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biopython/Tests/test_Align_codonalign.py
mdehoon 8d47923a20 update (#4820) 
Co-authored-by: Michiel de Hoon <michiel.dehoon@riken.jp>
2024-09-02 13:58:03 +09:00

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# Copyright (C) 2013 by Zheng Ruan (zruan1991@gmail.com)
# This code is part of the Biopython distribution and governed by its
# license. Please see the LICENSE file that should have been included
# as part of this package.
"""Unit tests for CodonAligner and Bio.Align.analysis."""
import unittest
try:
import numpy as np
except ImportError:
from Bio import MissingPythonDependencyError
raise MissingPythonDependencyError(
"Install numpy if you want to use Bio.Align."
) from None
from Bio import Align
from Bio import SeqIO
from Bio.Align import Alignment
from Bio.Align import CodonAligner
from Bio.Align.analysis import calculate_dn_ds
from Bio.Align.analysis import calculate_dn_ds_matrix
from Bio.Align.analysis import mktest
from Bio.Data import CodonTable
from Bio.Seq import Seq
from Bio.SeqRecord import SeqRecord
class TestBasic(unittest.TestCase):
def test_aligner(self):
aligner = CodonAligner()
self.assertEqual(
str(aligner),
"""\
Codon aligner with parameters
wildcard: 'X'
match_score: 1.0
mismatch_score: 0.0
frameshift_minus_two_score: -3.0
frameshift_minus_one_score: -3.0
frameshift_plus_one_score: -3.0
frameshift_plus_two_score: -3.0
""",
)
aligner.wildcard = "Y"
aligner.match_score = 2.0
aligner.mismatch_score = -1.0
aligner.frameshift_score = -5.0
aligner.frameshift_two_score = -2.0
aligner.frameshift_minus_score = -4.0
self.assertEqual(
str(aligner),
"""\
Codon aligner with parameters
wildcard: 'Y'
match_score: 2.0
mismatch_score: -1.0
frameshift_minus_two_score: -4.0
frameshift_minus_one_score: -4.0
frameshift_plus_one_score: -5.0
frameshift_plus_two_score: -2.0
""",
)
self.assertEqual(aligner.wildcard, "Y")
self.assertAlmostEqual(aligner.match_score, 2.0)
self.assertAlmostEqual(aligner.mismatch_score, -1.0)
self.assertAlmostEqual(aligner.frameshift_minus_two_score, -4.0)
self.assertAlmostEqual(aligner.frameshift_minus_one_score, -4.0)
self.assertAlmostEqual(aligner.frameshift_plus_one_score, -5.0)
self.assertAlmostEqual(aligner.frameshift_plus_two_score, -2.0)
def test_alignments(self):
aligner = CodonAligner()
aligner.frameshift_score = -1.0
dna = SeqRecord(Seq("TTTAAAAAAAAATTT"), id="dna")
pro = SeqRecord(Seq("FKKKF"), id="pro")
alignments = aligner.align(pro, dna)
self.assertEqual(len(alignments), 1)
self.assertAlmostEqual(alignments.score, 5.0)
alignment = alignments[0]
self.assertEqual(
str(alignment),
"""\
pro 0 F K K K F 5
dna 0 TTTAAAAAAAAATTT 15
""",
)
dna = SeqRecord(Seq("TTTAAAAAAAATTT"), id="dna")
score = aligner.score(pro, dna)
self.assertAlmostEqual(score, 4.0)
alignments = aligner.align(pro, dna)
self.assertEqual(len(alignments), 2)
self.assertAlmostEqual(alignments.score, 4.0)
alignment = alignments[0]
self.assertEqual(
str(alignment),
"""\
pro 0 F K K 3
dna 0 TTTAAAAAA 9
pro 3 K F 5
dna 8 AAATTT 14
""",
)
alignment = alignments[1]
self.assertEqual(
str(alignment),
"""\
pro 0 F K 2
dna 0 TTTAAA 6
pro 2 K K F 5
dna 5 AAAAAATTT 14
""",
)
dna = SeqRecord(Seq("TTTAAAAAAATTT"), id="dna")
score = aligner.score(pro, dna)
self.assertAlmostEqual(score, 4.0)
alignments = aligner.align(pro, dna)
self.assertEqual(len(alignments), 2)
self.assertAlmostEqual(alignments.score, 4.0)
alignment = alignments[0]
self.assertEqual(
str(alignment),
"""\
pro 0 F K K 3
dna 0 TTTAAAAAA 9
pro 3 K F 5
dna 7 AAATTT 13
""",
)
alignment = alignments[1]
self.assertEqual(
str(alignment),
"""\
pro 0 F K 2
dna 0 TTTAAA 6
pro 2 K K F 5
dna 4 AAAAAATTT 13
""",
)
dna = SeqRecord(Seq("TTTAAAAAATTT"), id="dna")
score = aligner.score(pro, dna)
self.assertAlmostEqual(score, 3.0)
alignments = aligner.align(pro, dna)
self.assertEqual(len(alignments), 2)
self.assertAlmostEqual(alignments.score, 3.0)
alignment = alignments[0]
self.assertEqual(
str(alignment),
"""\
pro 0 F K 2
dna 0 TTTAAA 6
pro 2 K 3
dna 5 AAA 8
pro 3 K F 5
dna 6 AAATTT 12
""",
)
alignment = alignments[1]
self.assertEqual(
str(alignment),
"""\
pro 0 F K 2
dna 0 TTTAAA 6
pro 2 K 3
dna 4 AAA 7
pro 3 K F 5
dna 6 AAATTT 12
""",
)
dna = SeqRecord(Seq("TTTAAAAATTT"), id="dna")
score = aligner.score(pro, dna)
self.assertAlmostEqual(score, 3.0)
alignments = aligner.align(pro, dna)
self.assertEqual(len(alignments), 1)
self.assertAlmostEqual(alignments.score, 3.0)
alignment = alignments[0]
self.assertEqual(
str(alignment),
"""\
pro 0 F K 2
dna 0 TTTAAA 6
pro 2 K 3
dna 4 AAA 7
pro 3 K F 5
dna 5 AAATTT 11
""",
)
dna = SeqRecord(Seq("TTTAAAAAAAAAATTT"), id="dna")
alignments = aligner.align(pro, dna)
self.assertEqual(len(alignments), 6)
self.assertAlmostEqual(alignments.score, 4.0)
alignment = alignments[0]
self.assertEqual(
str(alignment),
"""\
pro 0 F K K K F 5
dna 0 TTTAAAAAAAAAATT 15
""",
)
alignment = alignments[1]
self.assertEqual(
str(alignment),
"""\
pro 0 F K K K F 5
dna 1 TTAAAAAAAAAATTT 16
""",
)
alignment = alignments[2]
self.assertEqual(
str(alignment),
"""\
pro 0 F -K K K F 5
dna 0 TTTAAAAAAAAAATTT 16
""",
)
alignment = alignments[3]
self.assertEqual(
str(alignment),
"""\
pro 0 F K -K K F 5
dna 0 TTTAAAAAAAAAATTT 16
""",
)
alignment = alignments[4]
self.assertEqual(
str(alignment),
"""\
pro 0 F K K -K F 5
dna 0 TTTAAAAAAAAAATTT 16
""",
)
alignment = alignments[5]
self.assertEqual(
str(alignment),
"""\
pro 0 F K K K -F 5
dna 0 TTTAAAAAAAAAATTT 16
""",
)
dna = SeqRecord(Seq("TTTAAAAAAAAAAATTT"), id="dna")
alignments = aligner.align(pro, dna)
self.assertEqual(len(alignments), 6)
self.assertAlmostEqual(alignments.score, 4.0)
alignment = alignments[0]
self.assertEqual(
str(alignment),
"""\
pro 0 F K K K F 5
dna 0 TTTAAAAAAAAAAAT 15
""",
)
alignment = alignments[1]
self.assertEqual(
str(alignment),
"""\
pro 0 F K K K F 5
dna 2 TAAAAAAAAAAATTT 17
""",
)
alignment = alignments[2]
self.assertEqual(
str(alignment),
"""\
pro 0 F --K K K F 5
dna 0 TTTAAAAAAAAAAATTT 17
""",
)
alignment = alignments[3]
self.assertEqual(
str(alignment),
"""\
pro 0 F K --K K F 5
dna 0 TTTAAAAAAAAAAATTT 17
""",
)
alignment = alignments[4]
self.assertEqual(
str(alignment),
"""\
pro 0 F K K --K F 5
dna 0 TTTAAAAAAAAAAATTT 17
""",
)
alignment = alignments[5]
self.assertEqual(
str(alignment),
"""\
pro 0 F K K K --F 5
dna 0 TTTAAAAAAAAAAATTT 17
""",
)
dna = SeqRecord(Seq("TTTAAAAAAAAAAAATTT"), id="dna")
alignments = aligner.align(pro, dna)
self.assertEqual(len(alignments), 2)
self.assertAlmostEqual(alignments.score, 4.0)
alignment = alignments[0]
self.assertEqual(
str(alignment),
"""\
pro 0 F K K K F 5
dna 0 TTTAAAAAAAAAAAA 15
""",
)
alignment = alignments[1]
self.assertEqual(
str(alignment),
"""\
pro 0 F K K K F 5
dna 3 AAAAAAAAAAAATTT 18
""",
)
class TestBuildAndIO(unittest.TestCase):
def test1(self):
aligner = CodonAligner()
nucleotide_records = SeqIO.parse("codonalign/nucl1.fa", "fasta")
protein_alignment = Align.read("codonalign/pro1.aln", "clustal")
self.assertEqual(len(protein_alignment.sequences), 3)
codon_alignments = []
nucleotide_record = next(nucleotide_records)
protein_record = protein_alignment.sequences[0]
self.assertEqual(nucleotide_record.id, protein_record.id)
alignments = aligner.align(protein_record, nucleotide_record)
self.assertEqual(len(alignments), 1)
alignment = next(alignments)
codon_alignments.append(alignment)
self.assertTrue(
np.array_equal(alignment.coordinates, np.array([[0, 183], [0, 549]]))
)
self.assertEqual(
str(alignment),
"""\
isotig697 0 R G D Q R S N F Q L S P S T M Q I S T G
isotig697 0 AGAGGCGATCAACGCAGCAACTTCCAGCTGTCTCCCTCCACCATGCAGATCTCCACAGGG
isotig697 20 L L C L L L V A T G F T S Q V L A H P G
isotig697 60 CTTCTGTGCcTGCTGCTTGTGGCCACTGGCTTCACTTCCCAGGTGCTGGCTCACCCAGGC
isotig697 40 S I P S T Y C F V M T S K K I P K S L L
isotig697 120 TCTATCCCATCTACCTaCTGCTTTGTTATGACCAGTAAGAaGATCCCCAAATCACTACTG
isotig697 60 K S Y K R I S N S R C T L K A I L F K T
isotig697 180 AaGAGCTACAAAaGAATCTCCAACAGCAGATGCACCcTGAAAGCCATACTCTTCAAGACC
isotig697 80 K S G K E I C A D P K K K W V Q D A T K
isotig697 240 AAGTCGGGCAAAGAGATCTGTGCTGACCCCAAGAAGAAGTGGGTCcAGGATGCCACAAAG
isotig697 100 H L D Q I L Q T P K P T I P S F E T H P
isotig697 300 CACCTGGACCAAATCCTTCAAACTCCAAAACCGACAATCCCCTCTTTTGAGACTCACCCA
isotig697 120 E T K K C F I H S P F L R R A P R S T Q
isotig697 360 GAGACTAAGAAATGCTTCATTCATTCTCCATTCCTAAGACGTGCTCCAAGGTCAACTCAG
isotig697 140 H H S P R T W L H L V M D R T E S H Y V
isotig697 420 CACCATTCCCCAAGGACTTGGCTTCATTTAGTTATGGATAGAACTGAAAGTCATTATGTT
isotig697 160 Q N K P D L K R L C N F L N M Q N L K R
isotig697 480 CAGAATAAGCCAGACTTGAAGAGGTTGTGTAATTTCTTGAATATGCAAAATCTTAAAAGG
isotig697 180 G A C 183
isotig697 540 GGGGCATGC 549
""",
)
nucleotide_record = next(nucleotide_records)
protein_record = protein_alignment.sequences[1]
self.assertEqual(nucleotide_record.id, protein_record.id)
alignments = aligner.align(protein_record, nucleotide_record)
self.assertEqual(len(alignments), 1)
alignment = next(alignments)
codon_alignments.append(alignment)
self.assertTrue(
np.array_equal(alignment.coordinates, np.array([[0, 65], [0, 195]]))
)
self.assertEqual(
str(alignment),
"""\
ENSG00000 0 M K V S A A L L C L L L I A A T F I P Q
ENSG00000 0 ATGAAAGTCTCTGCCGCCCTTCTGTGCCTGCTGCTCATAGCAGCCACCTTCATTCCCCAA
ENSG00000 20 G L A Q P D A I N A P V T C C Y N F T N
ENSG00000 60 GGGCTCGCTCAGCCAGATGCAATCAATGCCCCAGTCACCTGCTGTTATAACTTCACCAAT
ENSG00000 40 R K I S V Q R L A S Y R R I T S S K C P
ENSG00000 120 AGGAAGATCTCAGTGCAGAGGCTCGCGAGCTATAGAAGAATCACCAGCAGCAAGTGTCCC
ENSG00000 60 K E A V M 65
ENSG00000 180 AAAGAAGCTGTGATG 195
""",
)
nucleotide_record = next(nucleotide_records)
protein_record = protein_alignment.sequences[2]
self.assertEqual(nucleotide_record.id, protein_record.id)
alignments = aligner.align(protein_record, nucleotide_record)
self.assertEqual(len(alignments), 1)
alignment = next(alignments)
codon_alignments.append(alignment)
self.assertTrue(
np.array_equal(alignment.coordinates, np.array([[0, 99], [9, 306]]))
)
self.assertEqual(
str(alignment),
"""\
ENSG00000 0 M K V S A A L L C L L L I A A T F I P Q
ENSG00000 9 ATGAAAGTCTCTGCCGCCCTTCTGTGCCTGCTGCTCATAGCAGCCACCTTCATTCCCCAA
ENSG00000 20 G L A Q P D A I N A P V T C C Y N F T N
ENSG00000 69 GGGCTCGCTCAGCCAGATGCAATCAATGCCCCAGTCACCTGCTGTTATAACTTCACCAAT
ENSG00000 40 R K I S V Q R L A S Y R R I T S S K C P
ENSG00000 129 AGGAAGATCTCAGTGCAGAGGCTCGCGAGCTATAGAAGAATCACCAGCAGCAAGTGTCCC
ENSG00000 60 K E A V I F K T I V A K E I C A D P K Q
ENSG00000 189 AAAGAAGCTGTGATCTTCAAGACCATTGTGGCCAAGGAGATCTGTGCTGACCCCAAGCAG
ENSG00000 80 K W V Q D S M D H L D K Q T Q T P K T
ENSG00000 249 AAGTGGGTTCAGGATTCCATGGACCACCTGGACAAGCAAACCCAAACTCCGAAGACT
ENSG00000 99
ENSG00000 306
""",
)
alignment = protein_alignment.mapall(codon_alignments)
self.assertTrue(
np.array_equal(
alignment.coordinates,
# fmt: off
np.array([[0, 42, 126, 126, 231, 333, 549],
[0, 0, 84, 90, 195, 195, 195],
[9, 9, 93, 99, 204, 306, 306]])
# fmt: on
)
)
self.assertEqual(
format(alignment, "clustal"),
"""\
isotig69710 AGAGGCGATCAACGCAGCAACTTCCAGCTGTCTCCCTCCACCATGCAGAT
ENSG00000108691:ENST0000058090 ------------------------------------------ATGAAAGT
ENSG00000108691:ENST0000022583 ------------------------------------------ATGAAAGT
isotig69710 CTCCACAGGGCTTCTGTGCcTGCTGCTTGTGGCCACTGGCTTCACTTCCC
ENSG00000108691:ENST0000058090 CTCTGCCGCCCTTCTGTGCCTGCTGCTCATAGCAGCCACCTTCATTCCCC
ENSG00000108691:ENST0000022583 CTCTGCCGCCCTTCTGTGCCTGCTGCTCATAGCAGCCACCTTCATTCCCC
isotig69710 AGGTGCTGGCTCACCCAGGCTCTATC------CCATCTACCTaCTGCTTT
ENSG00000108691:ENST0000058090 AAGGGCTCGCTCAGCCAGATGCAATCAATGCCCCAGTCACCTGCTGTTAT
ENSG00000108691:ENST0000022583 AAGGGCTCGCTCAGCCAGATGCAATCAATGCCCCAGTCACCTGCTGTTAT
isotig69710 GTTATGACCAGTAAGAaGATCCCCAAATCACTACTGAaGAGCTACAAAaG
ENSG00000108691:ENST0000058090 AACTTCACCAATAGGAAGATCTCAGTGCAGAGGCTCGCGAGCTATAGAAG
ENSG00000108691:ENST0000022583 AACTTCACCAATAGGAAGATCTCAGTGCAGAGGCTCGCGAGCTATAGAAG
isotig69710 AATCTCCAACAGCAGATGCACCcTGAAAGCCATACTCTTCAAGACCAAGT
ENSG00000108691:ENST0000058090 AATCACCAGCAGCAAGTGTCCCAAAGAAGCTGTGATG-------------
ENSG00000108691:ENST0000022583 AATCACCAGCAGCAAGTGTCCCAAAGAAGCTGTGATCTTCAAGACCATTG
isotig69710 CGGGCAAAGAGATCTGTGCTGACCCCAAGAAGAAGTGGGTCcAGGATGCC
ENSG00000108691:ENST0000058090 --------------------------------------------------
ENSG00000108691:ENST0000022583 TGGCCAAGGAGATCTGTGCTGACCCCAAGCAGAAGTGGGTTCAGGATTCC
isotig69710 ACAAAGCACCTGGACCAAATCCTTCAAACTCCAAAACCGACAATCCCCTC
ENSG00000108691:ENST0000058090 --------------------------------------------------
ENSG00000108691:ENST0000022583 ATGGACCACCTGGACAAGCAAACCCAAACTCCGAAGACT-----------
isotig69710 TTTTGAGACTCACCCAGAGACTAAGAAATGCTTCATTCATTCTCCATTCC
ENSG00000108691:ENST0000058090 --------------------------------------------------
ENSG00000108691:ENST0000022583 --------------------------------------------------
isotig69710 TAAGACGTGCTCCAAGGTCAACTCAGCACCATTCCCCAAGGACTTGGCTT
ENSG00000108691:ENST0000058090 --------------------------------------------------
ENSG00000108691:ENST0000022583 --------------------------------------------------
isotig69710 CATTTAGTTATGGATAGAACTGAAAGTCATTATGTTCAGAATAAGCCAGA
ENSG00000108691:ENST0000058090 --------------------------------------------------
ENSG00000108691:ENST0000022583 --------------------------------------------------
isotig69710 CTTGAAGAGGTTGTGTAATTTCTTGAATATGCAAAATCTTAAAAGGGGGG
ENSG00000108691:ENST0000058090 --------------------------------------------------
ENSG00000108691:ENST0000022583 --------------------------------------------------
isotig69710 CATGC
ENSG00000108691:ENST0000058090 -----
ENSG00000108691:ENST0000022583 -----
""",
)
def test2(self):
aligner = CodonAligner()
nucleotide_records = SeqIO.parse("codonalign/nucl2.fa", "fasta")
protein_alignment = Align.read("codonalign/pro2.aln", "clustal")
self.assertEqual(len(protein_alignment.sequences), 3)
codon_alignments = []
nucleotide_record = next(nucleotide_records)
protein_record = protein_alignment.sequences[0]
self.assertEqual(nucleotide_record.id, protein_record.id)
alignments = aligner.align(protein_record, nucleotide_record)
self.assertEqual(len(alignments), 1)
alignment = next(alignments)
codon_alignments.append(alignment)
self.assertTrue(
np.array_equal(alignment.coordinates, np.array([[0, 1094], [0, 3282]]))
)
self.assertEqual(
str(alignment),
"""\
isotig351 0 E R Q G R W C V P G E A V E A R V S R S
isotig351 0 GAAAGGCAGGGTCGctGGTGCGTGCCCGGCGAGGCTGTGGAGGCCcgTGTGTCTAGAAGC
isotig351 20 C V R E M A E P G R R R G P R S R G G G
isotig351 60 TGTGTGAGAGAGATGGCGGAACCCGGGAGGAGACGGGGTCCGAGGTCCCGCGGTGGCGGC
isotig351 40 A G R G A R R A R V A R G R R P R A P Q
isotig351 120 GCCGGCCGAGGCgCTCGAAGAGCCCGGGTCGCCCGTGGCCGGCGTCCTCGCGCCCCGCAG
isotig351 60 S L S R L I P D T V L V D L V S D S D E
isotig351 180 TCTCTGTCCCGGCTCATTCCAGACACGGTGCTTGTGGACTTGGTCAGTGACAGCGACGAG
isotig351 80 E I L E V V A D P V E A P A A R A P A P
isotig351 240 GAGATCCTGGAAGTCGTCGCGGACCCGGTAGAAGCGCCCGCCGCCCGGGCcCCcGCGCCG
isotig351 100 A A H G Q D S D S D S A G A D E G P A G
isotig351 300 GCCGCACATGGGCAGGACAGCGACAGCGACAGTGCAGGGGCGgACGAGGGGCCTGCAGGA
isotig351 120 A P Q T L V R R R R R R L L D P G E A P
isotig351 360 GCCCCTCAGACCTTGGTCCGGCGGCGGCGCCGGCGGCTGCTGGATCCCGGCGAGGCACCG
isotig351 140 V V P V Y S G K V Q S S L N L I P D N S
isotig351 420 GTGGTTCCTGTGTACTCCGGGAAGGTACAAAGCAGCCTCAACCTCATCCCAGATAATTCA
isotig351 160 S L L K L C P S E P E D E A D V T D C G
isotig351 480 TCCCTCTTGAAACTTTGCCCCTCAGAGCCTGAAGATGAGGCAGATGTGACAGATTGTGGC
isotig351 180 S P P P E D A L I P G S P W K K K L R N
isotig351 540 AGTCCTCCTCCTGAGGATGCCCTAATTCCAGGTTCTCCCTGGAAGAAGAAGCTGAGGAAT
isotig351 200 K H E K E E M K M E E F P D Q D I S P L
isotig351 600 AAGCATGAAAAaGAAGAGATGAAGATGGAAGAGTTtCCGGACCAGGACATCTCTCCTTTG
isotig351 220 P R P S S R N K S R K H T E A L Q K L R
isotig351 660 CCCCGACCTTCATCAAGAAaCAAAAGCAGAAAGCATACCGAGGCACTCCAGAAGTTGAGG
isotig351 240 E V N K R L Q D L R S C L S P K Q H Q S
isotig351 720 GAAGTGAACAAGCGCCTCCAAGATCTCCGATCCTGCCTGAGCCCCAAGCAGCACCAGAGT
isotig351 260 P A L Q N P D D E V V L V D G P V L S Q
isotig351 780 CCAGCCCTTCAGAACCCAGATGATGAGGTGGTCCTCGTGGACGGGCCTGtCTTGTCACAG
isotig351 280 S P R L F T L K I R C R A D L V R L P V
isotig351 840 AGCCCGAGACTCTTCACCCTCAAGATCCGGTGCCGGGCTGACCTAGTCAGATTGCCCGTC
isotig351 300 M T S E P L Q N V V D Y M A N H L G V S
isotig351 900 ATGACATCGGAACCCCTTCAGAATGTGGTGGATTACATGGCCAATCATCTTGGGGTGTCT
isotig351 320 P S R I L L L F G E T E L S P T A T P R
isotig351 960 CCAAGCAGGATTCTTTTACTCTTTGGAGAGACAGAACTGTCCCCTACTGCCACCCCTAGG
isotig351 340 T L K L G V A D I I D C V V L T S S S E
isotig351 1020 ACCCTAAAGCTTGGTGTGGCTGACATCATTGATTGTGTGGTGCTGACAAGTTCTTCAGAG
isotig351 360 A T E T T Q Q L C L R V Q G K E K H Q M
isotig351 1080 GCCACAGAGACAACCCAGCAGCTCTGCCTCCGGGTGCAGGGGAAGGAGAAGCACCAGATG
isotig351 380 L E I S L S P D S P L E V L M A H Y E E
isotig351 1140 TTGGAGATCTCACTCTCTCCTGACTCtCCTCTTGAGGTCCTCATGGCGCACTATGAGGAG
isotig351 400 A M G L S G H K L S F F F D G T K L S G
isotig351 1200 GCCATGGGACTCTCCGGACACAAGCTCTCCTTCTTCTTCGATGGGACAAAGCTGTCGGGC
isotig351 420 K E L P A D L G M E S G D L I E V W G S
isotig351 1260 AAGGAGCTGCCAGCTGATCTGGGCATGGAATCCGGGGATCTCATTGAAGTTTGGGGCAGC
isotig351 440 F L L L F G C R A K T W G Q Q L P L L L
isotig351 1320 TTCCTCCTCCTGTTTGGATGCAGAGCCAAGACTTGGGGACAACAGCTCCCACTTTtATTA
isotig351 460 L F F A P G L T E T E L E L V Y L F P A
isotig351 1380 TTATTTTTtGCCCcAGGGCTAACAGAAACCGAATTAGAACTCGTTTATTTATTTCCGGCA
isotig351 480 L G I E P R A V H M L R M C E V E V K P
isotig351 1440 CTGGGGATTGAACCCAGGGCTGTGCATATGCTAAGGATGTGTGAAGTTGAGGTAAAaCCA
isotig351 500 R H D L C P V S L T V V S S G L I G N C
isotig351 1500 AGGCATGACCTTTGCCcTGTCTCGTTGACCGTAGTCTCAAGCGGTCTGATTGGTAATTGT
isotig351 520 V T V A A L G G L W L C V L V L C T A A
isotig351 1560 GTGACTGTGGCTGCCCTGGGTGgCCTGTGGCTGTGTGTGTTGGTGCTGTGTACAGCAGCT
isotig351 540 P G A W R R G I G F P T I S F S S A Q M
isotig351 1620 CCTGGGGCATGGAGAAGGGGTATTGGCTTCCCTACCATTTCGTTCAGTAGTGCACAAATG
isotig351 560 S L A F G C P G L F M P H W G P T G I L
isotig351 1680 AGCCTTGCATTTGGGTGCCCAGGCTTGTTTATGCCACATTGGGGACCAACAGGGATTTTA
isotig351 580 I L I W G L R C R Y L P W W G S V A G K
isotig351 1740 ATTCTCATTTGGGGGCTGAGATGCAGGTACCTTCCCTGGTGGGGATCGGTTGCAGGGAAA
isotig351 600 T S N D I Y A E A E D V D S G F L K A N
isotig351 1800 ACAAGCAATGACATCTATGCTGAAGCTGAGGACGTAGACAGTGGGTTTTTAAAGGCTAAC
isotig351 620 R S G V F S P G H P L S Q D S A S I W Y
isotig351 1860 AGGAGTGGTGTCTTCAGCCCTGGGCATCCACTCTCCCAGGACTCGGCCAGCATCTGGTAC
isotig351 640 I L P G M H I P H L S T C S C V C L L F
isotig351 1920 ATACTTCCTGGCATGCACATCCCACATCTGAGCACATGCAGCTGTGTTTGTTTACTCTTC
isotig351 660 R P P A L S C Q H P L G I F V S E C L Y
isotig351 1980 cGTCCTCCCGCCCTCTCCTGTCAGCACCCACTTGGTATATTTGTATCTGAATGTCTTTAT
isotig351 680 K M I F M C V I L V Y V H G T V Q T F C
isotig351 2040 AAGATGATTTTCATGTGTGTGATTTTAGTGTATGTACATGGTACTGTGCAAACATTCTGT
isotig351 700 L H S V V T G P C H L L D L L L F R S A
isotig351 2100 CTTCACTCAGTGGTGACAGGCCCATGTCACCTTCTAGATCTGTTGTTGTTCCGATCTGCT
isotig351 720 V A A P W H M I L L T H C L N W R D T V
isotig351 2160 GTGGCTGCCCCATGGCATATGATATTACTCACACATTGCCTTAATTGGAGGGATACCGTC
isotig351 740 A S S E P N S R P Q Q T S F C V F P S G
isotig351 2220 GCCAGCTCCGAACCAAATTCCAGACCACAGCAAACATCTTTTTGTGTGTTCCCTTCTGGG
isotig351 760 P G V I V W H T C P G W D C G L R R F I
isotig351 2280 CCAGGGGTAATTGTCTGGCATACTTGCCCAGGATGGGACTgTGGGTTACGCAGGTTCATT
isotig351 780 S L V F L G F S S E C G L L F L E L L F
isotig351 2340 TcTCTGGTTTTTCTAGGgTTTTCTTCAGAATGTGGACTGCTTTTCTTGGAGCTTCTcTTT
isotig351 800 P S L D Q Y L V L L Y F L I C Q S T V Y
isotig351 2400 CCTTcTCTTGACCAGTATTTAGTGTTGttgTACTTTCTGATTTGCCAGTCTACTGTGTAT
isotig351 820 K A L H I L I S F I P P F L I N V H L L
isotig351 2460 AAAGCACTGCATATCTTAATATCCTTTATCCCACCATTTCTTATCAATGTCCACCTTCTG
isotig351 840 V F L C L L V F L G F L L C V F S V R S
isotig351 2520 GTTTTTCTTTGTCTGCTTGTTTTCTTGGGCTTCCTTTTGTGTGTTTTTtCTGTGAGGAGT
isotig351 860 C L C S R Q L Q I T F R I A L C V P R G
isotig351 2580 TGCTTGTGTTCTaGgCAATTGCAAATAACCTTCAGAATAGCACTTTGTGTACCCAGGGGG
isotig351 880 I F T K Q T F L T L M Q T A G F C K G F
isotig351 2640 ATTTTCACCAAACAGACATTCTTAACTTTAATGCAGACAGCTGGCTTTTGTAAAGGGTTT
isotig351 900 F V L C F F F F C F C F C F L R E N E K
isotig351 2700 TTTGTTTTGTGTTTtTTTTTtttttGCTTTTGTTTTtGcTTTTTAAGGGAAAATGAGAAA
isotig351 920 E L P E W Q G F R G V S G L L L L D L T
isotig351 2760 GAACTTCCAGAATGGCAGGGGTTCCGGGGAGTCTCAGGATTGCTACTTTTGGATCTCACT
isotig351 940 S E T F I V F C L A S F L F F C F Y L S
isotig351 2820 AGTGAAACTTTCATTGTCTTCTGTCTTGCTAGTTTTTTGTTCTTTTGTTTTTATCTCTCA
isotig351 960 Y D H M R I E F L I C C G V D T D C S E
isotig351 2880 TATGACCACATGAGAATAGAGTTCCTGATCTGCTGTGGTGTGGATaCTGACTGTTCTGAa
isotig351 980 L S T L L L T G Y S T V L V P D Y C M L
isotig351 2940 CTTTCCACTCTGCTTCTCACTGGTTACAGCACTGTACTGGTTCCTGACTATTGTATGTtA
isotig351 1000 R L N H L K C T F V W E S K F Y C V L I
isotig351 3000 CGTCTAAACCATCTGAAATGCACCTTTGTGTGGGAGAGCAAATTTTATTGTGTTTTAATT
isotig351 1020 I M S Q F S K L C L L K N Y V V L S Q E
isotig351 3060 ATAATGAGCCAGTTTTCtAAGCTTTGTCTaCTAAAAAATTATGTAGTCCTTTCACAAGAA
isotig351 1040 V C Q L L K N F F C E N M L Y L I L I F
isotig351 3120 GTATGTCAACTTCTtAAAAATTTTTTTtGtGAGAATATGTTATACCTTATTTTAATATTT
isotig351 1060 K N S M T Y S F Q V S Q L L Y D N I T H
isotig351 3180 AAAAATTCCATGACATATAGCTTCCAGGTTTCTCAGCTCTTGTATGACAATATCACACAT
isotig351 1080 Y Y Y V F N L S Q R E M P L 1094
isotig351 3240 TaCTATTATGTATTCAATCTCAGCCAAAGGGAGATGCCTTTA 3282
""",
)
nucleotide_record = next(nucleotide_records)
protein_record = protein_alignment.sequences[1]
self.assertEqual(nucleotide_record.id, protein_record.id)
alignments = aligner.align(protein_record, nucleotide_record)
self.assertEqual(len(alignments), 1)
alignment = next(alignments)
codon_alignments.append(alignment)
self.assertTrue(
np.array_equal(alignment.coordinates, np.array([[0, 1104], [0, 3312]]))
)
self.assertEqual(
str(alignment),
"""\
isotig351 0 E R Q G R W C V P G E A V E A R V S R S
isotig351 0 GAAAGGCAGGGTCGctGGTGCGTGCCCGGCGAGGCTGTGGAGGCCcgTGTGTCTAGAAGC
isotig351 20 C V R E M A E P G R R R G P R S R G G G
isotig351 60 TGTGTGAGAGAGATGGCGGAACCCGGGAGGAGACGGGGTCCGAGGTCCCGCGGTGGCGGC
isotig351 40 A G R G A R R A R V A R G R R P R A P Q
isotig351 120 GCCGGCCGAGGCgCTCGAAGAGCCCGGGTCGCCCGTGGCCGGCGTCCTCGCGCCCCGCAG
isotig351 60 S L S R L I P D T V L V D L V S D S D E
isotig351 180 TCTCTGTCCCGGCTCATTCCAGACACGGTGCTTGTGGACTTGGTCAGTGACAGCGACGAG
isotig351 80 E I L E V V A D P V E A P A A R A P A P
isotig351 240 GAGATCCTGGAAGTCGTCGCGGACCCGGTAGAAGCGCCCGCCGCCCGGGCcCCcGCGCCG
isotig351 100 A A H G Q D S D S D S A G A D E G P A G
isotig351 300 GCCGCACATGGGCAGGACAGCGACAGCGACAGTGCAGGGGCGgACGAGGGGCCTGCAGGA
isotig351 120 A P Q T L V R R R R R R L L D P G E A P
isotig351 360 GCCCCTCAGACCTTGGTCCGGCGGCGGCGCCGGCGGCTGCTGGATCCCGGCGAGGCACCG
isotig351 140 V V P V Y S G K V Q S S L N L I P D N S
isotig351 420 GTGGTTCCTGTGTACTCCGGGAAGGTACAAAGCAGCCTCAACCTCATCCCAGATAATTCA
isotig351 160 S L L K L C P S E P E D E A D V T D C G
isotig351 480 TCCCTCTTGAAACTTTGCCCCTCAGAGCCTGAAGATGAGGCAGATGTGACAGATTGTGGC
isotig351 180 S P P P E D A L I P G S P W K K K L R N
isotig351 540 AGTCCTCCTCCTGAGGATGCCCTAATTCCAGGTTCTCCCTGGAAGAAGAAGCTGAGGAAT
isotig351 200 K H E K E E M K M E E F P D Q D I S P L
isotig351 600 AAGCATGAAAAaGAAGAGATGAAGATGGAAGAGTTtCCGGACCAGGACATCTCTCCTTTG
isotig351 220 P R P S S R N K S R K H T E A L Q K L R
isotig351 660 CCCCGACCTTCATCAAGAAaCAAAAGCAGAAAGCATACCGAGGCACTCCAGAAGTTGAGG
isotig351 240 E V N K R L Q D L R S C L S P K Q H Q S
isotig351 720 GAAGTGAACAAGCGCCTCCAAGATCTCCGATCCTGCCTGAGCCCCAAGCAGCACCAGAGT
isotig351 260 P A L Q N P D D E V V L V D G P V L S Q
isotig351 780 CCAGCCCTTCAGAACCCAGATGATGAGGTGGTCCTCGTGGACGGGCCTGtCTTGTCACAG
isotig351 280 S P R L F T L K I R C R A D L V R L P V
isotig351 840 AGCCCGAGACTCTTCACCCTCAAGATCCGGTGCCGGGCTGACCTAGTCAGATTGCCCGTC
isotig351 300 M T S E P L Q N V V D Y M A N H L G V S
isotig351 900 ATGACATCGGAACCCCTTCAGAATGTGGTGGATTACATGGCCAATCATCTTGGGGTGTCT
isotig351 320 P S R I L L L F G E T E L S P T A T P R
isotig351 960 CCAAGCAGGATTCTTTTACTCTTTGGAGAGACAGAACTGTCCCCTACTGCCACCCCTAGG
isotig351 340 T L K L G V A D I I D C V V L T S S S E
isotig351 1020 ACCCTAAAGCTTGGTGTGGCTGACATCATTGATTGTGTGGTGCTGACAAGTTCTTCAGAG
isotig351 360 A T E T T Q Q L C L R V Q G K E K H Q M
isotig351 1080 GCCACAGAGACAACCCAGCAGCTCTGCCTCCGGGTGCAGGGGAAGGAGAAGCACCAGATG
isotig351 380 L E I S L S P D S P L E V L M A H Y E E
isotig351 1140 TTGGAGATCTCACTCTCTCCTGACTCgCCTCTTGAGGTCCTCATGGCGCACTATGAGGAG
isotig351 400 A M G L S G H K L S F F F D G T K L S G
isotig351 1200 GCCATGGGACTCTCCGGACACAAGCTCTCCTTCTTCTTCGATGGGACAAAGCTGTCGGGC
isotig351 420 K E L P A D L G M E S G D L I E V W G S
isotig351 1260 AAGGAACTGCCAGCTGATCTGGGCATGGAATCCGGGGATCTCATTGAAGTTTGGGGCAGC
isotig351 440 F L L L F G C R A K T W G Q Q L P L L L
isotig351 1320 TTCCTCCTCCTGTTTGGATGCAGAGCCAAGACTTGGGGACAACAGCTCCCACTTTTATTA
isotig351 460 L F F A P G L T E T E L E L V Y L F P A
isotig351 1380 TTATTTTTTGCCCCAGGGCTAACAGAAACCGAATTAGAACTCGTTTATTTATTTCCGGCA
isotig351 480 L G I E P W A V H M L R M C E V E V K P
isotig351 1440 CTGGGGATTGAACCCTGGGCTGTGCATATGCTAAGGATGTGTGAAGTTGAGGTAAAACCA
isotig351 500 R H D L C P V S L T D W L C D C G C P G
isotig351 1500 AGGCATGACCTTTGCCCTGTCTCGTTGACCGATTGGTTGTGTGACTGTGGCTGCCCTGGG
isotig351 520 W P V A V C V G A V D S S S W G M E K G
isotig351 1560 TGGCCTGTGGCTGTGTGTGTTGGTGCTGTGGACAGCAGCTCCTGGGGCATGGAGAAGGGG
isotig351 540 Y W L P Y H F V Q C T N E P C I W V P R
isotig351 1620 TATTGGCTTCCCTACCATTTCGTTCAGTGCACAAATGAGCCTTGCATTTGGGTGCCCAGG
isotig351 560 L V I Y A T L G T N R D F N S H L G A E
isotig351 1680 CTTGTGATTTATGCCACATTGGGGACCAACAGGGATTTTAATTCTCATTTGGGGGCTGAG
isotig351 580 M Q V P S L V G I V G C R E I N K Q H L
isotig351 1740 ATGCAGGTACCTTCCCTGGTGGGGATAGTCGGTTGCAGGGAAATAAACAAGCAACATCTA
isotig351 600 C S G L G R Q W V I F K G Q E W C L Q P
isotig351 1800 TGCAGCGGACTAGGTAGACAGTGGGTAATTTTTAAAGGCCAGGAGTGGTGTCTTCAGCCC
isotig351 620 W A S T L P G L G Q H L V H T S W H A H
isotig351 1860 TGGGCATCCACTCTCCCAGGACTCGGCCAGCATCTGGTACATACTTCCTGGCATGCACAT
isotig351 640 L A T S E H M Q L L S L M F T L V P S S
isotig351 1920 CTAGCCACATCTGAGCACATGCAGCTGTTGAGTTTGATGTTTACTCTAGTTCcGTCCTCC
isotig351 660 R P L L S A P T W Y I C I M S L D D F L
isotig351 1980 CGCCCTCTCCTGTCAGCACCCACTTGGTATATTTGTATCATGTCTTTAGATGATTTTCTG
isotig351 680 N V C D F S V C T W Y C A I D I L S S L
isotig351 2040 AATGTGTGTGATTTTAGTGTATGTACATGGTACTGTGCAATAGACATTCTGTCTTCACTC
isotig351 700 S V S D R L A M L A P S R S V V V P I C
isotig351 2100 AGTGTGAGTGACAGGCTAGCCATGTTAGCACCTTCTAGATCTGTTGTTGTTCCGATCTGC
isotig351 720 C G C P I V A L D D I T H T L P L E G Y
isotig351 2160 TGTGGCTGCCCCATAGTGGCATTAGATGATATTACTCACACATTGCCTTTGGAGGGATAC
isotig351 740 L S R Q L L G T K F Q T T A N I F L C V
isotig351 2220 CTGAGTCGCCAGCTCCTAGGAACCAAATTCCAGACCACAGCAAACATCTTTTTGTGTGTT
isotig351 760 P F W A R V G N C L A Y L P R M G L W V
isotig351 2280 CCCTTCTGGGCCAGGGTAGGTAATTGTCTGGCATACTTGCCCAGGATGGGACTgTGGGTT
isotig351 780 T Q V H F S G F S R V F F R M W T A F L
isotig351 2340 ACGCAGGTTCATTTcTCTGGTTTTTCTAGGgTTTTCTTCAGAATGTGGACTGCTTTTCTT
isotig351 800 G A S L S F S P V F S V V V L S D L P V
isotig351 2400 GGAGCTTCTcTTTCCTTcTCTCCAGTATTTAGTGTTGttgTACTTTCTGATTTGCCAGTC
isotig351 820 Y C V S T A Y L N I L Y L T T I S Y Q C
isotig351 2460 TACTGTGTAAGCACTGCATATCTTAATATCCTTTATCTGACCACCATTTCTTATCAATGT
isotig351 840 P P S G F S L L A A C F L V R L P F V C
isotig351 2520 CCACCTTCTGGTTTTTCTTTGTTAGCTGCTTGTTTTCTTGTGAGGCTTCCTTTTGTGTGT
isotig351 860 F F C E E L L V F A I A N N L Q N S T L
isotig351 2580 TTTTtCTGTGAGGAGTTGCTTGTGTTCgCAATTGCAAATAACCTTCAGAATAGCACTTTG
isotig351 880 C T Q G D F H Q T D I L N F N A D S W L
isotig351 2640 TGTACCCAGGGGGATTTTCACCAAACAGACATTCTTAACTTTAATGCAGACAGCTGGCTT
isotig351 900 L L E R V F C F V F F F F L L L F L L F
isotig351 2700 TTGTTAGAAAGGGTTTTTTGTTTTGTGTTTtTTTTTtttttGCTTTTGTTTTtGcTTTTT
isotig351 920 K G K E R T S R M A G V L A G S L R I A
isotig351 2760 AAGGGAAAAGAAAGAACTTCCAGAATGGCAGGGGTTCTAGCGGGGAGTCTCAGGATTGCT
isotig351 940 T F G S L N L R N F H C L L L A C F F V
isotig351 2820 ACTTTTGGATCTCTAAACTTAAGAAACTTTCATTGTCTTCTGTTAGCTTGCTTTTTTGTT
isotig351 960 L L F L S L I L R P L N E N R V L T D L
isotig351 2880 CTTTTGTTTTTATCTCTCATATTGAGACCACTAAATGAGAATAGAGTTCTAACTGATCTG
isotig351 980 L W C G Y L F T F H S A S H W L Q L D C
isotig351 2940 CTGTGGTGTGGATaCCTGTTCaCTTTCCACTCTGCTTCTCACTGGTTACAGCTAGACTGT
isotig351 1000 T G S L L Y V T S K P S E M H L C V G E
isotig351 3000 ACTGGTTCCCTATTGTATGTtACGTCTAAACCATCTGAAATGCACCTTTGTGTGGGAGAG
isotig351 1020 Q I L L C F N Y N E P V F A L S T K K L
isotig351 3060 CAAATTTTATTGTGTTTTAATTATAATGAGCCAGTTTTCGCTTTGTCTaCTAAAAAATTA
isotig351 1040 I C S L T F T R S M S T S K F F L E Y V
isotig351 3120 ATATGTAGTCTGACTTTCACAAGAAGTATGTCAACTTCTAAATTTTTTTtGGAATATGTT
isotig351 1060 I P L N F N I K F H D I V L P G F S A L
isotig351 3180 ATACCTTTGAATTTTAATATTAAATTCCATGACATAGTACTTCCAGGTTTCTCAGCTCTT
isotig351 1080 V Q L M N L N T L L L C I Q S Q P I K G
isotig351 3240 GTACAATTAATGAATCTGAACACATTaCTATTATGTATTCAATCTCAGCCAATAAAGGGA
isotig351 1100 D A F N 1104
isotig351 3300 GATGCCTTTAAC 3312
""",
)
nucleotide_record = next(nucleotide_records)
protein_record = protein_alignment.sequences[2]
self.assertEqual(nucleotide_record.id, protein_record.id)
alignments = aligner.align(protein_record, nucleotide_record)
self.assertEqual(len(alignments), 1)
alignment = next(alignments)
codon_alignments.append(alignment)
self.assertTrue(
np.array_equal(alignment.coordinates, np.array([[0, 419], [0, 1257]]))
)
self.assertEqual(
str(alignment),
"""\
ENSG00000 0 M A E P V G K R G R W S G G S G A G R G
ENSG00000 0 ATGGCGGAGCCTGTGGGGAAGCGGGGCCGCTGGTCCGGAGGTAGCGGTGCCGGCCGAGGG
ENSG00000 20 G R G G W G G R G R R P R A Q R S P S R
ENSG00000 60 GGTCGGGGCGGCTGGGGCGGTCGGGGCCGGCGTCCTCGGGCCCAGCGGTCTCCATCCCGG
ENSG00000 40 G T L D V V S V D L V T D S D E E I L E
ENSG00000 120 GGCACGCTGGACGTAGTGTCTGTGGACTTGGTCACCGACAGCGATGAGGAAATTCTGGAG
ENSG00000 60 V A T A R G A A D E V E V E P P E P P G
ENSG00000 180 GTCGCCACCGCTCGCGGTGCCGCGGACGAGGTTGAGGTGGAGCCCCCGGAGCCCCCGGGG
ENSG00000 80 P V A S R D N S N S D S E G E D R R P A
ENSG00000 240 CCGGTCGCGTCCCGGGATAACAGCAACAGTGACAGCGAAGGGGAGGACAGGCGGCCCGCA
ENSG00000 100 G P P R E P V R R R R R L V L D P G E A
ENSG00000 300 GGACCCCCGCGGGAGCCGGTCAGGCGGCGGCGGCGGCTGGTGCTGGATCCGGGGGAGGCG
ENSG00000 120 P L V P V Y S G K V K S S L R L I P D D
ENSG00000 360 CCGCTGGTTCCGGTGTACTCGGGGAAGGTTAAAAGCAGCCTTCGCCTTATCCCAGATGAT
ENSG00000 140 L S L L K L Y P P G D E E E A E L A D S
ENSG00000 420 CTATCCCTCCTGAAACTCTACCCTCCAGGGGATGAGGAAGAGGCAGAGCTGGCAGATTCG
ENSG00000 160 S G L Y H E G S P S P G S P W K T K L R
ENSG00000 480 AGTGGTCTCTACCATGAGGGCTCCCCATCACCAGGCTCTCCCTGGAAGACAAAGCTGAGG
ENSG00000 180 T K D K E E K K K T E F L D L D N S P L
ENSG00000 540 ACTAAGGATAAAGAAGAGAAGAAAAAGACAGAGTTTCTGGATCTGGACAACTCTCCTCTG
ENSG00000 200 S P P S P R T K S R T H T R A L K K L S
ENSG00000 600 TCCCCACCTTCACCAAGGACCAAAAGCAGAACGCATACTCGGGCACTCAAGAAGTTAAGT
ENSG00000 220 E V N K R L Q D L R S C L S P K P P Q G
ENSG00000 660 GAGGTGAACAAGCGCCTCCAGGATCTCCGTTCCTGTCTGAGCCCCAAGCCACCTCAGGGT
ENSG00000 240 Q E Q Q G Q E D E V V L V E G P T L P E
ENSG00000 720 CAAGAGCAACAGGGCCAAGAGGATGAAGTGGTCTTGGTGGAAGGGCCCACCCTCCCAGAG
ENSG00000 260 T P R L F P L K I R C R A D L V R L P L
ENSG00000 780 ACCCCCCGACTCTTCCCACTCAAAATCCGTTGCCGGGCTGACCTGGTCAGATTGCCCCTC
ENSG00000 280 R M S E P L Q S V V D H M A T H L G V S
ENSG00000 840 AGGATGTCGGAGCCCCTGCAGAGTGTGGTGGACCACATGGCCACCCACCTTGGGGTGTCC
ENSG00000 300 P S R I L L L F G E T E L S P T A T P R
ENSG00000 900 CCAAGCAGGATCCTTTTGCTTTTTGGAGAGACAGAGCTATCACCTACTGCCACTCCCAGG
ENSG00000 320 T L K L G V A D I I D C V V L T S S P E
ENSG00000 960 ACCCTAAAGCTCGGAGTGGCTGACATCATTGACTGTGTGGTACTAACAAGTTCTCCAGAG
ENSG00000 340 A T E T S Q Q L Q L R V Q G K E K H Q T
ENSG00000 1020 GCCACAGAGACGTCCCAACAGCTCCAGCTCCGGGTGCAGGGAAAGGAGAAACACCAGACA
ENSG00000 360 L E V S L S R D S P L K T L M S H Y E E
ENSG00000 1080 CTGGAAGTCTCACTGTCTCGAGATTCCCCTCTAAAGACCCTCATGTCCCACTATGAGGAG
ENSG00000 380 A M G L S G R K L S F F F D G T K L S G
ENSG00000 1140 GCCATGGGACTGTCGGGACGGAAGCTCTCCTTCTTCTTTGATGGGACAAAGCTTTCAGGC
ENSG00000 400 R E L P A D L G M E S G D L I E V W G
ENSG00000 1200 AGGGAGCTGCCAGCTGACCTGGGCATGGAATCTGGGGACCTCATTGAGGTCTGGGGC
ENSG00000 419
ENSG00000 1257
""",
)
alignment = protein_alignment.mapall(codon_alignments)
self.assertTrue(
np.array_equal(
alignment.coordinates,
# fmt: off
np.array([[ 0, 72, 255, 255, 603, 606, 1317, 1530,
1530, 1737, 1737, 1902, 1902, 1926, 1926, 2031,
2088, 2343, 2346, 2418, 2442, 2556, 2562, 2763,
2784, 2853, 2859, 3165, 3165, 3282, 3282],
[ 0, 72, 255, 255, 603, 606, 1317, 1530,
1569, 1776, 1821, 1986, 1992, 2016, 2031, 2136,
2136, 2391, 2391, 2463, 2463, 2577, 2577, 2778,
2778, 2847, 2847, 3153, 3162, 3279, 3312],
[ 0, 0, 183, 198, 546, 546, 1257, 1257,
1257, 1257, 1257, 1257, 1257, 1257, 1257, 1257,
1257, 1257, 1257, 1257, 1257, 1257, 1257, 1257,
1257, 1257, 1257, 1257, 1257, 1257, 1257]])
# fmt: on
)
)
self.assertEqual(
format(alignment, "clustal"),
"""\
isotig35100 GAAAGGCAGGGTCGctGGTGCGTGCCCGGCGAGGCTGTGGAGGCCcgTGT
isotig35101 GAAAGGCAGGGTCGctGGTGCGTGCCCGGCGAGGCTGTGGAGGCCcgTGT
ENSG00000176953:ENST0000032080 --------------------------------------------------
isotig35100 GTCTAGAAGCTGTGTGAGAGAGATGGCGGAACCCGGGAGGAGACGGGGTC
isotig35101 GTCTAGAAGCTGTGTGAGAGAGATGGCGGAACCCGGGAGGAGACGGGGTC
ENSG00000176953:ENST0000032080 ----------------------ATGGCGGAGCCTGTGGGGAAGCGGGGCC
isotig35100 CGAGGTCCCGCGGTGGCGGCGCCGGCCGAGGCgCTCGAAGAGCCCGGGTC
isotig35101 CGAGGTCCCGCGGTGGCGGCGCCGGCCGAGGCgCTCGAAGAGCCCGGGTC
ENSG00000176953:ENST0000032080 GCTGGTCCGGAGGTAGCGGTGCCGGCCGAGGGGGTCGGGGCGGCTGGGGC
isotig35100 GCCCGTGGCCGGCGTCCTCGCGCCCCGCAGTCTCTGTCCCGGCTCATTCC
isotig35101 GCCCGTGGCCGGCGTCCTCGCGCCCCGCAGTCTCTGTCCCGGCTCATTCC
ENSG00000176953:ENST0000032080 GGTCGGGGCCGGCGTCCTCGGGCCCAGCGGTCTCCATCCCGGGGCACGCT
isotig35100 AGACACGGTGCTTGTGGACTTGGTCAGTGACAGCGACGAGGAGATCCTGG
isotig35101 AGACACGGTGCTTGTGGACTTGGTCAGTGACAGCGACGAGGAGATCCTGG
ENSG00000176953:ENST0000032080 GGACGTAGTGTCTGTGGACTTGGTCACCGACAGCGATGAGGAAATTCTGG
isotig35100 AAGTC---------------GTCGCGGACCCGGTAGAAGCGCCCGCCGCC
isotig35101 AAGTC---------------GTCGCGGACCCGGTAGAAGCGCCCGCCGCC
ENSG00000176953:ENST0000032080 AGGTCGCCACCGCTCGCGGTGCCGCGGACGAGGTTGAGGTGGAGCCCCCG
isotig35100 CGGGCcCCcGCGCCGGCCGCACATGGGCAGGACAGCGACAGCGACAGTGC
isotig35101 CGGGCcCCcGCGCCGGCCGCACATGGGCAGGACAGCGACAGCGACAGTGC
ENSG00000176953:ENST0000032080 GAGCCCCCGGGGCCGGTCGCGTCCCGGGATAACAGCAACAGTGACAGCGA
isotig35100 AGGGGCGgACGAGGGGCCTGCAGGAGCCCCTCAGACCTTGGTCCGGCGGC
isotig35101 AGGGGCGgACGAGGGGCCTGCAGGAGCCCCTCAGACCTTGGTCCGGCGGC
ENSG00000176953:ENST0000032080 AGGGGAGGACAGGCGGCCCGCAGGACCCCCGCGGGAGCCGGTCAGGCGGC
isotig35100 GGCGCCGGCGGCTGCTGGATCCCGGCGAGGCACCGGTGGTTCCTGTGTAC
isotig35101 GGCGCCGGCGGCTGCTGGATCCCGGCGAGGCACCGGTGGTTCCTGTGTAC
ENSG00000176953:ENST0000032080 GGCGGCGGCTGGTGCTGGATCCGGGGGAGGCGCCGCTGGTTCCGGTGTAC
isotig35100 TCCGGGAAGGTACAAAGCAGCCTCAACCTCATCCCAGATAATTCATCCCT
isotig35101 TCCGGGAAGGTACAAAGCAGCCTCAACCTCATCCCAGATAATTCATCCCT
ENSG00000176953:ENST0000032080 TCGGGGAAGGTTAAAAGCAGCCTTCGCCTTATCCCAGATGATCTATCCCT
isotig35100 CTTGAAACTTTGCCCCTCAGAGCCTGAAGATGAGGCAGATGTGACAGATT
isotig35101 CTTGAAACTTTGCCCCTCAGAGCCTGAAGATGAGGCAGATGTGACAGATT
ENSG00000176953:ENST0000032080 CCTGAAACTCTACCCTCCAGGGGATGAGGAAGAGGCAGAGCTGGCAGATT
isotig35100 GTGGCAGTCCTCCTCCTGAGGATGCCCTAATTCCAGGTTCTCCCTGGAAG
isotig35101 GTGGCAGTCCTCCTCCTGAGGATGCCCTAATTCCAGGTTCTCCCTGGAAG
ENSG00000176953:ENST0000032080 CGAGTGGTCTCTACCATGAGGGCTCCCCATCACCAGGCTCTCCCTGGAAG
isotig35100 AAGAAGCTGAGGAATAAGCATGAAAAaGAAGAGATGAAGATGGAAGAGTT
isotig35101 AAGAAGCTGAGGAATAAGCATGAAAAaGAAGAGATGAAGATGGAAGAGTT
ENSG00000176953:ENST0000032080 ACAAAGCTGAGGACTAAG---GATAAAGAAGAGAAGAAAAAGACAGAGTT
isotig35100 tCCGGACCAGGACATCTCTCCTTTGCCCCGACCTTCATCAAGAAaCAAAA
isotig35101 tCCGGACCAGGACATCTCTCCTTTGCCCCGACCTTCATCAAGAAaCAAAA
ENSG00000176953:ENST0000032080 TCTGGATCTGGACAACTCTCCTCTGTCCCCACCTTCACCAAGGACCAAAA
isotig35100 GCAGAAAGCATACCGAGGCACTCCAGAAGTTGAGGGAAGTGAACAAGCGC
isotig35101 GCAGAAAGCATACCGAGGCACTCCAGAAGTTGAGGGAAGTGAACAAGCGC
ENSG00000176953:ENST0000032080 GCAGAACGCATACTCGGGCACTCAAGAAGTTAAGTGAGGTGAACAAGCGC
isotig35100 CTCCAAGATCTCCGATCCTGCCTGAGCCCCAAGCAGCACCAGAGTCCAGC
isotig35101 CTCCAAGATCTCCGATCCTGCCTGAGCCCCAAGCAGCACCAGAGTCCAGC
ENSG00000176953:ENST0000032080 CTCCAGGATCTCCGTTCCTGTCTGAGCCCCAAGCCACCTCAGGGTCAAGA
isotig35100 CCTTCAGAACCCAGATGATGAGGTGGTCCTCGTGGACGGGCCTGtCTTGT
isotig35101 CCTTCAGAACCCAGATGATGAGGTGGTCCTCGTGGACGGGCCTGtCTTGT
ENSG00000176953:ENST0000032080 GCAACAGGGCCAAGAGGATGAAGTGGTCTTGGTGGAAGGGCCCACCCTCC
isotig35100 CACAGAGCCCGAGACTCTTCACCCTCAAGATCCGGTGCCGGGCTGACCTA
isotig35101 CACAGAGCCCGAGACTCTTCACCCTCAAGATCCGGTGCCGGGCTGACCTA
ENSG00000176953:ENST0000032080 CAGAGACCCCCCGACTCTTCCCACTCAAAATCCGTTGCCGGGCTGACCTG
isotig35100 GTCAGATTGCCCGTCATGACATCGGAACCCCTTCAGAATGTGGTGGATTA
isotig35101 GTCAGATTGCCCGTCATGACATCGGAACCCCTTCAGAATGTGGTGGATTA
ENSG00000176953:ENST0000032080 GTCAGATTGCCCCTCAGGATGTCGGAGCCCCTGCAGAGTGTGGTGGACCA
isotig35100 CATGGCCAATCATCTTGGGGTGTCTCCAAGCAGGATTCTTTTACTCTTTG
isotig35101 CATGGCCAATCATCTTGGGGTGTCTCCAAGCAGGATTCTTTTACTCTTTG
ENSG00000176953:ENST0000032080 CATGGCCACCCACCTTGGGGTGTCCCCAAGCAGGATCCTTTTGCTTTTTG
isotig35100 GAGAGACAGAACTGTCCCCTACTGCCACCCCTAGGACCCTAAAGCTTGGT
isotig35101 GAGAGACAGAACTGTCCCCTACTGCCACCCCTAGGACCCTAAAGCTTGGT
ENSG00000176953:ENST0000032080 GAGAGACAGAGCTATCACCTACTGCCACTCCCAGGACCCTAAAGCTCGGA
isotig35100 GTGGCTGACATCATTGATTGTGTGGTGCTGACAAGTTCTTCAGAGGCCAC
isotig35101 GTGGCTGACATCATTGATTGTGTGGTGCTGACAAGTTCTTCAGAGGCCAC
ENSG00000176953:ENST0000032080 GTGGCTGACATCATTGACTGTGTGGTACTAACAAGTTCTCCAGAGGCCAC
isotig35100 AGAGACAACCCAGCAGCTCTGCCTCCGGGTGCAGGGGAAGGAGAAGCACC
isotig35101 AGAGACAACCCAGCAGCTCTGCCTCCGGGTGCAGGGGAAGGAGAAGCACC
ENSG00000176953:ENST0000032080 AGAGACGTCCCAACAGCTCCAGCTCCGGGTGCAGGGAAAGGAGAAACACC
isotig35100 AGATGTTGGAGATCTCACTCTCTCCTGACTCtCCTCTTGAGGTCCTCATG
isotig35101 AGATGTTGGAGATCTCACTCTCTCCTGACTCgCCTCTTGAGGTCCTCATG
ENSG00000176953:ENST0000032080 AGACACTGGAAGTCTCACTGTCTCGAGATTCCCCTCTAAAGACCCTCATG
isotig35100 GCGCACTATGAGGAGGCCATGGGACTCTCCGGACACAAGCTCTCCTTCTT
isotig35101 GCGCACTATGAGGAGGCCATGGGACTCTCCGGACACAAGCTCTCCTTCTT
ENSG00000176953:ENST0000032080 TCCCACTATGAGGAGGCCATGGGACTGTCGGGACGGAAGCTCTCCTTCTT
isotig35100 CTTCGATGGGACAAAGCTGTCGGGCAAGGAGCTGCCAGCTGATCTGGGCA
isotig35101 CTTCGATGGGACAAAGCTGTCGGGCAAGGAACTGCCAGCTGATCTGGGCA
ENSG00000176953:ENST0000032080 CTTTGATGGGACAAAGCTTTCAGGCAGGGAGCTGCCAGCTGACCTGGGCA
isotig35100 TGGAATCCGGGGATCTCATTGAAGTTTGGGGCAGCTTCCTCCTCCTGTTT
isotig35101 TGGAATCCGGGGATCTCATTGAAGTTTGGGGCAGCTTCCTCCTCCTGTTT
ENSG00000176953:ENST0000032080 TGGAATCTGGGGACCTCATTGAGGTCTGGGGC------------------
isotig35100 GGATGCAGAGCCAAGACTTGGGGACAACAGCTCCCACTTTtATTATTATT
isotig35101 GGATGCAGAGCCAAGACTTGGGGACAACAGCTCCCACTTTTATTATTATT
ENSG00000176953:ENST0000032080 --------------------------------------------------
isotig35100 TTTtGCCCcAGGGCTAACAGAAACCGAATTAGAACTCGTTTATTTATTTC
isotig35101 TTTTGCCCCAGGGCTAACAGAAACCGAATTAGAACTCGTTTATTTATTTC
ENSG00000176953:ENST0000032080 --------------------------------------------------
isotig35100 CGGCACTGGGGATTGAACCCAGGGCTGTGCATATGCTAAGGATGTGTGAA
isotig35101 CGGCACTGGGGATTGAACCCTGGGCTGTGCATATGCTAAGGATGTGTGAA
ENSG00000176953:ENST0000032080 --------------------------------------------------
isotig35100 GTTGAGGTAAAaCCAAGGCATGACCTTTGCCcTGTCTCGTTGACC-----
isotig35101 GTTGAGGTAAAACCAAGGCATGACCTTTGCCCTGTCTCGTTGACCGATTG
ENSG00000176953:ENST0000032080 --------------------------------------------------
isotig35100 ----------------------------------GTAGTCTCAAGCGGTC
isotig35101 GTTGTGTGACTGTGGCTGCCCTGGGTGGCCTGTGGCTGTGTGTGTTGGTG
ENSG00000176953:ENST0000032080 --------------------------------------------------
isotig35100 TGATTGGTAATTGTGTGACTGTGGCTGCCCTGGGTGgCCTGTGGCTGTGT
isotig35101 CTGTGGACAGCAGCTCCTGGGGCATGGAGAAGGGGTATTGGCTTCCCTAC
ENSG00000176953:ENST0000032080 --------------------------------------------------
isotig35100 GTGTTGGTGCTGTGTACAGCAGCTCCTGGGGCATGGAGAAGGGGTATTGG
isotig35101 CATTTCGTTCAGTGCACAAATGAGCCTTGCATTTGGGTGCCCAGGCTTGT
ENSG00000176953:ENST0000032080 --------------------------------------------------
isotig35100 CTTCCCTACCATTTCGTTCAGTAGTGCACAAATGAGCCTTGCATTTGGGT
isotig35101 GATTTATGCCACATTGGGGACCAACAGGGATTTTAATTCTCATTTGGGGG
ENSG00000176953:ENST0000032080 --------------------------------------------------
isotig35100 GCCCAGGCTTGTTTATGCCACATTGGGGACCAACAGGGATT---------
isotig35101 CTGAGATGCAGGTACCTTCCCTGGTGGGGATAGTCGGTTGCAGGGAAATA
ENSG00000176953:ENST0000032080 --------------------------------------------------
isotig35100 ------------------------------------TTAATTCTCATTTG
isotig35101 AACAAGCAACATCTATGCAGCGGACTAGGTAGACAGTGGGTAATTTTTAA
ENSG00000176953:ENST0000032080 --------------------------------------------------
isotig35100 GGGGCTGAGATGCAGGTACCTTCCCTGGTGGGGATCGGTTGCAGGGAAAA
isotig35101 AGGCCAGGAGTGGTGTCTTCAGCCCTGGGCATCCACTCTCCCAGGACTCG
ENSG00000176953:ENST0000032080 --------------------------------------------------
isotig35100 CAAGCAATGACATCTATGCTGAAGCTGAGGACGTAGACAGTGGGTTTTTA
isotig35101 GCCAGCATCTGGTACATACTTCCTGGCATGCACATCTAGCCACATCTGAG
ENSG00000176953:ENST0000032080 --------------------------------------------------
isotig35100 AAGGCTAACAGGAGTGGTGTCTTCAGCCCTGGGCATCCACTCTCCCAGGA
isotig35101 CACATGCAGCTGTTGAGTTTGATGTTTACTCTAGTTCcGTCCTCCCGCCC
ENSG00000176953:ENST0000032080 --------------------------------------------------
isotig35100 C------TCGGCCAGCATCTGGTACATACTT---------------CCTG
isotig35101 TCTCCTGTCAGCACCCACTTGGTATATTTGTATCATGTCTTTAGATGATT
ENSG00000176953:ENST0000032080 --------------------------------------------------
isotig35100 GCATGCACATCCCACATCTGAGCACATGCAGCTGTGTTTGTTTACTCTTC
isotig35101 TTCTGAATGTGTGTGATTTTAGTGTATGTACATGGTACTGTGCAATAGAC
ENSG00000176953:ENST0000032080 --------------------------------------------------
isotig35100 cGTCCTCCCGCCCTCTCCTGTCAGCACCCACTTGGTATATTTGTATCTGA
isotig35101 ATTCTGTCTTCACTCAGTGTGAGTGACAGGCTAGCCATGTTAGCACCTTC
ENSG00000176953:ENST0000032080 --------------------------------------------------
isotig35100 ATGTCTTTATAAGATGATTTTCATGTGTGTGATTTTAGTGTATGTACATG
isotig35101 T-------------------------------------------------
ENSG00000176953:ENST0000032080 --------------------------------------------------
isotig35100 GTACTGTGCAAACATTCTGTCTTCACTCAGTGGTGACAGGCCCATGTCAC
isotig35101 --------AGATCTGTTGTTGTTCCGATCTGCTGTGGCTGCCCCATAGTG
ENSG00000176953:ENST0000032080 --------------------------------------------------
isotig35100 CTTCTAGATCTGTTGTTGTTCCGATCTGCTGTGGCTGCCCCATGGCATAT
isotig35101 GCATTAGATGATATTACTCACACATTGCCTTTGGAGGGATACCTGAGTCG
ENSG00000176953:ENST0000032080 --------------------------------------------------
isotig35100 GATATTACTCACACATTGCCTTAATTGGAGGGATACCGTCGCCAGCTCCG
isotig35101 CCAGCTCCTAGGAACCAAATTCCAGACCACAGCAAACATCTTTTTGTGTG
ENSG00000176953:ENST0000032080 --------------------------------------------------
isotig35100 AACCAAATTCCAGACCACAGCAAACATCTTTTTGTGTGTTCCCTTCTGGG
isotig35101 TTCCCTTCTGGGCCAGGGTAGGTAATTGTCTGGCATACTTGCCCAGGATG
ENSG00000176953:ENST0000032080 --------------------------------------------------
isotig35100 CCAGGGGTAATTGTCTGGCATACTTGCCCAGGATGGGACTgTGGGTTACG
isotig35101 GGACTgTGGGTTACGCAGGTTCATTTcTCTGGTTTTTCTAGGgTTTTCTT
ENSG00000176953:ENST0000032080 --------------------------------------------------
isotig35100 CAGGTTCATTTcTCTGGTTTTTCTAGGgTTTTCTTCAGAATGTGGACTGC
isotig35101 CAGAATGTGGACT---GCTTTTCTTGGAGCTTCTcTTTCCTTcTCTCCAG
ENSG00000176953:ENST0000032080 --------------------------------------------------
isotig35100 TTTTCTTGGAGCTTCTcTTTCCTTcTCTTGACCAGTATTTAGTGTTGttg
isotig35101 TATTTAGTGTTGttgTACTTTCTGATTTGCCAGTCTAC------------
ENSG00000176953:ENST0000032080 --------------------------------------------------
isotig35100 TACTTTCTGATTTGCCAGTCTACTGTGTATAAAGCACTGCATATCTTAAT
isotig35101 ------------TGTGTAAGCACTGCATATCTTAATATCCTTTATCTGAC
ENSG00000176953:ENST0000032080 --------------------------------------------------
isotig35100 ATCCTTTATCCCACCATTTCTTATCAATGTCCACCTTCTGGTTTTTCTTT
isotig35101 CACCATTTCTTATCAATGTCCACCTTCTGGTTTTTCTTTGTTAGCTGCTT
ENSG00000176953:ENST0000032080 --------------------------------------------------
isotig35100 GTCTGCTTGTTTTCTTGGGCTTCCTTTTGTGTGTTTTTtCTGTGAGGAGT
isotig35101 GTTTTCTTGTGAGGCTTCCTTTTGTG------TGTTTTTtCTGTGAGGAG
ENSG00000176953:ENST0000032080 --------------------------------------------------
isotig35100 TGCTTGTGTTCTaGgCAATTGCAAATAACCTTCAGAATAGCACTTTGTGT
isotig35101 TTGCTTGTGTTCgCAATTGCAAATAACCTTCAGAATAGCACTTTGTGTAC
ENSG00000176953:ENST0000032080 --------------------------------------------------
isotig35100 ACCCAGGGGGATTTTCACCAAACAGACATTCTTAACTTTAATGCAGACAG
isotig35101 CCAGGGGGATTTTCACCAAACAGACATTCTTAACTTTAATGCAGACAGCT
ENSG00000176953:ENST0000032080 --------------------------------------------------
isotig35100 CTGGCTTTTGTAAAGGGTTTTTTGTTTTGTGTTTtTTTTTtttttGCTTT
isotig35101 GGCTTTTGTTAGAAAGGGTTTTTTGTTTTGTGTTTtTTTTTtttttGCTT
ENSG00000176953:ENST0000032080 --------------------------------------------------
isotig35100 TGTTTTtGcTTTTTAAGGGAAAATGAGAAAGAACTTCCAGAATGGCAGGG
isotig35101 TTGTTTTtGcTTTTTAAGGGAAAAGAAAGAACT-----------------
ENSG00000176953:ENST0000032080 --------------------------------------------------
isotig35100 GTTCCGGGGAGTCTCAGGATTGCTACTTTTGGATCTCACTAGTGAAACTT
isotig35101 ----TCCAGAATGGCAGGGGTTCTAGCGGGGAGTCTCAGGATTGCTACTT
ENSG00000176953:ENST0000032080 --------------------------------------------------
isotig35100 TCATTGTCTTCTGTCTTGCTAGTTTTTTGTTCTTTTGTTTTTATCTCTCA
isotig35101 TTGGATCTCTAAACTTAAGAAAC------TTTCATTGTCTTCTGTTAGCT
ENSG00000176953:ENST0000032080 --------------------------------------------------
isotig35100 TATGACCACATGAGAATAGAGTTCCTGATCTGCTGTGGTGTGGATaCTGA
isotig35101 TGCTTTTTTGTTCTTTTGTTTTTATCTCTCATATTGAGACCACTAAATGA
ENSG00000176953:ENST0000032080 --------------------------------------------------
isotig35100 CTGTTCTGAaCTTTCCACTCTGCTTCTCACTGGTTACAGCACTGTACTGG
isotig35101 GAATAGAGTTCTAACTGATCTGCTGTGGTGTGGATaCCTGTTCaCTTTCC
ENSG00000176953:ENST0000032080 --------------------------------------------------
isotig35100 TTCCTGACTATTGTATGTtACGTCTAAACCATCTGAAATGCACCTTTGTG
isotig35101 ACTCTGCTTCTCACTGGTTACAGCTAGACTGTACTGGTTCCCTATTGTAT
ENSG00000176953:ENST0000032080 --------------------------------------------------
isotig35100 TGGGAGAGCAAATTTTATTGTGTTTTAATTATAATGAGCCAGTTTTCtAA
isotig35101 GTtACGTCTAAACCATCTGAAATGCACCTTTGTGTGGGAGAGCAAATTTT
ENSG00000176953:ENST0000032080 --------------------------------------------------
isotig35100 GCTTTGTCTaCTAAAAAATTATGTAGTCCTTTCACAAGAAGTATGTCAAC
isotig35101 ATTGTGTTTTAATTATAATGAGCCAGTTTTCGCTTTGTCTaCTAAAAAAT
ENSG00000176953:ENST0000032080 --------------------------------------------------
isotig35100 TTCTtAAAAATTTTTTTtGtGAGAATATGTTATAC---------CTTATT
isotig35101 TAATATGTAGTCTGACTTTCACAAGAAGTATGTCAACTTCTAAATTTTTT
ENSG00000176953:ENST0000032080 --------------------------------------------------
isotig35100 TTAATATTTAAAAATTCCATGACATATAGCTTCCAGGTTTCTCAGCTCTT
isotig35101 TtGGAATATGTTATACCTTTGAATTTTAATATTAAATTCCATGACATAGT
ENSG00000176953:ENST0000032080 --------------------------------------------------
isotig35100 GTATGACAATATCACACATTaCTATTATGTATTCAATCTCAGCCAAAGGG
isotig35101 ACTTCCAGGTTTCTCAGCTCTTGTACAATTAATGAATCTGAACACATTaC
ENSG00000176953:ENST0000032080 --------------------------------------------------
isotig35100 AGATGCCTTTA---------------------------------
isotig35101 TATTATGTATTCAATCTCAGCCAATAAAGGGAGATGCCTTTAAC
ENSG00000176953:ENST0000032080 --------------------------------------------
""",
)
def test3(self):
aligner = CodonAligner()
nucleotide_records = SeqIO.index("codonalign/nucl3.fa", "fasta")
protein_alignment = Align.read("codonalign/pro3.aln", "clustal")
self.assertEqual(len(protein_alignment.sequences), 10)
codon_alignments = []
protein_record = protein_alignment.sequences[0]
nucleotide_record = nucleotide_records[protein_record.id]
self.assertEqual(nucleotide_record.id, protein_record.id)
alignments = aligner.align(protein_record, nucleotide_record)
self.assertEqual(len(alignments), 1)
alignment = next(alignments)
codon_alignments.append(alignment)
self.assertTrue(
np.array_equal(alignment.coordinates, np.array([[0, 847], [0, 2541]]))
)
self.assertEqual(
str(alignment),
"""\
ENSG00000 0 M S L W G L V S K M P P E K V Q R L Y V
ENSG00000 0 ATGTCTCTGTGGGGTCTGGTCTCCAAGATGCCCCCAGAAAAAGTGCAGCGGCTCTATGTC
ENSG00000 20 D F P Q H L R H L L G D W L E S Q P W E
ENSG00000 60 GACTTTCCCCAACACCTGCGGCATCTTCTGGGTGACTGGCTGGAGAGCCAGCCCTGGGAG
ENSG00000 40 F L V G S D A F C C N L A S A L L S D T
ENSG00000 120 TTCCTGGTCGGCTCCGACGCCTTCTGCTGCAACTTGGCTAGTGCCCTACTTTCAGACACT
ENSG00000 60 V Q H L Q A S V G E Q G E G S T I L Q H
ENSG00000 180 GTCCAGCACCTTCAGGCCTCGGTGGGAGAGCAGGGGGAGGGGAGCACCATCTTGCAACAC
ENSG00000 80 I S T L E S I Y Q R D P L K L V A T F R
ENSG00000 240 ATCAGCACCCTTGAGAGCATATATCAGAGGGACCCCCTGAAGCTGGTGGCCACTTTCAGA
ENSG00000 100 Q I L Q G E K K A V M E Q F R H L P M P
ENSG00000 300 CAAATACTTCAAGGAGAGAAAAAAGCTGTTATGGAACAGTTCCGCCACTTGCCAATGCCT
ENSG00000 120 F H W K Q E E L K F K T G L R R L Q H R
ENSG00000 360 TTCCACTGGAAGCAGGAAGAACTCAAGTTTAAGACAGGCTTGCGGAGGCTGCAGCACCGA
ENSG00000 140 V G E I H L L R E A L Q K G A E A G Q V
ENSG00000 420 GTAGGGGAGATCCACCTTCTCCGAGAAGCCCTGCAGAAGGGGGCTGAGGCTGGCCAAGTG
ENSG00000 160 S L H S L I E T P A N G T G P S E A L A
ENSG00000 480 TCTCTGCACAGCTTGATAGAAACTCCTGCTAATGGGACTGGGCCAAGTGAGGCCCTGGCC
ENSG00000 180 M L L Q E T T G E L E A A K A L V L K R
ENSG00000 540 ATGCTACTGCAGGAGACCACTGGAGAGCTAGAGGCAGCCAAAGCCCTAGTGCTGAAGAGG
ENSG00000 200 I Q I W K R Q Q Q L A G N G A P F E E S
ENSG00000 600 ATCCAGATTTGGAAACGGCAGCAGCAGCTGGCAGGGAATGGCGCACCGTTTGAGGAGAGC
ENSG00000 220 L A P L Q E R C E S L V D I Y S Q L Q Q
ENSG00000 660 CTGGCCCCACTCCAGGAGAGGTGTGAAAGCCTGGTGGACATTTATTCCCAGCTACAGCAG
ENSG00000 240 E V G A A G G E L E P K T R A S L T G R
ENSG00000 720 GAGGTAGGGGCGGCTGGTGGGGAGCTTGAGCCCAAGACCCGGGCATCGCTGACTGGCCGG
ENSG00000 260 L D E V L R T L V T S C F L V E K Q P P
ENSG00000 780 CTGGATGAAGTCCTGAGAACCCTCGTCACCAGTTGCTTCCTGGTGGAGAAGCAGCCCCCC
ENSG00000 280 Q V L K T Q T K F Q A G V R F L L G L R
ENSG00000 840 CAGGTACTGAAGACTCAGACCAAGTTCCAGGCTGGAGTTCGATTCCTGTTGGGCTTGAGG
ENSG00000 300 F L G A P A K P P L V R A D M V T E K Q
ENSG00000 900 TTCCTGGGGGCCCCAGCCAAGCCTCCGCTGGTCAGGGCCGACATGGTGACAGAGAAGCAG
ENSG00000 320 A R E L S V P Q G P G A G A E S T G E I
ENSG00000 960 GCGCGGGAGCTGAGTGTGCCTCAGGGTCCTGGGGCTGGAGCAGAAAGCACTGGAGAAATC
ENSG00000 340 I N N T V P L E N S I P G N C C S A L F
ENSG00000 1020 ATCAACAACACTGTGCCCTTGGAGAACAGCATTCCTGGGAACTGCTGCTCTGCCCTGTTC
ENSG00000 360 K N L L L K K I K R C E R K G T E S V T
ENSG00000 1080 AAGAACCTGCTTCTCAAGAAGATCAAGCGGTGTGAGCGGAAGGGCACTGAGTCTGTCACA
ENSG00000 380 E E K C A V L F S A S F T L G P G K L P
ENSG00000 1140 GAGGAGAAGTGCGCTGTGCTCTTCTCTGCCAGCTTCACACTTGGCCCCGGCAAACTCCCC
ENSG00000 400 I Q L Q A L S L P L V V I V H G N Q D N
ENSG00000 1200 ATCCAGCTCCAGGCCCTGTCTCTGCCCCTGGTGGTCATCGTCCATGGCAACCAAGACAAC
ENSG00000 420 N A K A T I L W D N A F S E M D R V P F
ENSG00000 1260 AATGCCAAAGCCACTATCCTGTGGGACAATGCCTTCTCTGAGATGGACCGCGTGCCCTTT
ENSG00000 440 V V A E R V P W E K M C E T L N L K F M
ENSG00000 1320 GTGGTGGCTGAGCGGGTGCCCTGGGAGAAGATGTGTGAAACTCTGAACCTGAAGTTCATG
ENSG00000 460 A E V G T N R G L L P E H F L F L A Q K
ENSG00000 1380 GCTGAGGTGGGGACCAACCGGGGGCTGCTCCCAGAGCACTTCCTCTTCCTGGCCCAGAAG
ENSG00000 480 I F N D N S L S M E A F Q H R S V S W S
ENSG00000 1440 ATCTTCAATGACAACAGCCTCAGTATGGAGGCCTTCCAGCACCGTTCTGTGTCCTGGTCG
ENSG00000 500 Q F N K E I L L G R G F T F W Q W F D G
ENSG00000 1500 CAGTTCAACAAGGAGATCCTGCTGGGCCGTGGCTTCACCTTTTGGCAGTGGTTTGATGGT
ENSG00000 520 V L D L T K R C L R S Y W S D R L I I G
ENSG00000 1560 GTCCTGGACCTCACCAAACGCTGTCTCCGGAGCTACTGGTCTGACCGGCTGATCATTGGC
ENSG00000 540 F I S K Q Y V T S L L L N E P D G T F L
ENSG00000 1620 TTCATCAGCAAACAGTACGTTACTAGCCTTCTTCTCAATGAGCCCGACGGAACCTTTCTC
ENSG00000 560 L R F S D S E I G G I T I A H V I R G Q
ENSG00000 1680 CTCCGCTTCAGCGACTCAGAGATTGGGGGCATCACCATTGCCCATGTCATCCGGGGCCAG
ENSG00000 580 D G S P Q I E N I Q P F S A K D L S I R
ENSG00000 1740 GATGGCTCTCCACAGATAGAGAACATCCAGCCATTCTCTGCCAAAGACCTGTCCATTCGC
ENSG00000 600 S L G D R I R D L A Q L K N L Y P K K P
ENSG00000 1800 TCACTGGGGGACCGAATCCGGGATCTTGCTCAGCTCAAAAATCTCTATCCCAAGAAGCCC
ENSG00000 620 K D E A F R S H Y K P E Q M G K D G R G
ENSG00000 1860 AAGGATGAGGCTTTCCGGAGCCACTACAAGCCTGAACAGATGGGTAAGGATGGCAGGGGT
ENSG00000 640 Y V P A T I K M T V E R D Q P L P T P E
ENSG00000 1920 TATGTCCCAGCTACCATCAAGATGACCGTGGAAAGGGACCAACCACTTCCTACCCCAGAG
ENSG00000 660 L Q M P T M V P S Y D L G M A P D S S M
ENSG00000 1980 CTCCAGATGCCTACCATGGTGCCTTCTTATGACCTTGGAATGGCCCCTGATTCCTCCATG
ENSG00000 680 S M Q L G P D M V P Q V Y P P H S H S I
ENSG00000 2040 AGCATGCAGCTTGGCCCAGATATGGTGCCCCAGGTGTACCCACCACACTCTCACTCCATC
ENSG00000 700 P P Y Q G L S P E E S V N V L S A F Q E
ENSG00000 2100 CCCCCGTATCAAGGCCTCTCCCCAGAAGAATCAGTCAACGTGTTGTCAGCCTTCCAGGAG
ENSG00000 720 P H L Q M P P S L G Q M S L P F D Q P H
ENSG00000 2160 CCTCACCTGCAGATGCCCCCCAGCCTGGGCCAGATGAGCCTGCCCTTTGACCAGCCTCAC
ENSG00000 740 P Q G L L P C Q P Q E H A V S S P D P L
ENSG00000 2220 CCCCAGGGCCTGCTGCCGTGCCAGCCTCAGGAGCATGCTGTGTCCAGCCCTGACCCCCTG
ENSG00000 760 L C S D V T M V E D S C L S Q P V T A F
ENSG00000 2280 CTCTGCTCAGATGTGACCATGGTGGAAGACAGCTGCCTGAGCCAGCCAGTGACAGCGTTT
ENSG00000 780 P Q G T W I G E D I F P P L L P P T E Q
ENSG00000 2340 CCTCAGGGCACTTGGATTGGTGAAGACATATTCCCTCCTCTGCTGCCTCCCACTGAACAG
ENSG00000 800 D L T K L L L E G Q G E S G G G S L G A
ENSG00000 2400 GACCTCACTAAGCTTCTCCTGGAGGGGCAAGGGGAGTCGGGGGGAGGGTCCTTGGGGGCA
ENSG00000 820 Q P L L Q P S H Y G Q S G I S M S H M D
ENSG00000 2460 CAGCCCCTCCTGCAGCCCTCCCACTATGGGCAATCTGGGATCTCAATGTCCCACATGGAC
ENSG00000 840 L R A N P S W 847
ENSG00000 2520 CTAAGGGCCAACCCCAGTTGG 2541
""",
)
protein_record = protein_alignment.sequences[1]
nucleotide_record = nucleotide_records[protein_record.id]
self.assertEqual(nucleotide_record.id, protein_record.id)
alignments = aligner.align(protein_record, nucleotide_record)
self.assertEqual(len(alignments), 1)
alignment = next(alignments)
codon_alignments.append(alignment)
self.assertTrue(
np.array_equal(alignment.coordinates, np.array([[0, 847], [0, 2541]]))
)
self.assertEqual(
str(alignment),
"""\
ENSG00000 0 M S L W G L V S K M P P E K V Q R L Y V
ENSG00000 0 ATGTCTCTGTGGGGTCTGGTCTCCAAGATGCCCCCAGAAAAAGTGCAGCGGCTCTATGTC
ENSG00000 20 D F P Q H L R H L L G D W L E S Q P W E
ENSG00000 60 GACTTTCCCCAACACCTGCGGCATCTTCTGGGTGACTGGCTGGAGAGCCAGCCCTGGGAG
ENSG00000 40 F L V G S D A F C C N L A S A L L S D T
ENSG00000 120 TTCCTGGTCGGCTCCGACGCCTTCTGCTGCAACTTGGCTAGTGCCCTACTTTCAGACACT
ENSG00000 60 V Q H L Q A S V G E Q G E G S T I L Q H
ENSG00000 180 GTCCAGCACCTTCAGGCCTCGGTGGGAGAGCAGGGGGAGGGGAGCACCATCTTGCAACAC
ENSG00000 80 I S T L E S I Y Q R D P L K L V A T F R
ENSG00000 240 ATCAGCACCCTTGAGAGCATATATCAGAGGGACCCCCTGAAGCTGGTGGCCACTTTCAGA
ENSG00000 100 Q I L Q G E K K A V M E Q F R H L P M P
ENSG00000 300 CAAATACTTCAAGGAGAGAAAAAAGCTGTTATGGAACAGTTCCGCCACTTGCCAATGCCT
ENSG00000 120 F H W K Q E E L K F K T G L R R L Q H R
ENSG00000 360 TTCCACTGGAAGCAGGAAGAACTCAAGTTTAAGACAGGCTTGCGGAGGCTGCAGCACCGA
ENSG00000 140 V G E I H L L R E A L Q K G A E A G Q V
ENSG00000 420 GTAGGGGAGATCCACCTTCTCCGAGAAGCCCTGCAGAAGGGGGCTGAGGCTGGCCAAGTG
ENSG00000 160 S L H S L I E T P A N G T G P S E A L A
ENSG00000 480 TCTCTGCACAGCTTGATAGAAACTCCTGCTAATGGGACTGGGCCAAGTGAGGCCCTGGCC
ENSG00000 180 M L L Q E T T G E L E A A K A L V L K R
ENSG00000 540 ATGCTACTGCAGGAGACCACTGGAGAGCTAGAGGCAGCCAAAGCCCTAGTGCTGAAGAGG
ENSG00000 200 I Q I W K R Q Q Q L A G N G A P F E E S
ENSG00000 600 ATCCAGATTTGGAAACGGCAGCAGCAGCTGGCAGGGAATGGCGCACCGTTTGAGGAGAGC
ENSG00000 220 L A P L Q E R C E S L V D I Y S Q L Q Q
ENSG00000 660 CTGGCCCCACTCCAGGAGAGGTGTGAAAGCCTGGTGGACATTTATTCCCAGCTACAGCAG
ENSG00000 240 E V G A A G G E L E P K T R A S L T G R
ENSG00000 720 GAGGTAGGGGCGGCTGGTGGGGAGCTTGAGCCCAAGACCCGGGCATCGCTGACTGGCCGG
ENSG00000 260 L D E V L R T L V T S C F L V E K Q P P
ENSG00000 780 CTGGATGAAGTCCTGAGAACCCTCGTCACCAGTTGCTTCCTGGTGGAGAAGCAGCCCCCC
ENSG00000 280 Q V L K T Q T K F Q A G V R F L L G L R
ENSG00000 840 CAGGTACTGAAGACTCAGACCAAGTTCCAGGCTGGAGTTCGATTCCTGTTGGGCTTGAGG
ENSG00000 300 F L G A P A K P P L V R A D M V T E K Q
ENSG00000 900 TTCCTGGGGGCCCCAGCCAAGCCTCCGCTGGTCAGGGCCGACATGGTGACAGAGAAGCAG
ENSG00000 320 A R E L S V P Q G P G A G A E S T G E I
ENSG00000 960 GCGCGGGAGCTGAGTGTGCCTCAGGGTCCTGGGGCTGGAGCAGAAAGCACTGGAGAAATC
ENSG00000 340 I N N T V P L E N S I P G N C C S A L F
ENSG00000 1020 ATCAACAACACTGTGCCCTTGGAGAACAGCATTCCTGGGAACTGCTGCTCTGCCCTGTTC
ENSG00000 360 K N L L L K K I K R C E R K G T E S V T
ENSG00000 1080 AAGAACCTGCTTCTCAAGAAGATCAAGCGGTGTGAGCGGAAGGGCACTGAGTCTGTCACA
ENSG00000 380 E E K C A V L F S A S F T L G P G K L P
ENSG00000 1140 GAGGAGAAGTGCGCTGTGCTCTTCTCTGCCAGCTTCACACTTGGCCCCGGCAAACTCCCC
ENSG00000 400 I Q L Q A L S L P L V V I V H G N Q D N
ENSG00000 1200 ATCCAGCTCCAGGCCCTGTCTCTGCCCCTGGTGGTCATCGTCCATGGCAACCAAGACAAC
ENSG00000 420 N A K A T I L W D N A F S E M D R V P F
ENSG00000 1260 AATGCCAAAGCCACTATCCTGTGGGACAATGCCTTCTCTGAGATGGACCGCGTGCCCTTT
ENSG00000 440 V V A E R V P W E K M C E T L N L K F M
ENSG00000 1320 GTGGTGGCTGAGCGGGTGCCCTGGGAGAAGATGTGTGAAACTCTGAACCTGAAGTTCATG
ENSG00000 460 A E V G T N R G L L P E H F L F L A Q K
ENSG00000 1380 GCTGAGGTGGGGACCAACCGGGGGCTGCTCCCAGAGCACTTCCTCTTCCTGGCCCAGAAG
ENSG00000 480 I F N D N S L S M E A F Q H R S V S W S
ENSG00000 1440 ATCTTCAATGACAACAGCCTCAGTATGGAGGCCTTCCAGCACCGTTCTGTGTCCTGGTCG
ENSG00000 500 Q F N K E I L L G R G F T F W Q W F D G
ENSG00000 1500 CAGTTCAACAAGGAGATCCTGCTGGGCCGTGGCTTCACCTTTTGGCAGTGGTTTGATGGT
ENSG00000 520 V L D L T K R C L R S Y W S D R L I I G
ENSG00000 1560 GTCCTGGACCTCACCAAACGCTGTCTCCGGAGCTACTGGTCTGACCGGCTGATCATTGGC
ENSG00000 540 F I S K Q Y V T S L L L N E P D G T F L
ENSG00000 1620 TTCATCAGCAAACAGTACGTTACTAGCCTTCTTCTCAATGAGCCCGACGGAACCTTTCTC
ENSG00000 560 L R F S D S E I G G I T I A H V I R G Q
ENSG00000 1680 CTCCGCTTCAGCGACTCAGAGATTGGGGGCATCACCATTGCCCATGTCATCCGGGGCCAG
ENSG00000 580 D G S P Q I E N I Q P F S A K D L S I R
ENSG00000 1740 GATGGCTCTCCACAGATAGAGAACATCCAGCCATTCTCTGCCAAAGACCTGTCCATTCGC
ENSG00000 600 S L G D R I R D L A Q L K N L Y P K K P
ENSG00000 1800 TCACTGGGGGACCGAATCCGGGATCTTGCTCAGCTCAAAAATCTCTATCCCAAGAAGCCC
ENSG00000 620 K D E A F R S H Y K P E Q M G K D G R G
ENSG00000 1860 AAGGATGAGGCTTTCCGGAGCCACTACAAGCCTGAACAGATGGGTAAGGATGGCAGGGGT
ENSG00000 640 Y V P A T I K M T V E R D Q P L P T P E
ENSG00000 1920 TATGTCCCAGCTACCATCAAGATGACCGTGGAAAGGGACCAACCACTTCCTACCCCAGAG
ENSG00000 660 L Q M P T M V P S Y D L G M A P D S S M
ENSG00000 1980 CTCCAGATGCCTACCATGGTGCCTTCTTATGACCTTGGAATGGCCCCTGATTCCTCCATG
ENSG00000 680 S M Q L G P D M V P Q V Y P P H S H S I
ENSG00000 2040 AGCATGCAGCTTGGCCCAGATATGGTGCCCCAGGTGTACCCACCACACTCTCACTCCATC
ENSG00000 700 P P Y Q G L S P E E S V N V L S A F Q E
ENSG00000 2100 CCCCCGTATCAAGGCCTCTCCCCAGAAGAATCAGTCAACGTGTTGTCAGCCTTCCAGGAG
ENSG00000 720 P H L Q M P P S L G Q M S L P F D Q P H
ENSG00000 2160 CCTCACCTGCAGATGCCCCCCAGCCTGGGCCAGATGAGCCTGCCCTTTGACCAGCCTCAC
ENSG00000 740 P Q G L L P C Q P Q E H A V S S P D P L
ENSG00000 2220 CCCCAGGGCCTGCTGCCGTGCCAGCCTCAGGAGCATGCTGTGTCCAGCCCTGACCCCCTG
ENSG00000 760 L C S D V T M V E D S C L S Q P V T A F
ENSG00000 2280 CTCTGCTCAGATGTGACCATGGTGGAAGACAGCTGCCTGAGCCAGCCAGTGACAGCGTTT
ENSG00000 780 P Q G T W I G E D I F P P L L P P T E Q
ENSG00000 2340 CCTCAGGGCACTTGGATTGGTGAAGACATATTCCCTCCTCTGCTGCCTCCCACTGAACAG
ENSG00000 800 D L T K L L L E G Q G E S G G G S L G A
ENSG00000 2400 GACCTCACTAAGCTTCTCCTGGAGGGGCAAGGGGAGTCGGGGGGAGGGTCCTTGGGGGCA
ENSG00000 820 Q P L L Q P S H Y G Q S G I S M S H M D
ENSG00000 2460 CAGCCCCTCCTGCAGCCCTCCCACTATGGGCAATCTGGGATCTCAATGTCCCACATGGAC
ENSG00000 840 L R A N P S W 847
ENSG00000 2520 CTAAGGGCCAACCCCAGTTGG 2541
""",
)
protein_record = protein_alignment.sequences[2]
nucleotide_record = nucleotide_records[protein_record.id]
self.assertEqual(nucleotide_record.id, protein_record.id)
alignments = aligner.align(protein_record, nucleotide_record)
self.assertEqual(len(alignments), 1)
alignment = next(alignments)
codon_alignments.append(alignment)
self.assertTrue(
np.array_equal(alignment.coordinates, np.array([[0, 847], [0, 2541]]))
)
self.assertEqual(
str(alignment),
"""\
ENSG00000 0 M S L W G L V S K M P P E K V Q R L Y V
ENSG00000 0 ATGTCTCTGTGGGGTCTGGTCTCCAAGATGCCCCCAGAAAAAGTGCAGCGGCTCTATGTC
ENSG00000 20 D F P Q H L R H L L G D W L E S Q P W E
ENSG00000 60 GACTTTCCCCAACACCTGCGGCATCTTCTGGGTGACTGGCTGGAGAGCCAGCCCTGGGAG
ENSG00000 40 F L V G S D A F C C N L A S A L L S D T
ENSG00000 120 TTCCTGGTCGGCTCCGACGCCTTCTGCTGCAACTTGGCTAGTGCCCTACTTTCAGACACT
ENSG00000 60 V Q H L Q A S V G E Q G E G S T I L Q H
ENSG00000 180 GTCCAGCACCTTCAGGCCTCGGTGGGAGAGCAGGGGGAGGGGAGCACCATCTTGCAACAC
ENSG00000 80 I S T L E S I Y Q R D P L K L V A T F R
ENSG00000 240 ATCAGCACCCTTGAGAGCATATATCAGAGGGACCCCCTGAAGCTGGTGGCCACTTTCAGA
ENSG00000 100 Q I L Q G E K K A V M E Q F R H L P M P
ENSG00000 300 CAAATACTTCAAGGAGAGAAAAAAGCTGTTATGGAACAGTTCCGCCACTTGCCAATGCCT
ENSG00000 120 F H W K Q E E L K F K T G L R R L Q H R
ENSG00000 360 TTCCACTGGAAGCAGGAAGAACTCAAGTTTAAGACAGGCTTGCGGAGGCTGCAGCACCGA
ENSG00000 140 V G E I H L L R E A L Q K G A E A G Q V
ENSG00000 420 GTAGGGGAGATCCACCTTCTCCGAGAAGCCCTGCAGAAGGGGGCTGAGGCTGGCCAAGTG
ENSG00000 160 S L H S L I E T P A N G T G P S E A L A
ENSG00000 480 TCTCTGCACAGCTTGATAGAAACTCCTGCTAATGGGACTGGGCCAAGTGAGGCCCTGGCC
ENSG00000 180 M L L Q E T T G E L E A A K A L V L K R
ENSG00000 540 ATGCTACTGCAGGAGACCACTGGAGAGCTAGAGGCAGCCAAAGCCCTAGTGCTGAAGAGG
ENSG00000 200 I Q I W K R Q Q Q L A G N G A P F E E S
ENSG00000 600 ATCCAGATTTGGAAACGGCAGCAGCAGCTGGCAGGGAATGGCGCACCGTTTGAGGAGAGC
ENSG00000 220 L A P L Q E R C E S L V D I Y S Q L Q Q
ENSG00000 660 CTGGCCCCACTCCAGGAGAGGTGTGAAAGCCTGGTGGACATTTATTCCCAGCTACAGCAG
ENSG00000 240 E V G A A G G E L E P K T R A S L T G R
ENSG00000 720 GAGGTAGGGGCGGCTGGTGGGGAGCTTGAGCCCAAGACCCGGGCATCGCTGACTGGCCGG
ENSG00000 260 L D E V L R T L V T S C F L V E K Q P P
ENSG00000 780 CTGGATGAAGTCCTGAGAACCCTCGTCACCAGTTGCTTCCTGGTGGAGAAGCAGCCCCCC
ENSG00000 280 Q V L K T Q T K F Q A G V R F L L G L R
ENSG00000 840 CAGGTACTGAAGACTCAGACCAAGTTCCAGGCTGGAGTTCGATTCCTGTTGGGCTTGAGG
ENSG00000 300 F L G A P A K P P L V R A D M V T E K Q
ENSG00000 900 TTCCTGGGGGCCCCAGCCAAGCCTCCGCTGGTCAGGGCCGACATGGTGACAGAGAAGCAG
ENSG00000 320 A R E L S V P Q G P G A G A E S T G E I
ENSG00000 960 GCGCGGGAGCTGAGTGTGCCTCAGGGTCCTGGGGCTGGAGCAGAAAGCACTGGAGAAATC
ENSG00000 340 I N N T V P L E N S I P G N C C S A L F
ENSG00000 1020 ATCAACAACACTGTGCCCTTGGAGAACAGCATTCCTGGGAACTGCTGCTCTGCCCTGTTC
ENSG00000 360 K N L L L K K I K R C E R K G T E S V T
ENSG00000 1080 AAGAACCTGCTTCTCAAGAAGATCAAGCGGTGTGAGCGGAAGGGCACTGAGTCTGTCACA
ENSG00000 380 E E K C A V L F S A S F T L G P G K L P
ENSG00000 1140 GAGGAGAAGTGCGCTGTGCTCTTCTCTGCCAGCTTCACACTTGGCCCCGGCAAACTCCCC
ENSG00000 400 I Q L Q A L S L P L V V I V H G N Q D N
ENSG00000 1200 ATCCAGCTCCAGGCCCTGTCTCTGCCCCTGGTGGTCATCGTCCATGGCAACCAAGACAAC
ENSG00000 420 N A K A T I L W D N A F S E M D R V P F
ENSG00000 1260 AATGCCAAAGCCACTATCCTGTGGGACAATGCCTTCTCTGAGATGGACCGCGTGCCCTTT
ENSG00000 440 V V A E R V P W E K M C E T L N L K F M
ENSG00000 1320 GTGGTGGCTGAGCGGGTGCCCTGGGAGAAGATGTGTGAAACTCTGAACCTGAAGTTCATG
ENSG00000 460 A E V G T N R G L L P E H F L F L A Q K
ENSG00000 1380 GCTGAGGTGGGGACCAACCGGGGGCTGCTCCCAGAGCACTTCCTCTTCCTGGCCCAGAAG
ENSG00000 480 I F N D N S L S M E A F Q H R S V S W S
ENSG00000 1440 ATCTTCAATGACAACAGCCTCAGTATGGAGGCCTTCCAGCACCGTTCTGTGTCCTGGTCG
ENSG00000 500 Q F N K E I L L G R G F T F W Q W F D G
ENSG00000 1500 CAGTTCAACAAGGAGATCCTGCTGGGCCGTGGCTTCACCTTTTGGCAGTGGTTTGATGGT
ENSG00000 520 V L D L T K R C L R S Y W S D R L I I G
ENSG00000 1560 GTCCTGGACCTCACCAAACGCTGTCTCCGGAGCTACTGGTCTGACCGGCTGATCATTGGC
ENSG00000 540 F I S K Q Y V T S L L L N E P D G T F L
ENSG00000 1620 TTCATCAGCAAACAGTACGTTACTAGCCTTCTTCTCAATGAGCCCGACGGAACCTTTCTC
ENSG00000 560 L R F S D S E I G G I T I A H V I R G Q
ENSG00000 1680 CTCCGCTTCAGCGACTCAGAGATTGGGGGCATCACCATTGCCCATGTCATCCGGGGCCAG
ENSG00000 580 D G S P Q I E N I Q P F S A K D L S I R
ENSG00000 1740 GATGGCTCTCCACAGATAGAGAACATCCAGCCATTCTCTGCCAAAGACCTGTCCATTCGC
ENSG00000 600 S L G D R I R D L A Q L K N L Y P K K P
ENSG00000 1800 TCACTGGGGGACCGAATCCGGGATCTTGCTCAGCTCAAAAATCTCTATCCCAAGAAGCCC
ENSG00000 620 K D E A F R S H Y K P E Q M G K D G R G
ENSG00000 1860 AAGGATGAGGCTTTCCGGAGCCACTACAAGCCTGAACAGATGGGTAAGGATGGCAGGGGT
ENSG00000 640 Y V P A T I K M T V E R D Q P L P T P E
ENSG00000 1920 TATGTCCCAGCTACCATCAAGATGACCGTGGAAAGGGACCAACCACTTCCTACCCCAGAG
ENSG00000 660 L Q M P T M V P S Y D L G M A P D S S M
ENSG00000 1980 CTCCAGATGCCTACCATGGTGCCTTCTTATGACCTTGGAATGGCCCCTGATTCCTCCATG
ENSG00000 680 S M Q L G P D M V P Q V Y P P H S H S I
ENSG00000 2040 AGCATGCAGCTTGGCCCAGATATGGTGCCCCAGGTGTACCCACCACACTCTCACTCCATC
ENSG00000 700 P P Y Q G L S P E E S V N V L S A F Q E
ENSG00000 2100 CCCCCGTATCAAGGCCTCTCCCCAGAAGAATCAGTCAACGTGTTGTCAGCCTTCCAGGAG
ENSG00000 720 P H L Q M P P S L G Q M S L P F D Q P H
ENSG00000 2160 CCTCACCTGCAGATGCCCCCCAGCCTGGGCCAGATGAGCCTGCCCTTTGACCAGCCTCAC
ENSG00000 740 P Q G L L P C Q P Q E H A V S S P D P L
ENSG00000 2220 CCCCAGGGCCTGCTGCCGTGCCAGCCTCAGGAGCATGCTGTGTCCAGCCCTGACCCCCTG
ENSG00000 760 L C S D V T M V E D S C L S Q P V T A F
ENSG00000 2280 CTCTGCTCAGATGTGACCATGGTGGAAGACAGCTGCCTGAGCCAGCCAGTGACAGCGTTT
ENSG00000 780 P Q G T W I G E D I F P P L L P P T E Q
ENSG00000 2340 CCTCAGGGCACTTGGATTGGTGAAGACATATTCCCTCCTCTGCTGCCTCCCACTGAACAG
ENSG00000 800 D L T K L L L E G Q G E S G G G S L G A
ENSG00000 2400 GACCTCACTAAGCTTCTCCTGGAGGGGCAAGGGGAGTCGGGGGGAGGGTCCTTGGGGGCA
ENSG00000 820 Q P L L Q P S H Y G Q S G I S M S H M D
ENSG00000 2460 CAGCCCCTCCTGCAGCCCTCCCACTATGGGCAATCTGGGATCTCAATGTCCCACATGGAC
ENSG00000 840 L R A N P S W 847
ENSG00000 2520 CTAAGGGCCAACCCCAGTTGG 2541
""",
)
protein_record = protein_alignment.sequences[3]
nucleotide_record = nucleotide_records[protein_record.id]
self.assertEqual(nucleotide_record.id, protein_record.id)
alignments = aligner.align(protein_record, nucleotide_record)
self.assertEqual(len(alignments), 1)
alignment = next(alignments)
codon_alignments.append(alignment)
self.assertTrue(
np.array_equal(alignment.coordinates, np.array([[0, 847], [0, 2541]]))
)
self.assertEqual(
str(alignment),
"""\
ENSG00000 0 M S L W G L V S K M P P E K V Q R L Y V
ENSG00000 0 ATGTCTCTGTGGGGTCTGGTCTCCAAGATGCCCCCAGAAAAAGTGCAGCGGCTCTATGTC
ENSG00000 20 D F P Q H L R H L L G D W L E S Q P W E
ENSG00000 60 GACTTTCCCCAACACCTGCGGCATCTTCTGGGTGACTGGCTGGAGAGCCAGCCCTGGGAG
ENSG00000 40 F L V G S D A F C C N L A S A L L S D T
ENSG00000 120 TTCCTGGTCGGCTCCGACGCCTTCTGCTGCAACTTGGCTAGTGCCCTACTTTCAGACACT
ENSG00000 60 V Q H L Q A S V G E Q G E G S T I L Q H
ENSG00000 180 GTCCAGCACCTTCAGGCCTCGGTGGGAGAGCAGGGGGAGGGGAGCACCATCTTGCAACAC
ENSG00000 80 I S T L E S I Y Q R D P L K L V A T F R
ENSG00000 240 ATCAGCACCCTTGAGAGCATATATCAGAGGGACCCCCTGAAGCTGGTGGCCACTTTCAGA
ENSG00000 100 Q I L Q G E K K A V M E Q F R H L P M P
ENSG00000 300 CAAATACTTCAAGGAGAGAAAAAAGCTGTTATGGAACAGTTCCGCCACTTGCCAATGCCT
ENSG00000 120 F H W K Q E E L K F K T G L R R L Q H R
ENSG00000 360 TTCCACTGGAAGCAGGAAGAACTCAAGTTTAAGACAGGCTTGCGGAGGCTGCAGCACCGA
ENSG00000 140 V G E I H L L R E A L Q K G A E A G Q V
ENSG00000 420 GTAGGGGAGATCCACCTTCTCCGAGAAGCCCTGCAGAAGGGGGCTGAGGCTGGCCAAGTG
ENSG00000 160 S L H S L I E T P A N G T G P S E A L A
ENSG00000 480 TCTCTGCACAGCTTGATAGAAACTCCTGCTAATGGGACTGGGCCAAGTGAGGCCCTGGCC
ENSG00000 180 M L L Q E T T G E L E A A K A L V L K R
ENSG00000 540 ATGCTACTGCAGGAGACCACTGGAGAGCTAGAGGCAGCCAAAGCCCTAGTGCTGAAGAGG
ENSG00000 200 I Q I W K R Q Q Q L A G N G A P F E E S
ENSG00000 600 ATCCAGATTTGGAAACGGCAGCAGCAGCTGGCAGGGAATGGCGCACCGTTTGAGGAGAGC
ENSG00000 220 L A P L Q E R C E S L V D I Y S Q L Q Q
ENSG00000 660 CTGGCCCCACTCCAGGAGAGGTGTGAAAGCCTGGTGGACATTTATTCCCAGCTACAGCAG
ENSG00000 240 E V G A A G G E L E P K T R A S L T G R
ENSG00000 720 GAGGTAGGGGCGGCTGGTGGGGAGCTTGAGCCCAAGACCCGGGCATCGCTGACTGGCCGG
ENSG00000 260 L D E V L R T L V T S C F L V E K Q P P
ENSG00000 780 CTGGATGAAGTCCTGAGAACCCTCGTCACCAGTTGCTTCCTGGTGGAGAAGCAGCCCCCC
ENSG00000 280 Q V L K T Q T K F Q A G V R F L L G L R
ENSG00000 840 CAGGTACTGAAGACTCAGACCAAGTTCCAGGCTGGAGTTCGATTCCTGTTGGGCTTGAGG
ENSG00000 300 F L G A P A K P P L V R A D M V T E K Q
ENSG00000 900 TTCCTGGGGGCCCCAGCCAAGCCTCCGCTGGTCAGGGCCGACATGGTGACAGAGAAGCAG
ENSG00000 320 A R E L S V P Q G P G A G A E S T G E I
ENSG00000 960 GCGCGGGAGCTGAGTGTGCCTCAGGGTCCTGGGGCTGGAGCAGAAAGCACTGGAGAAATC
ENSG00000 340 I N N T V P L E N S I P G N C C S A L F
ENSG00000 1020 ATCAACAACACTGTGCCCTTGGAGAACAGCATTCCTGGGAACTGCTGCTCTGCCCTGTTC
ENSG00000 360 K N L L L K K I K R C E R K G T E S V T
ENSG00000 1080 AAGAACCTGCTTCTCAAGAAGATCAAGCGGTGTGAGCGGAAGGGCACTGAGTCTGTCACA
ENSG00000 380 E E K C A V L F S A S F T L G P G K L P
ENSG00000 1140 GAGGAGAAGTGCGCTGTGCTCTTCTCTGCCAGCTTCACACTTGGCCCCGGCAAACTCCCC
ENSG00000 400 I Q L Q A L S L P L V V I V H G N Q D N
ENSG00000 1200 ATCCAGCTCCAGGCCCTGTCTCTGCCCCTGGTGGTCATCGTCCATGGCAACCAAGACAAC
ENSG00000 420 N A K A T I L W D N A F S E M D R V P F
ENSG00000 1260 AATGCCAAAGCCACTATCCTGTGGGACAATGCCTTCTCTGAGATGGACCGCGTGCCCTTT
ENSG00000 440 V V A E R V P W E K M C E T L N L K F M
ENSG00000 1320 GTGGTGGCTGAGCGGGTGCCCTGGGAGAAGATGTGTGAAACTCTGAACCTGAAGTTCATG
ENSG00000 460 A E V G T N R G L L P E H F L F L A Q K
ENSG00000 1380 GCTGAGGTGGGGACCAACCGGGGGCTGCTCCCAGAGCACTTCCTCTTCCTGGCCCAGAAG
ENSG00000 480 I F N D N S L S M E A F Q H R S V S W S
ENSG00000 1440 ATCTTCAATGACAACAGCCTCAGTATGGAGGCCTTCCAGCACCGTTCTGTGTCCTGGTCG
ENSG00000 500 Q F N K E I L L G R G F T F W Q W F D G
ENSG00000 1500 CAGTTCAACAAGGAGATCCTGCTGGGCCGTGGCTTCACCTTTTGGCAGTGGTTTGATGGT
ENSG00000 520 V L D L T K R C L R S Y W S D R L I I G
ENSG00000 1560 GTCCTGGACCTCACCAAACGCTGTCTCCGGAGCTACTGGTCTGACCGGCTGATCATTGGC
ENSG00000 540 F I S K Q Y V T S L L L N E P D G T F L
ENSG00000 1620 TTCATCAGCAAACAGTACGTTACTAGCCTTCTTCTCAATGAGCCCGACGGAACCTTTCTC
ENSG00000 560 L R F S D S E I G G I T I A H V I R G Q
ENSG00000 1680 CTCCGCTTCAGCGACTCAGAGATTGGGGGCATCACCATTGCCCATGTCATCCGGGGCCAG
ENSG00000 580 D G S P Q I E N I Q P F S A K D L S I R
ENSG00000 1740 GATGGCTCTCCACAGATAGAGAACATCCAGCCATTCTCTGCCAAAGACCTGTCCATTCGC
ENSG00000 600 S L G D R I R D L A Q L K N L Y P K K P
ENSG00000 1800 TCACTGGGGGACCGAATCCGGGATCTTGCTCAGCTCAAAAATCTCTATCCCAAGAAGCCC
ENSG00000 620 K D E A F R S H Y K P E Q M G K D G R G
ENSG00000 1860 AAGGATGAGGCTTTCCGGAGCCACTACAAGCCTGAACAGATGGGTAAGGATGGCAGGGGT
ENSG00000 640 Y V P A T I K M T V E R D Q P L P T P E
ENSG00000 1920 TATGTCCCAGCTACCATCAAGATGACCGTGGAAAGGGACCAACCACTTCCTACCCCAGAG
ENSG00000 660 L Q M P T M V P S Y D L G M A P D S S M
ENSG00000 1980 CTCCAGATGCCTACCATGGTGCCTTCTTATGACCTTGGAATGGCCCCTGATTCCTCCATG
ENSG00000 680 S M Q L G P D M V P Q V Y P P H S H S I
ENSG00000 2040 AGCATGCAGCTTGGCCCAGATATGGTGCCCCAGGTGTACCCACCACACTCTCACTCCATC
ENSG00000 700 P P Y Q G L S P E E S V N V L S A F Q E
ENSG00000 2100 CCCCCGTATCAAGGCCTCTCCCCAGAAGAATCAGTCAACGTGTTGTCAGCCTTCCAGGAG
ENSG00000 720 P H L Q M P P S L G Q M S L P F D Q P H
ENSG00000 2160 CCTCACCTGCAGATGCCCCCCAGCCTGGGCCAGATGAGCCTGCCCTTTGACCAGCCTCAC
ENSG00000 740 P Q G L L P C Q P Q E H A V S S P D P L
ENSG00000 2220 CCCCAGGGCCTGCTGCCGTGCCAGCCTCAGGAGCATGCTGTGTCCAGCCCTGACCCCCTG
ENSG00000 760 L C S D V T M V E D S C L S Q P V T A F
ENSG00000 2280 CTCTGCTCAGATGTGACCATGGTGGAAGACAGCTGCCTGAGCCAGCCAGTGACAGCGTTT
ENSG00000 780 P Q G T W I G E D I F P P L L P P T E Q
ENSG00000 2340 CCTCAGGGCACTTGGATTGGTGAAGACATATTCCCTCCTCTGCTGCCTCCCACTGAACAG
ENSG00000 800 D L T K L L L E G Q G E S G G G S L G A
ENSG00000 2400 GACCTCACTAAGCTTCTCCTGGAGGGGCAAGGGGAGTCGGGGGGAGGGTCCTTGGGGGCA
ENSG00000 820 Q P L L Q P S H Y G Q S G I S M S H M D
ENSG00000 2460 CAGCCCCTCCTGCAGCCCTCCCACTATGGGCAATCTGGGATCTCAATGTCCCACATGGAC
ENSG00000 840 L R A N P S W 847
ENSG00000 2520 CTAAGGGCCAACCCCAGTTGG 2541
""",
)
protein_record = protein_alignment.sequences[4]
nucleotide_record = nucleotide_records[protein_record.id]
self.assertEqual(nucleotide_record.id, protein_record.id)
alignments = aligner.align(protein_record, nucleotide_record)
self.assertEqual(len(alignments), 1)
alignment = next(alignments)
codon_alignments.append(alignment)
self.assertTrue(
np.array_equal(alignment.coordinates, np.array([[0, 737], [0, 2211]]))
)
self.assertEqual(
str(alignment),
"""\
ENSG00000 0 M E Q F R H L P M P F H W K Q E E L K F
ENSG00000 0 ATGGAACAGTTCCGCCACTTGCCAATGCCTTTCCACTGGAAGCAGGAAGAACTCAAGTTT
ENSG00000 20 K T G L R R L Q H R V G E I H L L R E A
ENSG00000 60 AAGACAGGCTTGCGGAGGCTGCAGCACCGAGTAGGGGAGATCCACCTTCTCCGAGAAGCC
ENSG00000 40 L Q K G A E A G Q V S L H S L I E T P A
ENSG00000 120 CTGCAGAAGGGGGCTGAGGCTGGCCAAGTGTCTCTGCACAGCTTGATAGAAACTCCTGCT
ENSG00000 60 N G T G P S E A L A M L L Q E T T G E L
ENSG00000 180 AATGGGACTGGGCCAAGTGAGGCCCTGGCCATGCTACTGCAGGAGACCACTGGAGAGCTA
ENSG00000 80 E A A K A L V L K R I Q I W K R Q Q Q L
ENSG00000 240 GAGGCAGCCAAAGCCCTAGTGCTGAAGAGGATCCAGATTTGGAAACGGCAGCAGCAGCTG
ENSG00000 100 A G N G A P F E E S L A P L Q E R C E S
ENSG00000 300 GCAGGGAATGGCGCACCGTTTGAGGAGAGCCTGGCCCCACTCCAGGAGAGGTGTGAAAGC
ENSG00000 120 L V D I Y S Q L Q Q E V G A A G G E L E
ENSG00000 360 CTGGTGGACATTTATTCCCAGCTACAGCAGGAGGTAGGGGCGGCTGGTGGGGAGCTTGAG
ENSG00000 140 P K T R A S L T G R L D E V L R T L V T
ENSG00000 420 CCCAAGACCCGGGCATCGCTGACTGGCCGGCTGGATGAAGTCCTGAGAACCCTCGTCACC
ENSG00000 160 S C F L V E K Q P P Q V L K T Q T K F Q
ENSG00000 480 AGTTGCTTCCTGGTGGAGAAGCAGCCCCCCCAGGTACTGAAGACTCAGACCAAGTTCCAG
ENSG00000 180 A G V R F L L G L R F L G A P A K P P L
ENSG00000 540 GCTGGAGTTCGATTCCTGTTGGGCTTGAGGTTCCTGGGGGCCCCAGCCAAGCCTCCGCTG
ENSG00000 200 V R A D M V T E K Q A R E L S V P Q G P
ENSG00000 600 GTCAGGGCCGACATGGTGACAGAGAAGCAGGCGCGGGAGCTGAGTGTGCCTCAGGGTCCT
ENSG00000 220 G A G A E S T G E I I N N T V P L E N S
ENSG00000 660 GGGGCTGGAGCAGAAAGCACTGGAGAAATCATCAACAACACTGTGCCCTTGGAGAACAGC
ENSG00000 240 I P G N C C S A L F K N L L L K K I K R
ENSG00000 720 ATTCCTGGGAACTGCTGCTCTGCCCTGTTCAAGAACCTGCTTCTCAAGAAGATCAAGCGG
ENSG00000 260 C E R K G T E S V T E E K C A V L F S A
ENSG00000 780 TGTGAGCGGAAGGGCACTGAGTCTGTCACAGAGGAGAAGTGCGCTGTGCTCTTCTCTGCC
ENSG00000 280 S F T L G P G K L P I Q L Q A L S L P L
ENSG00000 840 AGCTTCACACTTGGCCCCGGCAAACTCCCCATCCAGCTCCAGGCCCTGTCTCTGCCCCTG
ENSG00000 300 V V I V H G N Q D N N A K A T I L W D N
ENSG00000 900 GTGGTCATCGTCCATGGCAACCAAGACAACAATGCCAAAGCCACTATCCTGTGGGACAAT
ENSG00000 320 A F S E M D R V P F V V A E R V P W E K
ENSG00000 960 GCCTTCTCTGAGATGGACCGCGTGCCCTTTGTGGTGGCTGAGCGGGTGCCCTGGGAGAAG
ENSG00000 340 M C E T L N L K F M A E V G T N R G L L
ENSG00000 1020 ATGTGTGAAACTCTGAACCTGAAGTTCATGGCTGAGGTGGGGACCAACCGGGGGCTGCTC
ENSG00000 360 P E H F L F L A Q K I F N D N S L S M E
ENSG00000 1080 CCAGAGCACTTCCTCTTCCTGGCCCAGAAGATCTTCAATGACAACAGCCTCAGTATGGAG
ENSG00000 380 A F Q H R S V S W S Q F N K E I L L G R
ENSG00000 1140 GCCTTCCAGCACCGTTCTGTGTCCTGGTCGCAGTTCAACAAGGAGATCCTGCTGGGCCGT
ENSG00000 400 G F T F W Q W F D G V L D L T K R C L R
ENSG00000 1200 GGCTTCACCTTTTGGCAGTGGTTTGATGGTGTCCTGGACCTCACCAAACGCTGTCTCCGG
ENSG00000 420 S Y W S D R L I I G F I S K Q Y V T S L
ENSG00000 1260 AGCTACTGGTCTGACCGGCTGATCATTGGCTTCATCAGCAAACAGTACGTTACTAGCCTT
ENSG00000 440 L L N E P D G T F L L R F S D S E I G G
ENSG00000 1320 CTTCTCAATGAGCCCGACGGAACCTTTCTCCTCCGCTTCAGCGACTCAGAGATTGGGGGC
ENSG00000 460 I T I A H V I R G Q D G S P Q I E N I Q
ENSG00000 1380 ATCACCATTGCCCATGTCATCCGGGGCCAGGATGGCTCTCCACAGATAGAGAACATCCAG
ENSG00000 480 P F S A K D L S I R S L G D R I R D L A
ENSG00000 1440 CCATTCTCTGCCAAAGACCTGTCCATTCGCTCACTGGGGGACCGAATCCGGGATCTTGCT
ENSG00000 500 Q L K N L Y P K K P K D E A F R S H Y K
ENSG00000 1500 CAGCTCAAAAATCTCTATCCCAAGAAGCCCAAGGATGAGGCTTTCCGGAGCCACTACAAG
ENSG00000 520 P E Q M G K D G R G Y V P A T I K M T V
ENSG00000 1560 CCTGAACAGATGGGTAAGGATGGCAGGGGTTATGTCCCAGCTACCATCAAGATGACCGTG
ENSG00000 540 E R D Q P L P T P E L Q M P T M V P S Y
ENSG00000 1620 GAAAGGGACCAACCACTTCCTACCCCAGAGCTCCAGATGCCTACCATGGTGCCTTCTTAT
ENSG00000 560 D L G M A P D S S M S M Q L G P D M V P
ENSG00000 1680 GACCTTGGAATGGCCCCTGATTCCTCCATGAGCATGCAGCTTGGCCCAGATATGGTGCCC
ENSG00000 580 Q V Y P P H S H S I P P Y Q G L S P E E
ENSG00000 1740 CAGGTGTACCCACCACACTCTCACTCCATCCCCCCGTATCAAGGCCTCTCCCCAGAAGAA
ENSG00000 600 S V N V L S A F Q E P H L Q M P P S L G
ENSG00000 1800 TCAGTCAACGTGTTGTCAGCCTTCCAGGAGCCTCACCTGCAGATGCCCCCCAGCCTGGGC
ENSG00000 620 Q M S L P F D Q P H P Q G L L P C Q P Q
ENSG00000 1860 CAGATGAGCCTGCCCTTTGACCAGCCTCACCCCCAGGGCCTGCTGCCGTGCCAGCCTCAG
ENSG00000 640 E H A V S S P D P L L C S D V T M V E D
ENSG00000 1920 GAGCATGCTGTGTCCAGCCCTGACCCCCTGCTCTGCTCAGATGTGACCATGGTGGAAGAC
ENSG00000 660 S C L S Q P V T A F P Q G T W I G E D I
ENSG00000 1980 AGCTGCCTGAGCCAGCCAGTGACAGCGTTTCCTCAGGGCACTTGGATTGGTGAAGACATA
ENSG00000 680 F P P L L P P T E Q D L T K L L L E G Q
ENSG00000 2040 TTCCCTCCTCTGCTGCCTCCCACTGAACAGGACCTCACTAAGCTTCTCCTGGAGGGGCAA
ENSG00000 700 G E S G G G S L G A Q P L L Q P S H Y G
ENSG00000 2100 GGGGAGTCGGGGGGAGGGTCCTTGGGGGCACAGCCCCTCCTGCAGCCCTCCCACTATGGG
ENSG00000 720 Q S G I S M S H M D L R A N P S W 737
ENSG00000 2160 CAATCTGGGATCTCAATGTCCCACATGGACCTAAGGGCCAACCCCAGTTGG 2211
""",
)
protein_record = protein_alignment.sequences[5]
nucleotide_record = nucleotide_records[protein_record.id]
self.assertEqual(nucleotide_record.id, protein_record.id)
alignments = aligner.align(protein_record, nucleotide_record)
self.assertEqual(len(alignments), 1)
alignment = next(alignments)
codon_alignments.append(alignment)
self.assertTrue(
np.array_equal(alignment.coordinates, np.array([[0, 737], [0, 2211]]))
)
self.assertEqual(
str(alignment),
"""\
ENSG00000 0 M E Q F R H L P M P F H W K Q E E L K F
ENSG00000 0 ATGGAACAGTTCCGCCACTTGCCAATGCCTTTCCACTGGAAGCAGGAAGAACTCAAGTTT
ENSG00000 20 K T G L R R L Q H R V G E I H L L R E A
ENSG00000 60 AAGACAGGCTTGCGGAGGCTGCAGCACCGAGTAGGGGAGATCCACCTTCTCCGAGAAGCC
ENSG00000 40 L Q K G A E A G Q V S L H S L I E T P A
ENSG00000 120 CTGCAGAAGGGGGCTGAGGCTGGCCAAGTGTCTCTGCACAGCTTGATAGAAACTCCTGCT
ENSG00000 60 N G T G P S E A L A M L L Q E T T G E L
ENSG00000 180 AATGGGACTGGGCCAAGTGAGGCCCTGGCCATGCTACTGCAGGAGACCACTGGAGAGCTA
ENSG00000 80 E A A K A L V L K R I Q I W K R Q Q Q L
ENSG00000 240 GAGGCAGCCAAAGCCCTAGTGCTGAAGAGGATCCAGATTTGGAAACGGCAGCAGCAGCTG
ENSG00000 100 A G N G A P F E E S L A P L Q E R C E S
ENSG00000 300 GCAGGGAATGGCGCACCGTTTGAGGAGAGCCTGGCCCCACTCCAGGAGAGGTGTGAAAGC
ENSG00000 120 L V D I Y S Q L Q Q E V G A A G G E L E
ENSG00000 360 CTGGTGGACATTTATTCCCAGCTACAGCAGGAGGTAGGGGCGGCTGGTGGGGAGCTTGAG
ENSG00000 140 P K T R A S L T G R L D E V L R T L V T
ENSG00000 420 CCCAAGACCCGGGCATCGCTGACTGGCCGGCTGGATGAAGTCCTGAGAACCCTCGTCACC
ENSG00000 160 S C F L V E K Q P P Q V L K T Q T K F Q
ENSG00000 480 AGTTGCTTCCTGGTGGAGAAGCAGCCCCCCCAGGTACTGAAGACTCAGACCAAGTTCCAG
ENSG00000 180 A G V R F L L G L R F L G A P A K P P L
ENSG00000 540 GCTGGAGTTCGATTCCTGTTGGGCTTGAGGTTCCTGGGGGCCCCAGCCAAGCCTCCGCTG
ENSG00000 200 V R A D M V T E K Q A R E L S V P Q G P
ENSG00000 600 GTCAGGGCCGACATGGTGACAGAGAAGCAGGCGCGGGAGCTGAGTGTGCCTCAGGGTCCT
ENSG00000 220 G A G A E S T G E I I N N T V P L E N S
ENSG00000 660 GGGGCTGGAGCAGAAAGCACTGGAGAAATCATCAACAACACTGTGCCCTTGGAGAACAGC
ENSG00000 240 I P G N C C S A L F K N L L L K K I K R
ENSG00000 720 ATTCCTGGGAACTGCTGCTCTGCCCTGTTCAAGAACCTGCTTCTCAAGAAGATCAAGCGG
ENSG00000 260 C E R K G T E S V T E E K C A V L F S A
ENSG00000 780 TGTGAGCGGAAGGGCACTGAGTCTGTCACAGAGGAGAAGTGCGCTGTGCTCTTCTCTGCC
ENSG00000 280 S F T L G P G K L P I Q L Q A L S L P L
ENSG00000 840 AGCTTCACACTTGGCCCCGGCAAACTCCCCATCCAGCTCCAGGCCCTGTCTCTGCCCCTG
ENSG00000 300 V V I V H G N Q D N N A K A T I L W D N
ENSG00000 900 GTGGTCATCGTCCATGGCAACCAAGACAACAATGCCAAAGCCACTATCCTGTGGGACAAT
ENSG00000 320 A F S E M D R V P F V V A E R V P W E K
ENSG00000 960 GCCTTCTCTGAGATGGACCGCGTGCCCTTTGTGGTGGCTGAGCGGGTGCCCTGGGAGAAG
ENSG00000 340 M C E T L N L K F M A E V G T N R G L L
ENSG00000 1020 ATGTGTGAAACTCTGAACCTGAAGTTCATGGCTGAGGTGGGGACCAACCGGGGGCTGCTC
ENSG00000 360 P E H F L F L A Q K I F N D N S L S M E
ENSG00000 1080 CCAGAGCACTTCCTCTTCCTGGCCCAGAAGATCTTCAATGACAACAGCCTCAGTATGGAG
ENSG00000 380 A F Q H R S V S W S Q F N K E I L L G R
ENSG00000 1140 GCCTTCCAGCACCGTTCTGTGTCCTGGTCGCAGTTCAACAAGGAGATCCTGCTGGGCCGT
ENSG00000 400 G F T F W Q W F D G V L D L T K R C L R
ENSG00000 1200 GGCTTCACCTTTTGGCAGTGGTTTGATGGTGTCCTGGACCTCACCAAACGCTGTCTCCGG
ENSG00000 420 S Y W S D R L I I G F I S K Q Y V T S L
ENSG00000 1260 AGCTACTGGTCTGACCGGCTGATCATTGGCTTCATCAGCAAACAGTACGTTACTAGCCTT
ENSG00000 440 L L N E P D G T F L L R F S D S E I G G
ENSG00000 1320 CTTCTCAATGAGCCCGACGGAACCTTTCTCCTCCGCTTCAGCGACTCAGAGATTGGGGGC
ENSG00000 460 I T I A H V I R G Q D G S P Q I E N I Q
ENSG00000 1380 ATCACCATTGCCCATGTCATCCGGGGCCAGGATGGCTCTCCACAGATAGAGAACATCCAG
ENSG00000 480 P F S A K D L S I R S L G D R I R D L A
ENSG00000 1440 CCATTCTCTGCCAAAGACCTGTCCATTCGCTCACTGGGGGACCGAATCCGGGATCTTGCT
ENSG00000 500 Q L K N L Y P K K P K D E A F R S H Y K
ENSG00000 1500 CAGCTCAAAAATCTCTATCCCAAGAAGCCCAAGGATGAGGCTTTCCGGAGCCACTACAAG
ENSG00000 520 P E Q M G K D G R G Y V P A T I K M T V
ENSG00000 1560 CCTGAACAGATGGGTAAGGATGGCAGGGGTTATGTCCCAGCTACCATCAAGATGACCGTG
ENSG00000 540 E R D Q P L P T P E L Q M P T M V P S Y
ENSG00000 1620 GAAAGGGACCAACCACTTCCTACCCCAGAGCTCCAGATGCCTACCATGGTGCCTTCTTAT
ENSG00000 560 D L G M A P D S S M S M Q L G P D M V P
ENSG00000 1680 GACCTTGGAATGGCCCCTGATTCCTCCATGAGCATGCAGCTTGGCCCAGATATGGTGCCC
ENSG00000 580 Q V Y P P H S H S I P P Y Q G L S P E E
ENSG00000 1740 CAGGTGTACCCACCACACTCTCACTCCATCCCCCCGTATCAAGGCCTCTCCCCAGAAGAA
ENSG00000 600 S V N V L S A F Q E P H L Q M P P S L G
ENSG00000 1800 TCAGTCAACGTGTTGTCAGCCTTCCAGGAGCCTCACCTGCAGATGCCCCCCAGCCTGGGC
ENSG00000 620 Q M S L P F D Q P H P Q G L L P C Q P Q
ENSG00000 1860 CAGATGAGCCTGCCCTTTGACCAGCCTCACCCCCAGGGCCTGCTGCCGTGCCAGCCTCAG
ENSG00000 640 E H A V S S P D P L L C S D V T M V E D
ENSG00000 1920 GAGCATGCTGTGTCCAGCCCTGACCCCCTGCTCTGCTCAGATGTGACCATGGTGGAAGAC
ENSG00000 660 S C L S Q P V T A F P Q G T W I G E D I
ENSG00000 1980 AGCTGCCTGAGCCAGCCAGTGACAGCGTTTCCTCAGGGCACTTGGATTGGTGAAGACATA
ENSG00000 680 F P P L L P P T E Q D L T K L L L E G Q
ENSG00000 2040 TTCCCTCCTCTGCTGCCTCCCACTGAACAGGACCTCACTAAGCTTCTCCTGGAGGGGCAA
ENSG00000 700 G E S G G G S L G A Q P L L Q P S H Y G
ENSG00000 2100 GGGGAGTCGGGGGGAGGGTCCTTGGGGGCACAGCCCCTCCTGCAGCCCTCCCACTATGGG
ENSG00000 720 Q S G I S M S H M D L R A N P S W 737
ENSG00000 2160 CAATCTGGGATCTCAATGTCCCACATGGACCTAAGGGCCAACCCCAGTTGG 2211
""",
)
protein_record = protein_alignment.sequences[6]
nucleotide_record = nucleotide_records[protein_record.id]
self.assertEqual(nucleotide_record.id, protein_record.id)
alignments = aligner.align(protein_record, nucleotide_record)
self.assertEqual(len(alignments), 1)
alignment = next(alignments)
codon_alignments.append(alignment)
self.assertTrue(
np.array_equal(alignment.coordinates, np.array([[0, 737], [0, 2211]]))
)
self.assertEqual(
str(alignment),
"""\
ENSG00000 0 M E Q F R H L P M P F H W K Q E E L K F
ENSG00000 0 ATGGAACAGTTCCGCCACTTGCCAATGCCTTTCCACTGGAAGCAGGAAGAACTCAAGTTT
ENSG00000 20 K T G L R R L Q H R V G E I H L L R E A
ENSG00000 60 AAGACAGGCTTGCGGAGGCTGCAGCACCGAGTAGGGGAGATCCACCTTCTCCGAGAAGCC
ENSG00000 40 L Q K G A E A G Q V S L H S L I E T P A
ENSG00000 120 CTGCAGAAGGGGGCTGAGGCTGGCCAAGTGTCTCTGCACAGCTTGATAGAAACTCCTGCT
ENSG00000 60 N G T G P S E A L A M L L Q E T T G E L
ENSG00000 180 AATGGGACTGGGCCAAGTGAGGCCCTGGCCATGCTACTGCAGGAGACCACTGGAGAGCTA
ENSG00000 80 E A A K A L V L K R I Q I W K R Q Q Q L
ENSG00000 240 GAGGCAGCCAAAGCCCTAGTGCTGAAGAGGATCCAGATTTGGAAACGGCAGCAGCAGCTG
ENSG00000 100 A G N G A P F E E S L A P L Q E R C E S
ENSG00000 300 GCAGGGAATGGCGCACCGTTTGAGGAGAGCCTGGCCCCACTCCAGGAGAGGTGTGAAAGC
ENSG00000 120 L V D I Y S Q L Q Q E V G A A G G E L E
ENSG00000 360 CTGGTGGACATTTATTCCCAGCTACAGCAGGAGGTAGGGGCGGCTGGTGGGGAGCTTGAG
ENSG00000 140 P K T R A S L T G R L D E V L R T L V T
ENSG00000 420 CCCAAGACCCGGGCATCGCTGACTGGCCGGCTGGATGAAGTCCTGAGAACCCTCGTCACC
ENSG00000 160 S C F L V E K Q P P Q V L K T Q T K F Q
ENSG00000 480 AGTTGCTTCCTGGTGGAGAAGCAGCCCCCCCAGGTACTGAAGACTCAGACCAAGTTCCAG
ENSG00000 180 A G V R F L L G L R F L G A P A K P P L
ENSG00000 540 GCTGGAGTTCGATTCCTGTTGGGCTTGAGGTTCCTGGGGGCCCCAGCCAAGCCTCCGCTG
ENSG00000 200 V R A D M V T E K Q A R E L S V P Q G P
ENSG00000 600 GTCAGGGCCGACATGGTGACAGAGAAGCAGGCGCGGGAGCTGAGTGTGCCTCAGGGTCCT
ENSG00000 220 G A G A E S T G E I I N N T V P L E N S
ENSG00000 660 GGGGCTGGAGCAGAAAGCACTGGAGAAATCATCAACAACACTGTGCCCTTGGAGAACAGC
ENSG00000 240 I P G N C C S A L F K N L L L K K I K R
ENSG00000 720 ATTCCTGGGAACTGCTGCTCTGCCCTGTTCAAGAACCTGCTTCTCAAGAAGATCAAGCGG
ENSG00000 260 C E R K G T E S V T E E K C A V L F S A
ENSG00000 780 TGTGAGCGGAAGGGCACTGAGTCTGTCACAGAGGAGAAGTGCGCTGTGCTCTTCTCTGCC
ENSG00000 280 S F T L G P G K L P I Q L Q A L S L P L
ENSG00000 840 AGCTTCACACTTGGCCCCGGCAAACTCCCCATCCAGCTCCAGGCCCTGTCTCTGCCCCTG
ENSG00000 300 V V I V H G N Q D N N A K A T I L W D N
ENSG00000 900 GTGGTCATCGTCCATGGCAACCAAGACAACAATGCCAAAGCCACTATCCTGTGGGACAAT
ENSG00000 320 A F S E M D R V P F V V A E R V P W E K
ENSG00000 960 GCCTTCTCTGAGATGGACCGCGTGCCCTTTGTGGTGGCTGAGCGGGTGCCCTGGGAGAAG
ENSG00000 340 M C E T L N L K F M A E V G T N R G L L
ENSG00000 1020 ATGTGTGAAACTCTGAACCTGAAGTTCATGGCTGAGGTGGGGACCAACCGGGGGCTGCTC
ENSG00000 360 P E H F L F L A Q K I F N D N S L S M E
ENSG00000 1080 CCAGAGCACTTCCTCTTCCTGGCCCAGAAGATCTTCAATGACAACAGCCTCAGTATGGAG
ENSG00000 380 A F Q H R S V S W S Q F N K E I L L G R
ENSG00000 1140 GCCTTCCAGCACCGTTCTGTGTCCTGGTCGCAGTTCAACAAGGAGATCCTGCTGGGCCGT
ENSG00000 400 G F T F W Q W F D G V L D L T K R C L R
ENSG00000 1200 GGCTTCACCTTTTGGCAGTGGTTTGATGGTGTCCTGGACCTCACCAAACGCTGTCTCCGG
ENSG00000 420 S Y W S D R L I I G F I S K Q Y V T S L
ENSG00000 1260 AGCTACTGGTCTGACCGGCTGATCATTGGCTTCATCAGCAAACAGTACGTTACTAGCCTT
ENSG00000 440 L L N E P D G T F L L R F S D S E I G G
ENSG00000 1320 CTTCTCAATGAGCCCGACGGAACCTTTCTCCTCCGCTTCAGCGACTCAGAGATTGGGGGC
ENSG00000 460 I T I A H V I R G Q D G S P Q I E N I Q
ENSG00000 1380 ATCACCATTGCCCATGTCATCCGGGGCCAGGATGGCTCTCCACAGATAGAGAACATCCAG
ENSG00000 480 P F S A K D L S I R S L G D R I R D L A
ENSG00000 1440 CCATTCTCTGCCAAAGACCTGTCCATTCGCTCACTGGGGGACCGAATCCGGGATCTTGCT
ENSG00000 500 Q L K N L Y P K K P K D E A F R S H Y K
ENSG00000 1500 CAGCTCAAAAATCTCTATCCCAAGAAGCCCAAGGATGAGGCTTTCCGGAGCCACTACAAG
ENSG00000 520 P E Q M G K D G R G Y V P A T I K M T V
ENSG00000 1560 CCTGAACAGATGGGTAAGGATGGCAGGGGTTATGTCCCAGCTACCATCAAGATGACCGTG
ENSG00000 540 E R D Q P L P T P E L Q M P T M V P S Y
ENSG00000 1620 GAAAGGGACCAACCACTTCCTACCCCAGAGCTCCAGATGCCTACCATGGTGCCTTCTTAT
ENSG00000 560 D L G M A P D S S M S M Q L G P D M V P
ENSG00000 1680 GACCTTGGAATGGCCCCTGATTCCTCCATGAGCATGCAGCTTGGCCCAGATATGGTGCCC
ENSG00000 580 Q V Y P P H S H S I P P Y Q G L S P E E
ENSG00000 1740 CAGGTGTACCCACCACACTCTCACTCCATCCCCCCGTATCAAGGCCTCTCCCCAGAAGAA
ENSG00000 600 S V N V L S A F Q E P H L Q M P P S L G
ENSG00000 1800 TCAGTCAACGTGTTGTCAGCCTTCCAGGAGCCTCACCTGCAGATGCCCCCCAGCCTGGGC
ENSG00000 620 Q M S L P F D Q P H P Q G L L P C Q P Q
ENSG00000 1860 CAGATGAGCCTGCCCTTTGACCAGCCTCACCCCCAGGGCCTGCTGCCGTGCCAGCCTCAG
ENSG00000 640 E H A V S S P D P L L C S D V T M V E D
ENSG00000 1920 GAGCATGCTGTGTCCAGCCCTGACCCCCTGCTCTGCTCAGATGTGACCATGGTGGAAGAC
ENSG00000 660 S C L S Q P V T A F P Q G T W I G E D I
ENSG00000 1980 AGCTGCCTGAGCCAGCCAGTGACAGCGTTTCCTCAGGGCACTTGGATTGGTGAAGACATA
ENSG00000 680 F P P L L P P T E Q D L T K L L L E G Q
ENSG00000 2040 TTCCCTCCTCTGCTGCCTCCCACTGAACAGGACCTCACTAAGCTTCTCCTGGAGGGGCAA
ENSG00000 700 G E S G G G S L G A Q P L L Q P S H Y G
ENSG00000 2100 GGGGAGTCGGGGGGAGGGTCCTTGGGGGCACAGCCCCTCCTGCAGCCCTCCCACTATGGG
ENSG00000 720 Q S G I S M S H M D L R A N P S W 737
ENSG00000 2160 CAATCTGGGATCTCAATGTCCCACATGGACCTAAGGGCCAACCCCAGTTGG 2211
""",
)
protein_record = protein_alignment.sequences[7]
nucleotide_record = nucleotide_records[protein_record.id]
self.assertEqual(nucleotide_record.id, protein_record.id)
nucleotide_record = nucleotide_record.upper()
alignments = aligner.align(protein_record, nucleotide_record)
self.assertEqual(len(alignments), 1)
alignment = next(alignments)
codon_alignments.append(alignment)
self.assertTrue(
np.array_equal(alignment.coordinates, np.array([[0, 1021], [0, 3063]]))
)
self.assertEqual(
str(alignment),
"""\
isotig466 0 E V T Q S R R K P V R E G R P W E P S Q
isotig466 0 GAGGTTACTCAGAGTAGGAGGAAGCCGGTCAGAGAGGGCAGACCCTGGGAACCTTCGCAG
isotig466 20 E L A Q T P E G G C P R Q E S R P E G G
isotig466 60 GAGTTGGCCCAAACCCCTGAGGGAGGCTGTCCTCGGCAGGAGAGCAGACCTGAGGGAGGT
isotig466 40 W C A G P G C P A L P S H P R A G S P E
isotig466 120 TGGTGTGCCGGTCCTGGTTGTCCAGCCCTCCCGTCCCATCCCAGGGCTGGCTCACCAGAA
isotig466 60 K S T G I P G P L G R E Q R V S S C P G
isotig466 180 AAAAGTACAGGCATCCCAGGCCCTCTGGGGCGGGAGCAGAGGGTCTCCTCTTGTCCGGGG
isotig466 80 E D K N K N K K R V C S P H W K S S G A
isotig466 240 GAAGACAAAAACAAAAACAAAAAACGAGTGTGTAGCCCTCACTGGAAGTCTTCTGGTGCT
isotig466 100 L G P F A L G S L A S G H G G R A P P G
isotig466 300 CTGGGGCCGTTTGCACTTGGGAGCCTGGCTTCTGGGCATGGTGGCCGGGCTCCGCCGGGG
isotig466 120 A S A L G K A F L E Q S G W E P T E V P
isotig466 360 GCTTCAGCCCTCGGCAAAGCGTTTCTAGAACAGAGTGGGTGGGAGCCGACTGAAGTCCCA
isotig466 140 E P R T L T H R K A S S G W R N A N P P
isotig466 420 GAACCGCGAACACTGACGCACAGGAAAGCCTCGAGTGGGTGGAGAAATGCAAATCCCCCA
isotig466 160 V A W P Q P L R T L T A D S D F G L E R
isotig466 480 GTGGCATGGCCTCAGCCGCTGCGGACCCTGACGGCCGATTCTGACTTCGGACTTGAGCGG
isotig466 180 D Q H P D P G R A S M S Q W N Q V Q Q L
isotig466 540 GACCAGCACCCGGACCCAGGGCGAGCCAGCATGTCTCAGTGGAATCAAGTCCAACAGTTA
isotig466 200 E I K F L E Q V D Q F Y D D N F P M E I
isotig466 600 GAAATCAAGTTTTTGGAGCAAGTTGATCAGTTCTATGATGACAACTTTCCCATGGAAATC
isotig466 220 R H L L A Q W I E H Q D W E V A S N N E
isotig466 660 CGACATCTGCTGGCCCAGTGGATTGAGCATCAAGACTGGGAGGTGGCCTCTAACAATGAA
isotig466 240 T M A T I L L Q N L L I Q L D E Q L G R
isotig466 720 ACTATGGCAACAATTCTTCTTCAAAACTTATTAATACAATTGGATGAACAGTTAGGTCGT
isotig466 260 V S K E K N L L L I H N L K R I R K V L
isotig466 780 GTTTCCAAAGAGAAAAACCTGCTATTGATCCACAATCTAAAGAGAATTAGAAAAGTACTT
isotig466 280 Q G K F H G N P M H V A V V I S N C L R
isotig466 840 CAGGGGAAGTTTCATGGAAATCCAATGCATGTAGCCGTGGTAATCTCAAATTGTTTAAGG
isotig466 300 E E R R I L A A A N M P I Q G P L E K S
isotig466 900 GAAGAGAGGAGAATACTGGCTGCAGCGAACATGCCTATCCAGGGACCTCTGGAGAAATCC
isotig466 320 L Q S S S V S E R Q R N V E H K V A A I
isotig466 960 TTACAAAGTTCGTCGGTTTCAGAAAGACAGAGAAATGTGGAACACAAAGTGGCTGCCATT
isotig466 340 K N S V Q M T E Q D T K Y L E D L Q D E
isotig466 1020 AAAAACAGTGTGCAGATGACAGAACAAGACACCAAATACTTGGAAGATCTGCAAGATGAA
isotig466 360 F D Y R Y K T I Q T M D Q G D K N S I L
isotig466 1080 TTTGACTACAGGTATAAAACAATTCAGACAATGGACCAGGGTGACAAGAATAGCATCCTA
isotig466 380 M N Q E V L T L Q E M L N S L D F K R K
isotig466 1140 ATGAACCAGGAGGTTTTGACACTCCAAGAAATGCTTAATAGCCTGGACTTCAAGAGAAAG
isotig466 400 E A L T K M T Q I V N E S D L L M S S M
isotig466 1200 GAAGCACTCACTAAGATGACACAGATAGTGAACGAGTCGGACCTGCTGATGAGCAGCATG
isotig466 420 L I E E L Q D W K R R Q Q I A C I G G P
isotig466 1260 CTCATAGAAGAGCTGCAGGACTGGAAGAGGAGGCAGCAGATCGCCTGCATCGGTGGCCCA
isotig466 440 L H N G L D Q L Q N C F T L L A E S L F
isotig466 1320 CTCCACAACGGGCTGGACCAGCTTCAGAACTGCTTTACCCTGTTGGCAGAAAGTCTTTTC
isotig466 460 Q L R R Q L E K L E E Q S S K M T Y E G
isotig466 1380 CAACTCAGACGACAGCTGGAGAAATTAGAGGAGCAGTCTTCCAAGATGACTTACGAAGGA
isotig466 480 D P I P T Q R A H L L E R A T F L I Y N
isotig466 1440 GACCCCATCCCCACGCAGAGAGCACACCTGCTGGAGAGAGCCACCTTCCTGATCTACAAC
isotig466 500 L F K N S F V V E R Q P C M P T H P Q R
isotig466 1500 CTTTTCAAGAACTCATTTGTGGTTGAGCGACAGCCCTGCATGCCAACACACCCTCAGAGG
isotig466 520 P L V L K T L I Q F T A K L R L L I K L
isotig466 1560 CCGCTGGTACTCAAAACCCTCATTCAGTTCACCGCGAAACTGAGACTACTAATAAAATTG
isotig466 540 P E L N Y Q V K V K A S I D K N V S T L
isotig466 1620 CCGGAACTCAACTATCAGGTGAAAGTAAAGGCATCGATCGACAAGAATGTTTCAACGCTA
isotig466 560 S N R R F V L C G T Q V K A M S I E E S
isotig466 1680 AGCAATAGAAGATTTGTGCTTTGTGGAACTCAAGTCAAAGCCATGTCCATCGAGGAATCC
isotig466 580 S N G S L S V E F R H L Q P K E M K S S
isotig466 1740 TCCAATGGGAGCCTCTCAGTAGAATTTAGACATTTGCAACCGAAGGAAATGAAATCCAGT
isotig466 600 A G S K G N E G C H M V T E E L H S I A
isotig466 1800 GCCGGAAGTAAAGGAAATGAGGGCTGCCACATGGTGACGGAAGAGCTGCATTCCATAGCC
isotig466 620 F E T Q I C L Y G L T I D L E T S S L P
isotig466 1860 TTTGAGACCCAGATCTGCCTCTATGGCCTCACCATCGACTTGGAGACAAGCTCATTACCT
isotig466 640 V V M I S N V S Q L P N A W A S I I W Y
isotig466 1920 GTGGTGATGATTTCTAATGTCAGCCAACTGCCTAATGCTTGGGCATCCATCATTTGGTAC
isotig466 660 N V S T N D C Q N L V F F N N P P P V T
isotig466 1980 AATGTGTCAACCAACGATTGCCAGAACTTGGTTTTCTTTAATAATCCTCCGCCTGTCACT
isotig466 680 L S Q L L E V M S W Q F S S Y V G R G L
isotig466 2040 TTGAGTCAACTCCTGGAAGTGATGAGCTGGCAGTTTTCATCCTATGTTGGTCGTGGCCTT
isotig466 700 N S D Q L N M L A E K L T V Q S N Y S D
isotig466 2100 AATTCAGACCAGCTCAACATGCTGGCAGAGAAGCTCACAGTTCAGTCTAACTACAGCGAT
isotig466 720 G H L T W A K F C K E H L P G K P F T F
isotig466 2160 GGTCACCTCACCTGGGCCAAGTTCTGCAAGGAACACTTGCCTGGCAAACCATTTACCTTC
isotig466 740 W T W L E A I L D L I K K H I L P L W I
isotig466 2220 TGGACCTGGCTTGAAGCAATATTGGACCTAATTAAAAAACACATTCTTCCCCTCTGGATT
isotig466 760 D G Y I M G F V S K E K E R F L L K D K
isotig466 2280 GATGGGTACATCATGGGCTTCGTGAGCAAAGAGAAGGAGAGGTTTCTGCTCAAGGATAAA
isotig466 780 M P G T F L L R F S E S H L G G I T F T
isotig466 2340 ATGCCCGGGACATTTTTGTTACGATTCAGTGAGAGCCATCTCGGAGGGATCACCTTCACC
isotig466 800 W V D H S E N G E V R F H S V E P Y N K
isotig466 2400 TGGGTGGACCACTCTGAAAACGGAGAAGTGAGATTCCACTCCGTAGAACCCTACAACAAA
isotig466 820 G R L S A L P F A D I L R D Y K V I M A
isotig466 2460 GGGCGTCTGTCGGCCCTGCCATTTGCTGACATCCTGCGGGACTACAAGGTCATCATGGCT
isotig466 840 E N I P E N P L K Y L Y P D I P K D K A
isotig466 2520 GAGAACATTCCCGAGAACCCTCTCAAGTACCTCTACCCCGACATCCCCAAAGACAAAGCC
isotig466 860 F G K H Y S S Q P C E V S R P T E R G D
isotig466 2580 TTCGGTAAACACTACAGCTCCCAGCCTTGCGAAGTTTCAAGGCCAACAGAACGGGGAGAC
isotig466 880 K G Y V P S V F I P I S T I R S D A M E
isotig466 2640 AAAGGTTATGTTCCTTCAGTTTTTATCCCTATTTCAACAATCCGCAGCGACGCCATGGAG
isotig466 900 P Q S P S D L L P M S P S V Y A V L R E
isotig466 2700 CCGCAGTCTCCTTCAGACCTTCTCCCCATGTCTCCGAGTGTATACGCTGTGCTGAGAGAA
isotig466 920 N L S P T T I E T A M K S P Y S E R Y K
isotig466 2760 AACCTGAGCCCTACCACAATTGAAACAGCAATGAAGTCTCCATATTCTGAGCGGTACAAA
isotig466 940 A T L Q G R E Q M K T E T A L C Q S P Q
isotig466 2820 GCGACTCTTCAAGGAAGAGAGCAGATGAAAACGGAGACTGCTCTTTGCCAAAGTCCACAA
isotig466 960 F I S S A L I L V S R K W H K S E A F L
isotig466 2880 TTCATTTCTTCAGCTTTGATACTGGTTTCTAGAAAATGGCACAAATCCGAAGCTTTCCTC
isotig466 980 S L G D I P Q L G V L L K C K P K L Q I
isotig466 2940 TCACTAGGTGACATTCCCCAACTGGGAGTGCTGCTGAAATGCAAACCAAAGCTTCAGATA
isotig466 1000 N T Q E K T A S R N L C S Q Y N R R L L
isotig466 3000 AACACGCAGGAAAAGACAGCTTCGAGAAACCTATGTTCGCAATATAACAGAAGGCTGCTT
isotig466 1020 C 1021
isotig466 3060 TGC 3063
""",
)
protein_record = protein_alignment.sequences[8]
nucleotide_record = nucleotide_records[protein_record.id]
self.assertEqual(nucleotide_record.id, protein_record.id)
nucleotide_record = nucleotide_record.upper()
alignments = aligner.align(protein_record, nucleotide_record)
self.assertEqual(len(alignments), 1)
alignment = next(alignments)
codon_alignments.append(alignment)
self.assertTrue(
np.array_equal(alignment.coordinates, np.array([[0, 806], [0, 2418]]))
)
self.assertEqual(
str(alignment),
"""\
isotig125 0 A R R G Q A A L G S P A A R T W S Q R S
isotig125 0 GCTAGGAGAGGCCAGGCGGCCCTCGGGAGCCCAGCTGCTCGCACCTGGAGCCAGCGCAGC
isotig125 20 P A S R A S A R E T V T P P D C G R M A
isotig125 60 CCGGCCAGTCGGGCCTCAGCCCGGGAGACAGTTACGCCCCCTGATTGCGGCAGGATGGCC
isotig125 40 Q W N Q L Q Q L D T R Y L E Q L H Q L Y
isotig125 120 CAGTGGAACCAGCTGCAGCAGCTGGACACTCGGTACCTGGAGCAGCTGCACCAGCTGTAC
isotig125 60 S D S F P M E L R Q F L A P W I E S Q D
isotig125 180 AGCGACAGCTTCCCCATGGAGCTGCGGCAGTTCCTGGCACCTTGGATTGAGAGTCAAGAT
isotig125 80 W A Y A A S K E S H A T L V F H N L L G
isotig125 240 TGGGCATATGCAGCCAGCAAAGAGTCACATGCCACACTGGTGTTTCATAATCTCTTGGGT
isotig125 100 E I D Q Q Y S R F L Q E S N V L Y Q H N
isotig125 300 GAGATTGACCAGCAGTACAGCCGATTCCTGCAAGAGTCCAACGTCCTCTATCAGCACAAC
isotig125 120 L R R I K Q F L Q S R Y L E K P M E I A
isotig125 360 CTTCGGAGGATCAAGCAGTTCCTACAGAGCAGGTATCTTGAGAAGCCGATGGAAATCGCC
isotig125 140 R I V A R C L W E E S R L L Q T A A T A
isotig125 420 CGCATCGTGGCCCGATGCCTGTGGGAAGAGTCTCGCCTCCTCCAGACGGCAGCCACTGCA
isotig125 160 A Q Q G G Q A N H P T A A V V T E K Q Q
isotig125 480 GCCCAGCAAGGAGGCCAGGCCAACCACCCAACAGCTGCTGTGGTGACGGAGAAACAGCAG
isotig125 180 M L E Q H L Q D V R K R V Q D L E Q K M
isotig125 540 ATGCTGGAGCAGCATCTTCAGGATGTCCGGAAACGTGTGCAGGATCTAGAACAGAAAATG
isotig125 200 K V V E N L Q D D F D F N Y K T L K S Q
isotig125 600 AAAGTGGTAGAGAATCTCCAGGATGACTTTGATTTCAACTATAAAACCCTCAAGAGTCAA
isotig125 220 G D M Q D L N G N N Q S V T R Q K M Q Q
isotig125 660 GGAGACATGCAGGATCTGAATGGAAACAACCAGTCTGTGACCAGGCAGAAGATGCAGCAG
isotig125 240 L E Q M L T A L D Q M R R S I V S E L A
isotig125 720 CTGGAACAGATGCTCACGGCGCTGGACCAGATGCGGAGAAGCATTGTGAGTGAGCTGGCG
isotig125 260 G L L S A M E Y V Q K T L T D E E L A D
isotig125 780 GGGCTTTTGTCGGCAATGGAGTACGTGCAGAAAACACTCACAGACGAGGAGCTGGCTGAC
isotig125 280 W K R R Q Q I A C I G G P P N I C L D R
isotig125 840 TGGAAGAGGCGGCAGCAGATCGCGTGCATTGGAGGCCCTCCCAACATCTGCCTGGATCGC
isotig125 300 L E N W I T S L A E S Q L Q T R Q Q I K
isotig125 900 CTGGAAAACTGGATAACTTCGTTAGCAGAATCTCAACTTCAGACCCGCCAACAAATTAAG
isotig125 320 K L E E L Q Q K V S Y K G D P I V Q H R
isotig125 960 AAACTGGAGGAGCTACAGCAGAAGGTGTCCTACAAGGGGGACCCCATTGTGCAGCACCGG
isotig125 340 P M L E E R I V E L F R N L M K S A F V
isotig125 1020 CCGATGCTGGAGGAGCGGATCGTGGAGCTGTTCAGAAACTTGATGAAGAGTGCCTTCGTG
isotig125 360 V E R Q P C M P M H P D R P L V I K T G
isotig125 1080 GTGGAGCGACAGCCCTGCATGCCGATGCACCCCGACCGGCCCTTGGTCATCAAGACTGGT
isotig125 380 V Q F T T K V R L L V K F P E L N Y Q L
isotig125 1140 GTCCAGTTCACTACTAAAGTCAGGTTGTTGGTCAAGTTTCCCGAGTTGAATTATCAGCTT
isotig125 400 K I K V C I D K D S G D V A A L R G S R
isotig125 1200 AAAATTAAAGTGTGCATTGACAAAGATTCTGGGGACGTTGCTGCTCTCAGAGGATCTCGG
isotig125 420 K F N I L G T N T K V M N M E E S N N G
isotig125 1260 AAATTTAACATTCTGGGCACAAACACGAAGGTGATGAACATGGAAGAATCCAACAACGGC
isotig125 440 S L S A E F K H L T L R E Q R C G N G G
isotig125 1320 AGCCTGTCTGCGGAGTTCAAGCACTTGACCCTGAGGGAGCAGAGATGTGGGAATGGAGGC
isotig125 460 R A N C D A S L I V T E E L H L I T F E
isotig125 1380 CGTGCCAATTGTGATGCCTCCTTGATTGTGACCGAGGAGCTGCATCTGATCACCTTCGAG
isotig125 480 T E V Y H Q G L K I D L E T H S L P V V
isotig125 1440 ACTGAGGTGTACCACCAAGGCCTCAAGATTGACCTGGAGACCCATTCTTTGCCAGTTGTG
isotig125 500 V I S N I C Q M P N A W A S I L W Y N M
isotig125 1500 GTGATCTCCAACATCTGTCAGATGCCAAATGCCTGGGCATCCATCCTGTGGTATAACATG
isotig125 520 L T N N P K N V N F F T K P P I G T W D
isotig125 1560 CTGACCAACAACCCCAAGAACGTGAACTTCTTCACCAAGCCACCAATCGGAACCTGGGAC
isotig125 540 Q V A E V L S W Q F S S T T K R G L S I
isotig125 1620 CAGGTGGCCGAGGTGCTCAGCTGGCAGTTCTCATCCACCACAAAGCGAGGGCTGAGCATC
isotig125 560 E Q L T T L A E K L L G P G V N Y S G C
isotig125 1680 GAGCAGCTGACTACGCTGGCCGAGAAGCTCCTAGGACCTGGTGTCAACTACTCCGGGTGT
isotig125 580 Q I T W A K F C K E N M A G K G F S F W
isotig125 1740 CAGATCACATGGGCTAAATTTTGCAAAGAAAACATGGCTGGCAAGGGCTTCTCCTTCTGG
isotig125 600 V W L D N I I D L V K K Y I L A L W N E
isotig125 1800 GTGTGGCTAGACAATATCATTGACCTTGTGAAAAAGTATATCTTGGCCCTCTGGAATGAA
isotig125 620 G Y I M G F I S K E R E R A I L S T K P
isotig125 1860 GGGTACATCATGGGCTTCATTAGCAAGGAGCGGGAGCGGGCGATCCTGAGCACGAAACCC
isotig125 640 P G T F L L R F S E S S K E G G V T F T
isotig125 1920 CCGGGCACCTTCCTGCTGAGATTCAGCGAGAGCAGCAAAGAAGGAGGGGTCACTTTCACT
isotig125 660 W V E K D I S G K T Q I Q S V E P Y T K
isotig125 1980 TGGGTGGAAAAGGACATCAGTGGCAAGACCCAGATCCAGTCTGTAGAGCCGTACACCAAG
isotig125 680 Q Q L N N M S F A E I I M G Y K I M D A
isotig125 2040 CAGCAGCTGAACAACATGTCCTTTGCTGAAATCATCATGGGCTACAAGATCATGGATGCC
isotig125 700 T N I L V S P L V Y L Y P D I P K E E A
isotig125 2100 ACCAACATCCTGGTGTCCCCATTGGTCTACCTCTACCCTGACATTCCCAAGGAGGAGGCG
isotig125 720 F G K Y C R P E S Q E H P E A D P G S A
isotig125 2160 TTCGGGAAGTACTGTCGACCAGAGAGCCAGGAGCATCCTGAAGCTGACCCCGGTAGTGCC
isotig125 740 A P Y L K T K F I C V T P T T C S N T I
isotig125 2220 GCCCCTTACCTGAAGACCAAGTTCATCTGTGTGACACCAACGACCTGCAGCAATACCATT
isotig125 760 D L P M S P P H F R F I D A V W K R R C
isotig125 2280 GACCTGCCGATGTCCCCCCCGCACTTTAGATTCATTGATGCAGTTTGGAAACGGAGGTGC
isotig125 780 A L G R R A V V T H V H G S D F G V R Y
isotig125 2340 GCCCTCGGCAGGAGGGCAGTTGTCACTCACGTTCATGGATCTGACTTCGGAGTGCGCTAC
isotig125 800 L P H V R S 806
isotig125 2400 CTCCCCCATGTGAGGAGC 2418
""",
)
protein_record = protein_alignment.sequences[9]
nucleotide_record = nucleotide_records[protein_record.id]
self.assertEqual(nucleotide_record.id, protein_record.id)
nucleotide_record = nucleotide_record.upper()
alignments = aligner.align(protein_record, nucleotide_record)
self.assertEqual(len(alignments), 1)
alignment = next(alignments)
codon_alignments.append(alignment)
self.assertTrue(
np.array_equal(alignment.coordinates, np.array([[0, 796], [0, 2388]]))
)
self.assertEqual(
str(alignment),
"""\
isotig125 0 A R R G Q A A L G S P A A R T W S Q R S
isotig125 0 GCTAGGAGAGGCCAGGCGGCCCTCGGGAGCCCAGCTGCTCGCACCTGGAGCCAGCGCAGC
isotig125 20 P A S R A S A R E T V T P P D C G R M A
isotig125 60 CCGGCCAGTCGGGCCTCAGCCCGGGAGACAGTTACGCCCCCTGATTGCGGCAGGATGGCC
isotig125 40 Q W N Q L Q Q L D T R Y L E Q L H Q L Y
isotig125 120 CAGTGGAACCAGCTGCAGCAGCTGGACACTCGGTACCTGGAGCAGCTGCACCAGCTGTAC
isotig125 60 S D S F P M E L R Q F L A P W I E S Q D
isotig125 180 AGCGACAGCTTCCCCATGGAGCTGCGGCAGTTCCTGGCACCTTGGATTGAGAGTCAAGAT
isotig125 80 W A Y A A S K E S H A T L V F H N L L G
isotig125 240 TGGGCATATGCAGCCAGCAAAGAGTCACATGCCACACTGGTGTTTCATAATCTCTTGGGT
isotig125 100 E I D Q Q Y S R F L Q E S N V L Y Q H N
isotig125 300 GAGATTGACCAGCAGTACAGCCGATTCCTGCAAGAGTCCAACGTCCTCTATCAGCACAAC
isotig125 120 L R R I K Q F L Q S R Y L E K P M E I A
isotig125 360 CTTCGGAGGATCAAGCAGTTCCTACAGAGCAGGTATCTTGAGAAGCCGATGGAAATCGCC
isotig125 140 R I V A R C L W E E S R L L Q T A A T A
isotig125 420 CGCATCGTGGCCCGATGCCTGTGGGAAGAGTCTCGCCTCCTCCAGACGGCAGCCACTGCA
isotig125 160 A Q Q G G Q A N H P T A A V V T E K Q Q
isotig125 480 GCCCAGCAAGGAGGCCAGGCCAACCACCCAACAGCTGCTGTGGTGACGGAGAAACAGCAG
isotig125 180 M L E Q H L Q D V R K R V Q D L E Q K M
isotig125 540 ATGCTGGAGCAGCATCTTCAGGATGTCCGGAAACGTGTGCAGGATCTAGAACAGAAAATG
isotig125 200 K V V E N L Q D D F D F N Y K T L K S Q
isotig125 600 AAAGTGGTAGAGAATCTCCAGGATGACTTTGATTTCAACTATAAAACCCTCAAGAGTCAA
isotig125 220 G D M Q D L N G N N Q S V T R Q K M Q Q
isotig125 660 GGAGACATGCAGGATCTGAATGGAAACAACCAGTCTGTGACCAGGCAGAAGATGCAGCAG
isotig125 240 L E Q M L T A L D Q M R R S I V S E L A
isotig125 720 CTGGAACAGATGCTCACGGCGCTGGACCAGATGCGGAGAAGCATTGTGAGTGAGCTGGCG
isotig125 260 G L L S A M E Y V Q K T L T D E E L A D
isotig125 780 GGGCTTTTGTCGGCAATGGAGTACGTGCAGAAAACACTCACAGACGAGGAGCTGGCTGAC
isotig125 280 W K R R Q Q I A C I G G P P N I C L D R
isotig125 840 TGGAAGAGGCGGCAGCAGATCGCGTGCATTGGAGGCCCTCCCAACATCTGCCTGGATCGC
isotig125 300 L E N W I T S L A E S Q L Q T R Q Q I K
isotig125 900 CTGGAAAACTGGATAACTTCGTTAGCAGAATCTCAACTTCAGACCCGCCAACAAATTAAG
isotig125 320 K L E E L Q Q K V S Y K G D P I V Q H R
isotig125 960 AAACTGGAGGAGCTACAGCAGAAGGTGTCCTACAAGGGGGACCCCATTGTGCAGCACCGG
isotig125 340 P M L E E R I V E L F R N L M K S A F V
isotig125 1020 CCGATGCTGGAGGAGCGGATCGTGGAGCTGTTCAGAAACTTGATGAAGAGTGCCTTCGTG
isotig125 360 V E R Q P C M P M H P D R P L V I K T G
isotig125 1080 GTGGAGCGACAGCCCTGCATGCCGATGCACCCCGACCGGCCCTTGGTCATCAAGACTGGT
isotig125 380 V Q F T T K V R L L V K F P E L N Y Q L
isotig125 1140 GTCCAGTTCACTACTAAAGTCAGGTTGTTGGTCAAGTTTCCCGAGTTGAATTATCAGCTT
isotig125 400 K I K V C I D K D S G D V A A L R G S R
isotig125 1200 AAAATTAAAGTGTGCATTGACAAAGATTCTGGGGACGTTGCTGCTCTCAGAGGATCTCGG
isotig125 420 K F N I L G T N T K V M N M E E S N N G
isotig125 1260 AAATTTAACATTCTGGGCACAAACACGAAGGTGATGAACATGGAAGAATCCAACAACGGC
isotig125 440 S L S A E F K H L T L R E Q R C G N G G
isotig125 1320 AGCCTGTCTGCGGAGTTCAAGCACTTGACCCTGAGGGAGCAGAGATGTGGGAATGGAGGC
isotig125 460 R A N C D A S L I V T E E L H L I T F E
isotig125 1380 CGTGCCAATTGTGATGCCTCCTTGATTGTGACCGAGGAGCTGCATCTGATCACCTTCGAG
isotig125 480 T E V Y H Q G L K I D L E T H S L P V V
isotig125 1440 ACTGAGGTGTACCACCAAGGCCTCAAGATTGACCTGGAGACCCATTCTTTGCCAGTTGTG
isotig125 500 V I S N I C Q M P N A W A S I L W Y N M
isotig125 1500 GTGATCTCCAACATCTGTCAGATGCCAAATGCCTGGGCATCCATCCTGTGGTATAACATG
isotig125 520 L T N N P K N V N F F T K P P I G T W D
isotig125 1560 CTGACCAACAACCCCAAGAACGTGAACTTCTTCACCAAGCCACCAATCGGAACCTGGGAC
isotig125 540 Q V A E V L S W Q F S S T T K R G L S I
isotig125 1620 CAGGTGGCCGAGGTGCTCAGCTGGCAGTTCTCATCCACCACAAAGCGAGGGCTGAGCATC
isotig125 560 E Q L T T L A E K L L G P G V N Y S G C
isotig125 1680 GAGCAGCTGACTACGCTGGCCGAGAAGCTCCTAGGACCTGGTGTCAACTACTCCGGGTGT
isotig125 580 Q I T W A K F C K E N M A G K G F S F W
isotig125 1740 CAGATCACATGGGCTAAATTTTGCAAAGAAAACATGGCTGGCAAGGGCTTCTCCTTCTGG
isotig125 600 V W L D N I I D L V K K Y I L A L W N E
isotig125 1800 GTGTGGCTAGACAATATCATTGACCTTGTGAAAAAGTATATCTTGGCCCTCTGGAATGAA
isotig125 620 G Y I M G F I S K E R E R A I L S T K P
isotig125 1860 GGGTACATCATGGGCTTCATTAGCAAGGAGCGGGAGCGGGCGATCCTGAGCACGAAACCC
isotig125 640 P G T F L L R F S E S S K E G G V T F T
isotig125 1920 CCGGGCACCTTCCTGCTGAGATTCAGCGAGAGCAGCAAAGAAGGAGGGGTCACTTTCACT
isotig125 660 W V E K D I S G K T Q I Q S V E P Y T K
isotig125 1980 TGGGTGGAAAAGGACATCAGTGGCAAGACCCAGATCCAGTCTGTAGAGCCGTACACCAAG
isotig125 680 Q Q L N N M S F A E I I M G Y K I M D A
isotig125 2040 CAGCAGCTGAACAACATGTCCTTTGCTGAAATCATCATGGGCTACAAGATCATGGATGCC
isotig125 700 T N I L V S P L V Y L Y P D I P K E E A
isotig125 2100 ACCAACATCCTGGTGTCCCCATTGGTCTACCTCTACCCTGACATTCCCAAGGAGGAGGCG
isotig125 720 F G K Y C R P E S Q E H P E A D P G S C
isotig125 2160 TTCGGGAAGTACTGTCGACCAGAGAGCCAGGAGCATCCTGAAGCTGACCCCGGTAGTTGT
isotig125 740 F S M V L V S L L G K G G Q C R S L E E
isotig125 2220 TTTTCCATGGTTCTGGTTTCGCTGTTAGGGAAAGGGGGACAGTGCAGGTCCTTGGAGGAG
isotig125 760 R Q G H D R V S G G E S C Y G R A V Y W
isotig125 2280 AGACAAGGACATGACCGGGTGTCTGGTGGTGAGTCCTGCTATGGAAGAGCTGTTTATTGG
isotig125 780 V L Q G D R D S R E D Q N Q A S 796
isotig125 2340 GTACTTCAGGGTGACCGGGATTCAAGAGAAGACCAGAATCAGGCCTCA 2388
""",
)
alignment = protein_alignment.mapall(codon_alignments)
self.assertTrue(
np.array_equal(
alignment.coordinates,
# fmt: off
np.array([[ 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 36, 36, 63, 63,
213, 222, 240, 240, 330, 330, 330, 405,
405, 438, 450, 579, 579, 729, 729, 837,
837, 897, 912, 975, 987, 1020, 1026, 1074,
1077, 1107, 1107, 1116, 1119, 1182, 1188, 1302,
1302, 1392, 1398, 1455, 1458, 1470, 1695, 1695,
1824, 1824, 1887, 1887, 1896, 1902, 1956, 1980,
2022, 2025, 2043, 2046, 2061, 2106, 2187, 2220,
2232, 2253, 2271, 2331, 2334, 2352, 2364, 2373,
2382, 2424, 2463, 2484, 2517, 2541],
[ 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 36, 36, 63, 63,
213, 222, 240, 240, 330, 330, 330, 405,
405, 438, 450, 579, 579, 729, 729, 837,
837, 897, 912, 975, 987, 1020, 1026, 1074,
1077, 1107, 1107, 1116, 1119, 1182, 1188, 1302,
1302, 1392, 1398, 1455, 1458, 1470, 1695, 1695,
1824, 1824, 1887, 1887, 1896, 1902, 1956, 1980,
2022, 2025, 2043, 2046, 2061, 2106, 2187, 2220,
2232, 2253, 2271, 2331, 2334, 2352, 2364, 2373,
2382, 2424, 2463, 2484, 2517, 2541],
[ 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 36, 36, 63, 63,
213, 222, 240, 240, 330, 330, 330, 405,
405, 438, 450, 579, 579, 729, 729, 837,
837, 897, 912, 975, 987, 1020, 1026, 1074,
1077, 1107, 1107, 1116, 1119, 1182, 1188, 1302,
1302, 1392, 1398, 1455, 1458, 1470, 1695, 1695,
1824, 1824, 1887, 1887, 1896, 1902, 1956, 1980,
2022, 2025, 2043, 2046, 2061, 2106, 2187, 2220,
2232, 2253, 2271, 2331, 2334, 2352, 2364, 2373,
2382, 2424, 2463, 2484, 2517, 2541],
[ 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 36, 36, 63, 63,
213, 222, 240, 240, 330, 330, 330, 405,
405, 438, 450, 579, 579, 729, 729, 837,
837, 897, 912, 975, 987, 1020, 1026, 1074,
1077, 1107, 1107, 1116, 1119, 1182, 1188, 1302,
1302, 1392, 1398, 1455, 1458, 1470, 1695, 1695,
1824, 1824, 1887, 1887, 1896, 1902, 1956, 1980,
2022, 2025, 2043, 2046, 2061, 2106, 2187, 2220,
2232, 2253, 2271, 2331, 2334, 2352, 2364, 2373,
2382, 2424, 2463, 2484, 2517, 2541],
[ 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 75,
75, 108, 120, 249, 249, 399, 399, 507,
507, 567, 582, 645, 657, 690, 696, 744,
747, 777, 777, 786, 789, 852, 858, 972,
972, 1062, 1068, 1125, 1128, 1140, 1365, 1365,
1494, 1494, 1557, 1557, 1566, 1572, 1626, 1650,
1692, 1695, 1713, 1716, 1731, 1776, 1857, 1890,
1902, 1923, 1941, 2001, 2004, 2022, 2034, 2043,
2052, 2094, 2133, 2154, 2187, 2211],
[ 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 75,
75, 108, 120, 249, 249, 399, 399, 507,
507, 567, 582, 645, 657, 690, 696, 744,
747, 777, 777, 786, 789, 852, 858, 972,
972, 1062, 1068, 1125, 1128, 1140, 1365, 1365,
1494, 1494, 1557, 1557, 1566, 1572, 1626, 1650,
1692, 1695, 1713, 1716, 1731, 1776, 1857, 1890,
1902, 1923, 1941, 2001, 2004, 2022, 2034, 2043,
2052, 2094, 2133, 2154, 2187, 2211],
[ 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 75,
75, 108, 120, 249, 249, 399, 399, 507,
507, 567, 582, 645, 657, 690, 696, 744,
747, 777, 777, 786, 789, 852, 858, 972,
972, 1062, 1068, 1125, 1128, 1140, 1365, 1365,
1494, 1494, 1557, 1557, 1566, 1572, 1626, 1650,
1692, 1695, 1713, 1716, 1731, 1776, 1857, 1890,
1902, 1923, 1941, 2001, 2004, 2022, 2034, 2043,
2052, 2094, 2133, 2154, 2187, 2211],
[ 0, 12, 21, 357, 378, 417, 444, 474,
516, 549, 564, 570, 606, 615, 642, 645,
795, 795, 813, 828, 918, 918, 999, 1074,
1077, 1110, 1110, 1239, 1251, 1401, 1428, 1536,
1560, 1620, 1620, 1683, 1683, 1716, 1716, 1764,
1764, 1794, 1809, 1818, 1818, 1881, 1881, 1995,
2001, 2091, 2091, 2148, 2148, 2148, 2373, 2373,
2502, 2532, 2595, 2619, 2628, 2628, 2682, 2706,
2706, 2709, 2727, 2727, 2727, 2772, 2772, 2805,
2817, 2817, 2835, 2895, 2898, 2916, 2928, 2937,
2946, 2946, 2985, 3006, 3039, 3063],
[ 0, 0, 9, 9, 30, 30, 57, 57,
99, 99, 114, 114, 150, 159, 186, 189,
339, 339, 357, 372, 462, 465, 546, 621,
624, 657, 669, 798, 810, 960, 987, 1095,
1119, 1179, 1179, 1242, 1254, 1287, 1287, 1335,
1335, 1365, 1380, 1389, 1392, 1455, 1455, 1569,
1575, 1665, 1665, 1722, 1725, 1725, 1950, 1953,
2082, 2112, 2175, 2175, 2184, 2184, 2184, 2208,
2208, 2208, 2226, 2226, 2226, 2271, 2271, 2304,
2304, 2304, 2304, 2304, 2307, 2325, 2337, 2346,
2346, 2346, 2385, 2385, 2418, 2418],
[ 0, 0, 9, 9, 30, 30, 57, 57,
99, 99, 114, 114, 150, 159, 186, 189,
339, 339, 357, 372, 462, 465, 546, 621,
624, 657, 669, 798, 810, 960, 987, 1095,
1119, 1179, 1179, 1242, 1254, 1287, 1287, 1335,
1335, 1365, 1380, 1389, 1392, 1455, 1455, 1569,
1575, 1665, 1665, 1722, 1725, 1725, 1950, 1953,
2082, 2112, 2175, 2175, 2184, 2184, 2184, 2208,
2208, 2208, 2226, 2229, 2229, 2229, 2229, 2262,
2274, 2274, 2274, 2334, 2337, 2337, 2349, 2349,
2349, 2349, 2388, 2388, 2388, 2388]])
# fmt: on
)
)
self.assertEqual(
format(alignment, "clustal"),
"""\
ENSG00000166888:ENST0000030013 --------------------------------------------------
ENSG00000166888:ENST0000054387 --------------------------------------------------
ENSG00000166888:ENST0000055615 --------------------------------------------------
ENSG00000166888:ENST0000045407 --------------------------------------------------
ENSG00000166888:ENST0000053891 --------------------------------------------------
ENSG00000166888:ENST0000053721 --------------------------------------------------
ENSG00000166888:ENST0000053520 --------------------------------------------------
isotig46679 GAGGTTACTCAGAGTAGGAGGAAGCCGGTCAGAGAGGGCAGACCCTGGGA
isotig12565 ------------GCTAGGAGA-----------------------------
isotig12566 ------------GCTAGGAGA-----------------------------
ENSG00000166888:ENST0000030013 --------------------------------------------------
ENSG00000166888:ENST0000054387 --------------------------------------------------
ENSG00000166888:ENST0000055615 --------------------------------------------------
ENSG00000166888:ENST0000045407 --------------------------------------------------
ENSG00000166888:ENST0000053891 --------------------------------------------------
ENSG00000166888:ENST0000053721 --------------------------------------------------
ENSG00000166888:ENST0000053520 --------------------------------------------------
isotig46679 ACCTTCGCAGGAGTTGGCCCAAACCCCTGAGGGAGGCTGTCCTCGGCAGG
isotig12565 --------------------------------------------------
isotig12566 --------------------------------------------------
ENSG00000166888:ENST0000030013 --------------------------------------------------
ENSG00000166888:ENST0000054387 --------------------------------------------------
ENSG00000166888:ENST0000055615 --------------------------------------------------
ENSG00000166888:ENST0000045407 --------------------------------------------------
ENSG00000166888:ENST0000053891 --------------------------------------------------
ENSG00000166888:ENST0000053721 --------------------------------------------------
ENSG00000166888:ENST0000053520 --------------------------------------------------
isotig46679 AGAGCAGACCTGAGGGAGGTTGGTGTGCCGGTCCTGGTTGTCCAGCCCTC
isotig12565 --------------------------------------------------
isotig12566 --------------------------------------------------
ENSG00000166888:ENST0000030013 --------------------------------------------------
ENSG00000166888:ENST0000054387 --------------------------------------------------
ENSG00000166888:ENST0000055615 --------------------------------------------------
ENSG00000166888:ENST0000045407 --------------------------------------------------
ENSG00000166888:ENST0000053891 --------------------------------------------------
ENSG00000166888:ENST0000053721 --------------------------------------------------
ENSG00000166888:ENST0000053520 --------------------------------------------------
isotig46679 CCGTCCCATCCCAGGGCTGGCTCACCAGAAAAAAGTACAGGCATCCCAGG
isotig12565 --------------------------------------------------
isotig12566 --------------------------------------------------
ENSG00000166888:ENST0000030013 --------------------------------------------------
ENSG00000166888:ENST0000054387 --------------------------------------------------
ENSG00000166888:ENST0000055615 --------------------------------------------------
ENSG00000166888:ENST0000045407 --------------------------------------------------
ENSG00000166888:ENST0000053891 --------------------------------------------------
ENSG00000166888:ENST0000053721 --------------------------------------------------
ENSG00000166888:ENST0000053520 --------------------------------------------------
isotig46679 CCCTCTGGGGCGGGAGCAGAGGGTCTCCTCTTGTCCGGGGGAAGACAAAA
isotig12565 --------------------------------------------------
isotig12566 --------------------------------------------------
ENSG00000166888:ENST0000030013 --------------------------------------------------
ENSG00000166888:ENST0000054387 --------------------------------------------------
ENSG00000166888:ENST0000055615 --------------------------------------------------
ENSG00000166888:ENST0000045407 --------------------------------------------------
ENSG00000166888:ENST0000053891 --------------------------------------------------
ENSG00000166888:ENST0000053721 --------------------------------------------------
ENSG00000166888:ENST0000053520 --------------------------------------------------
isotig46679 ACAAAAACAAAAAACGAGTGTGTAGCCCTCACTGGAAGTCTTCTGGTGCT
isotig12565 --------------------------------------------------
isotig12566 --------------------------------------------------
ENSG00000166888:ENST0000030013 --------------------------------------------------
ENSG00000166888:ENST0000054387 --------------------------------------------------
ENSG00000166888:ENST0000055615 --------------------------------------------------
ENSG00000166888:ENST0000045407 --------------------------------------------------
ENSG00000166888:ENST0000053891 --------------------------------------------------
ENSG00000166888:ENST0000053721 --------------------------------------------------
ENSG00000166888:ENST0000053520 --------------------------------------------------
isotig46679 CTGGGGCCGTTTGCACTTGGGAGCCTGGCTTCTGGGCATGGTGGCCGGGC
isotig12565 --------------------------------------------------
isotig12566 --------------------------------------------------
ENSG00000166888:ENST0000030013 --------------------------------------------------
ENSG00000166888:ENST0000054387 --------------------------------------------------
ENSG00000166888:ENST0000055615 --------------------------------------------------
ENSG00000166888:ENST0000045407 --------------------------------------------------
ENSG00000166888:ENST0000053891 --------------------------------------------------
ENSG00000166888:ENST0000053721 --------------------------------------------------
ENSG00000166888:ENST0000053520 --------------------------------------------------
isotig46679 TCCGCCGGGGGCTTCAGCCCTCGGCAAAGCGTTTCTAGAACAGAGTGGGT
isotig12565 -------GGCCAGGCGGCCCTCGGGAGC----------------------
isotig12566 -------GGCCAGGCGGCCCTCGGGAGC----------------------
ENSG00000166888:ENST0000030013 --------------------------------------------------
ENSG00000166888:ENST0000054387 --------------------------------------------------
ENSG00000166888:ENST0000055615 --------------------------------------------------
ENSG00000166888:ENST0000045407 --------------------------------------------------
ENSG00000166888:ENST0000053891 --------------------------------------------------
ENSG00000166888:ENST0000053721 --------------------------------------------------
ENSG00000166888:ENST0000053520 --------------------------------------------------
isotig46679 GGGAGCCGACTGAAGTCCCAGAACCGCGAACACTGACGCACAGGAAAGCC
isotig12565 -----------------CCAGCTGCTCGCACCTGGAGCCAGCGC------
isotig12566 -----------------CCAGCTGCTCGCACCTGGAGCCAGCGC------
ENSG00000166888:ENST0000030013 --------------------------------------------------
ENSG00000166888:ENST0000054387 --------------------------------------------------
ENSG00000166888:ENST0000055615 --------------------------------------------------
ENSG00000166888:ENST0000045407 --------------------------------------------------
ENSG00000166888:ENST0000053891 --------------------------------------------------
ENSG00000166888:ENST0000053721 --------------------------------------------------
ENSG00000166888:ENST0000053520 --------------------------------------------------
isotig46679 TCGAGTGGGTGGAGAAATGCAAATCCCCCAGTGGCATGGCCTCAGCCGCT
isotig12565 ------------------------AGCCCGGCCAGTCGGGCCTCAGCCCG
isotig12566 ------------------------AGCCCGGCCAGTCGGGCCTCAGCCCG
ENSG00000166888:ENST0000030013 --------------------------------------------------
ENSG00000166888:ENST0000054387 --------------------------------------------------
ENSG00000166888:ENST0000055615 --------------------------------------------------
ENSG00000166888:ENST0000045407 --------------------------------------------------
ENSG00000166888:ENST0000053891 --------------------------------------------------
ENSG00000166888:ENST0000053721 --------------------------------------------------
ENSG00000166888:ENST0000053520 --------------------------------------------------
isotig46679 GCGGACCCTGACGGCCGATTCTGACTTCGGACTTGAGCGGGACCAGCACC
isotig12565 GGAGACAGTTACGCCC---------------------------------C
isotig12566 GGAGACAGTTACGCCC---------------------------------C
ENSG00000166888:ENST0000030013 --------------------ATGTCTCTGTGGGGTCTGGTCTCCAAGATG
ENSG00000166888:ENST0000054387 --------------------ATGTCTCTGTGGGGTCTGGTCTCCAAGATG
ENSG00000166888:ENST0000055615 --------------------ATGTCTCTGTGGGGTCTGGTCTCCAAGATG
ENSG00000166888:ENST0000045407 --------------------ATGTCTCTGTGGGGTCTGGTCTCCAAGATG
ENSG00000166888:ENST0000053891 --------------------------------------------------
ENSG00000166888:ENST0000053721 --------------------------------------------------
ENSG00000166888:ENST0000053520 --------------------------------------------------
isotig46679 CGGACCCAGGGCGAGCCAGCATGTCTCAGTGGAATCAAGTCCAACAGTTA
isotig12565 CTGATTGCGGCAGG------ATGGCCCAGTGGAACCAGCTGCAGCAGCTG
isotig12566 CTGATTGCGGCAGG------ATGGCCCAGTGGAACCAGCTGCAGCAGCTG
ENSG00000166888:ENST0000030013 CCCCCA---------GAAAAAGTGCAGCGGCTCTATGTCGAC---TTTCC
ENSG00000166888:ENST0000054387 CCCCCA---------GAAAAAGTGCAGCGGCTCTATGTCGAC---TTTCC
ENSG00000166888:ENST0000055615 CCCCCA---------GAAAAAGTGCAGCGGCTCTATGTCGAC---TTTCC
ENSG00000166888:ENST0000045407 CCCCCA---------GAAAAAGTGCAGCGGCTCTATGTCGAC---TTTCC
ENSG00000166888:ENST0000053891 --------------------------------------------------
ENSG00000166888:ENST0000053721 --------------------------------------------------
ENSG00000166888:ENST0000053520 --------------------------------------------------
isotig46679 GAAATCAAGTTTTTGGAGCAAGTTGATCAGTTCTATGATGACAACTTTCC
isotig12565 GACACTCGGTACCTGGAGCAGCTGCACCAGCTGTACAGCGACAGCTTCCC
isotig12566 GACACTCGGTACCTGGAGCAGCTGCACCAGCTGTACAGCGACAGCTTCCC
ENSG00000166888:ENST0000030013 CCAACACCTGCGGCATCTTCTGGGTGACTGGCTGGAGAGCCAGCCCTGGG
ENSG00000166888:ENST0000054387 CCAACACCTGCGGCATCTTCTGGGTGACTGGCTGGAGAGCCAGCCCTGGG
ENSG00000166888:ENST0000055615 CCAACACCTGCGGCATCTTCTGGGTGACTGGCTGGAGAGCCAGCCCTGGG
ENSG00000166888:ENST0000045407 CCAACACCTGCGGCATCTTCTGGGTGACTGGCTGGAGAGCCAGCCCTGGG
ENSG00000166888:ENST0000053891 --------------------------------------------------
ENSG00000166888:ENST0000053721 --------------------------------------------------
ENSG00000166888:ENST0000053520 --------------------------------------------------
isotig46679 CATGGAAATCCGACATCTGCTGGCCCAGTGGATTGAGCATCAAGACTGGG
isotig12565 CATGGAGCTGCGGCAGTTCCTGGCACCTTGGATTGAGAGTCAAGATTGGG
isotig12566 CATGGAGCTGCGGCAGTTCCTGGCACCTTGGATTGAGAGTCAAGATTGGG
ENSG00000166888:ENST0000030013 AGTTCCTGGTCGGCTCCGACGCCTTCTGCTGCAACTTGGCTAGTGCCCTA
ENSG00000166888:ENST0000054387 AGTTCCTGGTCGGCTCCGACGCCTTCTGCTGCAACTTGGCTAGTGCCCTA
ENSG00000166888:ENST0000055615 AGTTCCTGGTCGGCTCCGACGCCTTCTGCTGCAACTTGGCTAGTGCCCTA
ENSG00000166888:ENST0000045407 AGTTCCTGGTCGGCTCCGACGCCTTCTGCTGCAACTTGGCTAGTGCCCTA
ENSG00000166888:ENST0000053891 --------------------------------------------------
ENSG00000166888:ENST0000053721 --------------------------------------------------
ENSG00000166888:ENST0000053520 --------------------------------------------------
isotig46679 AGGTGGCCTCTAACAATGAAACTATGGCAACAATTCTTCTTCAAAACTTA
isotig12565 CATATGCAGCCAGCAAAGAGTCACATGCCACACTGGTGTTTCATAATCTC
isotig12566 CATATGCAGCCAGCAAAGAGTCACATGCCACACTGGTGTTTCATAATCTC
ENSG00000166888:ENST0000030013 CTTTCAGACACTGTCCAGCACCTTCAGGCCTCGGTGGGAGAGCAGGGGGA
ENSG00000166888:ENST0000054387 CTTTCAGACACTGTCCAGCACCTTCAGGCCTCGGTGGGAGAGCAGGGGGA
ENSG00000166888:ENST0000055615 CTTTCAGACACTGTCCAGCACCTTCAGGCCTCGGTGGGAGAGCAGGGGGA
ENSG00000166888:ENST0000045407 CTTTCAGACACTGTCCAGCACCTTCAGGCCTCGGTGGGAGAGCAGGGGGA
ENSG00000166888:ENST0000053891 --------------------------------------------------
ENSG00000166888:ENST0000053721 --------------------------------------------------
ENSG00000166888:ENST0000053520 --------------------------------------------------
isotig46679 TTAATACAATTGGATGAACAGTTAGGTCGTGTTTCCAAAGAGAAA-----
isotig12565 TTGGGTGAGATTGACCAGCAGTACAGCCGATTCCTGCAAGAGTCC-----
isotig12566 TTGGGTGAGATTGACCAGCAGTACAGCCGATTCCTGCAAGAGTCC-----
ENSG00000166888:ENST0000030013 GGGGAGCACCATCTTGCAACAC---------------ATCAGCACCCTTG
ENSG00000166888:ENST0000054387 GGGGAGCACCATCTTGCAACAC---------------ATCAGCACCCTTG
ENSG00000166888:ENST0000055615 GGGGAGCACCATCTTGCAACAC---------------ATCAGCACCCTTG
ENSG00000166888:ENST0000045407 GGGGAGCACCATCTTGCAACAC---------------ATCAGCACCCTTG
ENSG00000166888:ENST0000053891 --------------------------------------------------
ENSG00000166888:ENST0000053721 --------------------------------------------------
ENSG00000166888:ENST0000053520 --------------------------------------------------
isotig46679 ----AACCTGCTATTGATCCACAATCTAAAGAGAATTAGAAAAGTACTTC
isotig12565 ----AACGTCCTCTATCAGCACAACCTTCGGAGGATCAAGCAGTTCCTAC
isotig12566 ----AACGTCCTCTATCAGCACAACCTTCGGAGGATCAAGCAGTTCCTAC
ENSG00000166888:ENST0000030013 AGAGCATATATCAGAGGGACCCCCTGAAGCTGGTGGCCACTTTCAGACAA
ENSG00000166888:ENST0000054387 AGAGCATATATCAGAGGGACCCCCTGAAGCTGGTGGCCACTTTCAGACAA
ENSG00000166888:ENST0000055615 AGAGCATATATCAGAGGGACCCCCTGAAGCTGGTGGCCACTTTCAGACAA
ENSG00000166888:ENST0000045407 AGAGCATATATCAGAGGGACCCCCTGAAGCTGGTGGCCACTTTCAGACAA
ENSG00000166888:ENST0000053891 --------------------------------------------------
ENSG00000166888:ENST0000053721 --------------------------------------------------
ENSG00000166888:ENST0000053520 --------------------------------------------------
isotig46679 AGGGGAAGTTTCATGGAAATCCAATGCATGTAGCCGTGGTAATCTCAAAT
isotig12565 AGAGCAGGTATCTTGAGAAGCCGATGGAAATCGCCCGCATCGTGGCCCGA
isotig12566 AGAGCAGGTATCTTGAGAAGCCGATGGAAATCGCCCGCATCGTGGCCCGA
ENSG00000166888:ENST0000030013 ATACTTCAAGGAGAGAAAAAAGCTGTT-----------------------
ENSG00000166888:ENST0000054387 ATACTTCAAGGAGAGAAAAAAGCTGTT-----------------------
ENSG00000166888:ENST0000055615 ATACTTCAAGGAGAGAAAAAAGCTGTT-----------------------
ENSG00000166888:ENST0000045407 ATACTTCAAGGAGAGAAAAAAGCTGTT-----------------------
ENSG00000166888:ENST0000053891 --------------------------------------------------
ENSG00000166888:ENST0000053721 --------------------------------------------------
ENSG00000166888:ENST0000053520 --------------------------------------------------
isotig46679 TGTTTAAGGGAAGAGAGGAGAATACTG---GCTGCAGCGAACATGCCTAT
isotig12565 TGCCTGTGGGAAGAGTCTCGCCTCCTCCAGACGGCAGCCACTGCAGCCCA
isotig12566 TGCCTGTGGGAAGAGTCTCGCCTCCTCCAGACGGCAGCCACTGCAGCCCA
ENSG00000166888:ENST0000030013 --------------------------------------------------
ENSG00000166888:ENST0000054387 --------------------------------------------------
ENSG00000166888:ENST0000055615 --------------------------------------------------
ENSG00000166888:ENST0000045407 --------------------------------------------------
ENSG00000166888:ENST0000053891 --------------------------------------------------
ENSG00000166888:ENST0000053721 --------------------------------------------------
ENSG00000166888:ENST0000053520 --------------------------------------------------
isotig46679 CCAGGGACCTCTGGAGAAATCCTTACAAAGTTCGTCGGTTTCAGAAAGAC
isotig12565 GCAAGGAGGCCAGGCCAACCACCCAACAGCTGCTGTGGTGACGGAGAAAC
isotig12566 GCAAGGAGGCCAGGCCAACCACCCAACAGCTGCTGTGGTGACGGAGAAAC
ENSG00000166888:ENST0000030013 -----------ATGGAACAGTTCCGCCACTTGCCAATGCCTTTCCACTGG
ENSG00000166888:ENST0000054387 -----------ATGGAACAGTTCCGCCACTTGCCAATGCCTTTCCACTGG
ENSG00000166888:ENST0000055615 -----------ATGGAACAGTTCCGCCACTTGCCAATGCCTTTCCACTGG
ENSG00000166888:ENST0000045407 -----------ATGGAACAGTTCCGCCACTTGCCAATGCCTTTCCACTGG
ENSG00000166888:ENST0000053891 -----------ATGGAACAGTTCCGCCACTTGCCAATGCCTTTCCACTGG
ENSG00000166888:ENST0000053721 -----------ATGGAACAGTTCCGCCACTTGCCAATGCCTTTCCACTGG
ENSG00000166888:ENST0000053520 -----------ATGGAACAGTTCCGCCACTTGCCAATGCCTTTCCACTGG
isotig46679 AGAGAAATGTGGAACACAAAGTGGCTGCCATTAAAAACAGTGTGCAGATG
isotig12565 AGCAGATGCTGGAGCAGCATCTTCAGGATGTCCGGAAACGTGTGCAGGAT
isotig12566 AGCAGATGCTGGAGCAGCATCTTCAGGATGTCCGGAAACGTGTGCAGGAT
ENSG00000166888:ENST0000030013 AAGCAGGAAGAACTCAAGTTTAAGACAGGCTTGCGG---AGGCTGCAGCA
ENSG00000166888:ENST0000054387 AAGCAGGAAGAACTCAAGTTTAAGACAGGCTTGCGG---AGGCTGCAGCA
ENSG00000166888:ENST0000055615 AAGCAGGAAGAACTCAAGTTTAAGACAGGCTTGCGG---AGGCTGCAGCA
ENSG00000166888:ENST0000045407 AAGCAGGAAGAACTCAAGTTTAAGACAGGCTTGCGG---AGGCTGCAGCA
ENSG00000166888:ENST0000053891 AAGCAGGAAGAACTCAAGTTTAAGACAGGCTTGCGG---AGGCTGCAGCA
ENSG00000166888:ENST0000053721 AAGCAGGAAGAACTCAAGTTTAAGACAGGCTTGCGG---AGGCTGCAGCA
ENSG00000166888:ENST0000053520 AAGCAGGAAGAACTCAAGTTTAAGACAGGCTTGCGG---AGGCTGCAGCA
isotig46679 ACAGAACAAGACACCAAATACTTGGAAGATCTGCAAGATGAATTTGACTA
isotig12565 CTAGAACAGAAAATGAAAGTGGTAGAGAATCTCCAGGATGACTTTGATTT
isotig12566 CTAGAACAGAAAATGAAAGTGGTAGAGAATCTCCAGGATGACTTTGATTT
ENSG00000166888:ENST0000030013 CCGAGTAGGGGAGATCCACCTTCTCCGAGAAGCCCTGCAGAAGGGGGCTG
ENSG00000166888:ENST0000054387 CCGAGTAGGGGAGATCCACCTTCTCCGAGAAGCCCTGCAGAAGGGGGCTG
ENSG00000166888:ENST0000055615 CCGAGTAGGGGAGATCCACCTTCTCCGAGAAGCCCTGCAGAAGGGGGCTG
ENSG00000166888:ENST0000045407 CCGAGTAGGGGAGATCCACCTTCTCCGAGAAGCCCTGCAGAAGGGGGCTG
ENSG00000166888:ENST0000053891 CCGAGTAGGGGAGATCCACCTTCTCCGAGAAGCCCTGCAGAAGGGGGCTG
ENSG00000166888:ENST0000053721 CCGAGTAGGGGAGATCCACCTTCTCCGAGAAGCCCTGCAGAAGGGGGCTG
ENSG00000166888:ENST0000053520 CCGAGTAGGGGAGATCCACCTTCTCCGAGAAGCCCTGCAGAAGGGGGCTG
isotig46679 CAGGTATAAAACAATTCAGACA------------ATGGACCAGGGTGACA
isotig12565 CAACTATAAAACCCTCAAGAGTCAAGGAGACATGCAGGATCTGAATGGAA
isotig12566 CAACTATAAAACCCTCAAGAGTCAAGGAGACATGCAGGATCTGAATGGAA
ENSG00000166888:ENST0000030013 AGGCTGGCCAAGTGTCTCTGCACAGCTTGATAGAAACTCCTGCTAATGGG
ENSG00000166888:ENST0000054387 AGGCTGGCCAAGTGTCTCTGCACAGCTTGATAGAAACTCCTGCTAATGGG
ENSG00000166888:ENST0000055615 AGGCTGGCCAAGTGTCTCTGCACAGCTTGATAGAAACTCCTGCTAATGGG
ENSG00000166888:ENST0000045407 AGGCTGGCCAAGTGTCTCTGCACAGCTTGATAGAAACTCCTGCTAATGGG
ENSG00000166888:ENST0000053891 AGGCTGGCCAAGTGTCTCTGCACAGCTTGATAGAAACTCCTGCTAATGGG
ENSG00000166888:ENST0000053721 AGGCTGGCCAAGTGTCTCTGCACAGCTTGATAGAAACTCCTGCTAATGGG
ENSG00000166888:ENST0000053520 AGGCTGGCCAAGTGTCTCTGCACAGCTTGATAGAAACTCCTGCTAATGGG
isotig46679 AGAATAGCATCCTAATGAACCAGGAGGTTTTGACACTCCAAGAAATGCTT
isotig12565 ACAACCAGTCTGTGACCAGGCAGAAGATGCAGCAGCTGGAACAGATGCTC
isotig12566 ACAACCAGTCTGTGACCAGGCAGAAGATGCAGCAGCTGGAACAGATGCTC
ENSG00000166888:ENST0000030013 ACTGGGCCAAGTGAGGCCCTGGCCATGCTACTGCAGGAGACCACTGGAGA
ENSG00000166888:ENST0000054387 ACTGGGCCAAGTGAGGCCCTGGCCATGCTACTGCAGGAGACCACTGGAGA
ENSG00000166888:ENST0000055615 ACTGGGCCAAGTGAGGCCCTGGCCATGCTACTGCAGGAGACCACTGGAGA
ENSG00000166888:ENST0000045407 ACTGGGCCAAGTGAGGCCCTGGCCATGCTACTGCAGGAGACCACTGGAGA
ENSG00000166888:ENST0000053891 ACTGGGCCAAGTGAGGCCCTGGCCATGCTACTGCAGGAGACCACTGGAGA
ENSG00000166888:ENST0000053721 ACTGGGCCAAGTGAGGCCCTGGCCATGCTACTGCAGGAGACCACTGGAGA
ENSG00000166888:ENST0000053520 ACTGGGCCAAGTGAGGCCCTGGCCATGCTACTGCAGGAGACCACTGGAGA
isotig46679 AATAGCCTGGACTTCAAGAGAAAGGAAGCACTCACTAAGATGACACAGAT
isotig12565 ACGGCGCTGGACCAGATGCGGAGAAGCATTGTGAGTGAGCTGGCGGGGCT
isotig12566 ACGGCGCTGGACCAGATGCGGAGAAGCATTGTGAGTGAGCTGGCGGGGCT
ENSG00000166888:ENST0000030013 GCTAGAGGCAGCC------------AAAGCCCTAGTGCTGAAGAGGATCC
ENSG00000166888:ENST0000054387 GCTAGAGGCAGCC------------AAAGCCCTAGTGCTGAAGAGGATCC
ENSG00000166888:ENST0000055615 GCTAGAGGCAGCC------------AAAGCCCTAGTGCTGAAGAGGATCC
ENSG00000166888:ENST0000045407 GCTAGAGGCAGCC------------AAAGCCCTAGTGCTGAAGAGGATCC
ENSG00000166888:ENST0000053891 GCTAGAGGCAGCC------------AAAGCCCTAGTGCTGAAGAGGATCC
ENSG00000166888:ENST0000053721 GCTAGAGGCAGCC------------AAAGCCCTAGTGCTGAAGAGGATCC
ENSG00000166888:ENST0000053520 GCTAGAGGCAGCC------------AAAGCCCTAGTGCTGAAGAGGATCC
isotig46679 AGTGAACGAGTCGGACCTGCTGATGAGCAGCATGCTCATAGAAGAGCTGC
isotig12565 TTTGTCGGCAATGGAGTACGTGCAGAAAACACTCACAGACGAGGAGCTGG
isotig12566 TTTGTCGGCAATGGAGTACGTGCAGAAAACACTCACAGACGAGGAGCTGG
ENSG00000166888:ENST0000030013 AGATTTGGAAACGGCAGCAGCAGCTGGCAGGGAATGGCGCACCGTTTGAG
ENSG00000166888:ENST0000054387 AGATTTGGAAACGGCAGCAGCAGCTGGCAGGGAATGGCGCACCGTTTGAG
ENSG00000166888:ENST0000055615 AGATTTGGAAACGGCAGCAGCAGCTGGCAGGGAATGGCGCACCGTTTGAG
ENSG00000166888:ENST0000045407 AGATTTGGAAACGGCAGCAGCAGCTGGCAGGGAATGGCGCACCGTTTGAG
ENSG00000166888:ENST0000053891 AGATTTGGAAACGGCAGCAGCAGCTGGCAGGGAATGGCGCACCGTTTGAG
ENSG00000166888:ENST0000053721 AGATTTGGAAACGGCAGCAGCAGCTGGCAGGGAATGGCGCACCGTTTGAG
ENSG00000166888:ENST0000053520 AGATTTGGAAACGGCAGCAGCAGCTGGCAGGGAATGGCGCACCGTTTGAG
isotig46679 AGGACTGGAAGAGGAGGCAGCAGATCGCCTGCATCGGTGGCCCACTCCAC
isotig12565 CTGACTGGAAGAGGCGGCAGCAGATCGCGTGCATTGGAGGCCCTCCCAAC
isotig12566 CTGACTGGAAGAGGCGGCAGCAGATCGCGTGCATTGGAGGCCCTCCCAAC
ENSG00000166888:ENST0000030013 GAGAGCCTGGCCCCACTCCAGGAGAGGTGTGAAAGCCTGGTGGACATTTA
ENSG00000166888:ENST0000054387 GAGAGCCTGGCCCCACTCCAGGAGAGGTGTGAAAGCCTGGTGGACATTTA
ENSG00000166888:ENST0000055615 GAGAGCCTGGCCCCACTCCAGGAGAGGTGTGAAAGCCTGGTGGACATTTA
ENSG00000166888:ENST0000045407 GAGAGCCTGGCCCCACTCCAGGAGAGGTGTGAAAGCCTGGTGGACATTTA
ENSG00000166888:ENST0000053891 GAGAGCCTGGCCCCACTCCAGGAGAGGTGTGAAAGCCTGGTGGACATTTA
ENSG00000166888:ENST0000053721 GAGAGCCTGGCCCCACTCCAGGAGAGGTGTGAAAGCCTGGTGGACATTTA
ENSG00000166888:ENST0000053520 GAGAGCCTGGCCCCACTCCAGGAGAGGTGTGAAAGCCTGGTGGACATTTA
isotig46679 AACGGGCTGGACCAGCTTCAGAACTGCTTTACCCTGTTGGCAGAAAGTCT
isotig12565 ATCTGCCTGGATCGCCTGGAAAACTGGATAACTTCGTTAGCAGAATCTCA
isotig12566 ATCTGCCTGGATCGCCTGGAAAACTGGATAACTTCGTTAGCAGAATCTCA
ENSG00000166888:ENST0000030013 TTCCCAGCTACAGCAGGAGGTAGGG-------------------------
ENSG00000166888:ENST0000054387 TTCCCAGCTACAGCAGGAGGTAGGG-------------------------
ENSG00000166888:ENST0000055615 TTCCCAGCTACAGCAGGAGGTAGGG-------------------------
ENSG00000166888:ENST0000045407 TTCCCAGCTACAGCAGGAGGTAGGG-------------------------
ENSG00000166888:ENST0000053891 TTCCCAGCTACAGCAGGAGGTAGGG-------------------------
ENSG00000166888:ENST0000053721 TTCCCAGCTACAGCAGGAGGTAGGG-------------------------
ENSG00000166888:ENST0000053520 TTCCCAGCTACAGCAGGAGGTAGGG-------------------------
isotig46679 TTTCCAACTCAGACGACAGCTGGAGAAATTAGAGGAGCAGTCTTCCAAGA
isotig12565 ACTTCAGACCCGCCAACAAATTAAGAAACTGGAGGAGCTACAGCAGAAGG
isotig12566 ACTTCAGACCCGCCAACAAATTAAGAAACTGGAGGAGCTACAGCAGAAGG
ENSG00000166888:ENST0000030013 --GCGGCTGGTGGGGAGCTTGAGCCCAAGACCCGGGCATCGCTGACTGGC
ENSG00000166888:ENST0000054387 --GCGGCTGGTGGGGAGCTTGAGCCCAAGACCCGGGCATCGCTGACTGGC
ENSG00000166888:ENST0000055615 --GCGGCTGGTGGGGAGCTTGAGCCCAAGACCCGGGCATCGCTGACTGGC
ENSG00000166888:ENST0000045407 --GCGGCTGGTGGGGAGCTTGAGCCCAAGACCCGGGCATCGCTGACTGGC
ENSG00000166888:ENST0000053891 --GCGGCTGGTGGGGAGCTTGAGCCCAAGACCCGGGCATCGCTGACTGGC
ENSG00000166888:ENST0000053721 --GCGGCTGGTGGGGAGCTTGAGCCCAAGACCCGGGCATCGCTGACTGGC
ENSG00000166888:ENST0000053520 --GCGGCTGGTGGGGAGCTTGAGCCCAAGACCCGGGCATCGCTGACTGGC
isotig46679 TGACTTACGAAGGAGACCCCATCCCCACGCAGAGAGCACACCTGCTGGAG
isotig12565 TGTCCTACAAGGGGGACCCCATTGTGCAGCACCGGCCGATGCTGGAGGAG
isotig12566 TGTCCTACAAGGGGGACCCCATTGTGCAGCACCGGCCGATGCTGGAGGAG
ENSG00000166888:ENST0000030013 CGGCTGGATGAAGTCCTGAGAACCCTCGTCACCAGTTGCTTCCTGGTGGA
ENSG00000166888:ENST0000054387 CGGCTGGATGAAGTCCTGAGAACCCTCGTCACCAGTTGCTTCCTGGTGGA
ENSG00000166888:ENST0000055615 CGGCTGGATGAAGTCCTGAGAACCCTCGTCACCAGTTGCTTCCTGGTGGA
ENSG00000166888:ENST0000045407 CGGCTGGATGAAGTCCTGAGAACCCTCGTCACCAGTTGCTTCCTGGTGGA
ENSG00000166888:ENST0000053891 CGGCTGGATGAAGTCCTGAGAACCCTCGTCACCAGTTGCTTCCTGGTGGA
ENSG00000166888:ENST0000053721 CGGCTGGATGAAGTCCTGAGAACCCTCGTCACCAGTTGCTTCCTGGTGGA
ENSG00000166888:ENST0000053520 CGGCTGGATGAAGTCCTGAGAACCCTCGTCACCAGTTGCTTCCTGGTGGA
isotig46679 AGAGCCACCTTCCTGATCTACAACCTTTTCAAGAACTCATTTGTGGTTGA
isotig12565 CGGATCGTGGAGCTGTTCAGAAACTTGATGAAGAGTGCCTTCGTGGTGGA
isotig12566 CGGATCGTGGAGCTGTTCAGAAACTTGATGAAGAGTGCCTTCGTGGTGGA
ENSG00000166888:ENST0000030013 GAAGCAGCCC------------------------CCCCAGGTACTGAAGA
ENSG00000166888:ENST0000054387 GAAGCAGCCC------------------------CCCCAGGTACTGAAGA
ENSG00000166888:ENST0000055615 GAAGCAGCCC------------------------CCCCAGGTACTGAAGA
ENSG00000166888:ENST0000045407 GAAGCAGCCC------------------------CCCCAGGTACTGAAGA
ENSG00000166888:ENST0000053891 GAAGCAGCCC------------------------CCCCAGGTACTGAAGA
ENSG00000166888:ENST0000053721 GAAGCAGCCC------------------------CCCCAGGTACTGAAGA
ENSG00000166888:ENST0000053520 GAAGCAGCCC------------------------CCCCAGGTACTGAAGA
isotig46679 GCGACAGCCCTGCATGCCAACACACCCTCAGAGGCCGCTGGTACTCAAAA
isotig12565 GCGACAGCCCTGCATGCCGATGCACCCCGACCGGCCCTTGGTCATCAAGA
isotig12566 GCGACAGCCCTGCATGCCGATGCACCCCGACCGGCCCTTGGTCATCAAGA
ENSG00000166888:ENST0000030013 CTCAGACCAAGTTCCAGGCTGGAGTTCGATTCCTGTTGGGCTTGAGGTTC
ENSG00000166888:ENST0000054387 CTCAGACCAAGTTCCAGGCTGGAGTTCGATTCCTGTTGGGCTTGAGGTTC
ENSG00000166888:ENST0000055615 CTCAGACCAAGTTCCAGGCTGGAGTTCGATTCCTGTTGGGCTTGAGGTTC
ENSG00000166888:ENST0000045407 CTCAGACCAAGTTCCAGGCTGGAGTTCGATTCCTGTTGGGCTTGAGGTTC
ENSG00000166888:ENST0000053891 CTCAGACCAAGTTCCAGGCTGGAGTTCGATTCCTGTTGGGCTTGAGGTTC
ENSG00000166888:ENST0000053721 CTCAGACCAAGTTCCAGGCTGGAGTTCGATTCCTGTTGGGCTTGAGGTTC
ENSG00000166888:ENST0000053520 CTCAGACCAAGTTCCAGGCTGGAGTTCGATTCCTGTTGGGCTTGAGGTTC
isotig46679 CCCTCATTCAGTTCACCGCGAAACTGAGACTACTAATAAAATTG------
isotig12565 CTGGTGTCCAGTTCACTACTAAAGTCAGGTTGTTGGTCAAGTTT------
isotig12566 CTGGTGTCCAGTTCACTACTAAAGTCAGGTTGTTGGTCAAGTTT------
ENSG00000166888:ENST0000030013 CTGGGGGCCCCAGCCAAGCCTCCGCTGGTCAGGGCCGACATGGTGACAGA
ENSG00000166888:ENST0000054387 CTGGGGGCCCCAGCCAAGCCTCCGCTGGTCAGGGCCGACATGGTGACAGA
ENSG00000166888:ENST0000055615 CTGGGGGCCCCAGCCAAGCCTCCGCTGGTCAGGGCCGACATGGTGACAGA
ENSG00000166888:ENST0000045407 CTGGGGGCCCCAGCCAAGCCTCCGCTGGTCAGGGCCGACATGGTGACAGA
ENSG00000166888:ENST0000053891 CTGGGGGCCCCAGCCAAGCCTCCGCTGGTCAGGGCCGACATGGTGACAGA
ENSG00000166888:ENST0000053721 CTGGGGGCCCCAGCCAAGCCTCCGCTGGTCAGGGCCGACATGGTGACAGA
ENSG00000166888:ENST0000053520 CTGGGGGCCCCAGCCAAGCCTCCGCTGGTCAGGGCCGACATGGTGACAGA
isotig46679 ---------CCGGAACTCAACTATCAGGTGAAAGTAAAGGCATCGATCGA
isotig12565 ---------CCCGAGTTGAATTATCAGCTTAAAATTAAAGTGTGCATTGA
isotig12566 ---------CCCGAGTTGAATTATCAGCTTAAAATTAAAGTGTGCATTGA
ENSG00000166888:ENST0000030013 GAAGCAGGCGCGGGAGCTGAGTGTGCCTCAGGGTCCTGGGGCTGGAGCAG
ENSG00000166888:ENST0000054387 GAAGCAGGCGCGGGAGCTGAGTGTGCCTCAGGGTCCTGGGGCTGGAGCAG
ENSG00000166888:ENST0000055615 GAAGCAGGCGCGGGAGCTGAGTGTGCCTCAGGGTCCTGGGGCTGGAGCAG
ENSG00000166888:ENST0000045407 GAAGCAGGCGCGGGAGCTGAGTGTGCCTCAGGGTCCTGGGGCTGGAGCAG
ENSG00000166888:ENST0000053891 GAAGCAGGCGCGGGAGCTGAGTGTGCCTCAGGGTCCTGGGGCTGGAGCAG
ENSG00000166888:ENST0000053721 GAAGCAGGCGCGGGAGCTGAGTGTGCCTCAGGGTCCTGGGGCTGGAGCAG
ENSG00000166888:ENST0000053520 GAAGCAGGCGCGGGAGCTGAGTGTGCCTCAGGGTCCTGGGGCTGGAGCAG
isotig46679 CAAGAATGTTTCAACGCTAAGC------------AATAGAAGATTTGTGC
isotig12565 CAAAGATTCTGGGGACGTTGCTGCTCTCAGAGGATCTCGGAAATTTAACA
isotig12566 CAAAGATTCTGGGGACGTTGCTGCTCTCAGAGGATCTCGGAAATTTAACA
ENSG00000166888:ENST0000030013 AAAGCACTGGAGAAATCATCAACAACACTGTGCCCTTGGAGAACAGCATT
ENSG00000166888:ENST0000054387 AAAGCACTGGAGAAATCATCAACAACACTGTGCCCTTGGAGAACAGCATT
ENSG00000166888:ENST0000055615 AAAGCACTGGAGAAATCATCAACAACACTGTGCCCTTGGAGAACAGCATT
ENSG00000166888:ENST0000045407 AAAGCACTGGAGAAATCATCAACAACACTGTGCCCTTGGAGAACAGCATT
ENSG00000166888:ENST0000053891 AAAGCACTGGAGAAATCATCAACAACACTGTGCCCTTGGAGAACAGCATT
ENSG00000166888:ENST0000053721 AAAGCACTGGAGAAATCATCAACAACACTGTGCCCTTGGAGAACAGCATT
ENSG00000166888:ENST0000053520 AAAGCACTGGAGAAATCATCAACAACACTGTGCCCTTGGAGAACAGCATT
isotig46679 TTTGTGGAACTCAAGTC------AAAGCCATGTCCATCGAGGAATCCTCC
isotig12565 TTCTGGGCACAAACACG------AAGGTGATGAACATGGAAGAATCCAAC
isotig12566 TTCTGGGCACAAACACG------AAGGTGATGAACATGGAAGAATCCAAC
ENSG00000166888:ENST0000030013 CCTGGGAACTGCTGCTCTGCCCTGTTCAAGAACCTGCTTCTCAAGAAGAT
ENSG00000166888:ENST0000054387 CCTGGGAACTGCTGCTCTGCCCTGTTCAAGAACCTGCTTCTCAAGAAGAT
ENSG00000166888:ENST0000055615 CCTGGGAACTGCTGCTCTGCCCTGTTCAAGAACCTGCTTCTCAAGAAGAT
ENSG00000166888:ENST0000045407 CCTGGGAACTGCTGCTCTGCCCTGTTCAAGAACCTGCTTCTCAAGAAGAT
ENSG00000166888:ENST0000053891 CCTGGGAACTGCTGCTCTGCCCTGTTCAAGAACCTGCTTCTCAAGAAGAT
ENSG00000166888:ENST0000053721 CCTGGGAACTGCTGCTCTGCCCTGTTCAAGAACCTGCTTCTCAAGAAGAT
ENSG00000166888:ENST0000053520 CCTGGGAACTGCTGCTCTGCCCTGTTCAAGAACCTGCTTCTCAAGAAGAT
isotig46679 AATGGGAGCCTCTCAGTAGAA---TTTAGACATTTGCAACCGAAGGAAAT
isotig12565 AACGGCAGCCTGTCTGCGGAG---TTCAAGCACTTGACCCTGAGGGAGCA
isotig12566 AACGGCAGCCTGTCTGCGGAG---TTCAAGCACTTGACCCTGAGGGAGCA
ENSG00000166888:ENST0000030013 CAAG---------------CGGTGTGAGCGGAAGGGCACTGAGTCTGTCA
ENSG00000166888:ENST0000054387 CAAG---------------CGGTGTGAGCGGAAGGGCACTGAGTCTGTCA
ENSG00000166888:ENST0000055615 CAAG---------------CGGTGTGAGCGGAAGGGCACTGAGTCTGTCA
ENSG00000166888:ENST0000045407 CAAG---------------CGGTGTGAGCGGAAGGGCACTGAGTCTGTCA
ENSG00000166888:ENST0000053891 CAAG---------------CGGTGTGAGCGGAAGGGCACTGAGTCTGTCA
ENSG00000166888:ENST0000053721 CAAG---------------CGGTGTGAGCGGAAGGGCACTGAGTCTGTCA
ENSG00000166888:ENST0000053520 CAAG---------------CGGTGTGAGCGGAAGGGCACTGAGTCTGTCA
isotig46679 GAAATCCAGTGCCGGAAGTAAAGGAAAT---GAGGGCTGCCACATGGTGA
isotig12565 GAGATGTGGGAATGGAGGCCGTGCCAATTGTGATGCCTCCTTGATTGTGA
isotig12566 GAGATGTGGGAATGGAGGCCGTGCCAATTGTGATGCCTCCTTGATTGTGA
ENSG00000166888:ENST0000030013 CAGAGGAGAAGTGCGCTGTGCTCTTCTCTGCCAGCTTCACACTTGGCCCC
ENSG00000166888:ENST0000054387 CAGAGGAGAAGTGCGCTGTGCTCTTCTCTGCCAGCTTCACACTTGGCCCC
ENSG00000166888:ENST0000055615 CAGAGGAGAAGTGCGCTGTGCTCTTCTCTGCCAGCTTCACACTTGGCCCC
ENSG00000166888:ENST0000045407 CAGAGGAGAAGTGCGCTGTGCTCTTCTCTGCCAGCTTCACACTTGGCCCC
ENSG00000166888:ENST0000053891 CAGAGGAGAAGTGCGCTGTGCTCTTCTCTGCCAGCTTCACACTTGGCCCC
ENSG00000166888:ENST0000053721 CAGAGGAGAAGTGCGCTGTGCTCTTCTCTGCCAGCTTCACACTTGGCCCC
ENSG00000166888:ENST0000053520 CAGAGGAGAAGTGCGCTGTGCTCTTCTCTGCCAGCTTCACACTTGGCCCC
isotig46679 CGGAAGAGCTGCATTCCATAGCCTTTGAGACCCAGATCTGCCTC------
isotig12565 CCGAGGAGCTGCATCTGATCACCTTCGAGACTGAGGTGTACCAC------
isotig12566 CCGAGGAGCTGCATCTGATCACCTTCGAGACTGAGGTGTACCAC------
ENSG00000166888:ENST0000030013 GGCAAACTCCCCATCCAGCTCCAGGCCCTGTCTCTGCCCCTGGTGGTCAT
ENSG00000166888:ENST0000054387 GGCAAACTCCCCATCCAGCTCCAGGCCCTGTCTCTGCCCCTGGTGGTCAT
ENSG00000166888:ENST0000055615 GGCAAACTCCCCATCCAGCTCCAGGCCCTGTCTCTGCCCCTGGTGGTCAT
ENSG00000166888:ENST0000045407 GGCAAACTCCCCATCCAGCTCCAGGCCCTGTCTCTGCCCCTGGTGGTCAT
ENSG00000166888:ENST0000053891 GGCAAACTCCCCATCCAGCTCCAGGCCCTGTCTCTGCCCCTGGTGGTCAT
ENSG00000166888:ENST0000053721 GGCAAACTCCCCATCCAGCTCCAGGCCCTGTCTCTGCCCCTGGTGGTCAT
ENSG00000166888:ENST0000053520 GGCAAACTCCCCATCCAGCTCCAGGCCCTGTCTCTGCCCCTGGTGGTCAT
isotig46679 TATGGCCTCACCATCGACTTGGAGACAAGCTCATTACCTGTGGTGATGAT
isotig12565 CAAGGCCTCAAGATTGACCTGGAGACCCATTCTTTGCCAGTTGTGGTGAT
isotig12566 CAAGGCCTCAAGATTGACCTGGAGACCCATTCTTTGCCAGTTGTGGTGAT
ENSG00000166888:ENST0000030013 CGTCCATGGCAACCAAGACAACAATGCCAAAGCCACTATCCTGTGGGACA
ENSG00000166888:ENST0000054387 CGTCCATGGCAACCAAGACAACAATGCCAAAGCCACTATCCTGTGGGACA
ENSG00000166888:ENST0000055615 CGTCCATGGCAACCAAGACAACAATGCCAAAGCCACTATCCTGTGGGACA
ENSG00000166888:ENST0000045407 CGTCCATGGCAACCAAGACAACAATGCCAAAGCCACTATCCTGTGGGACA
ENSG00000166888:ENST0000053891 CGTCCATGGCAACCAAGACAACAATGCCAAAGCCACTATCCTGTGGGACA
ENSG00000166888:ENST0000053721 CGTCCATGGCAACCAAGACAACAATGCCAAAGCCACTATCCTGTGGGACA
ENSG00000166888:ENST0000053520 CGTCCATGGCAACCAAGACAACAATGCCAAAGCCACTATCCTGTGGGACA
isotig46679 TTCTAATGTCAGCCAACTGCCTAATGCTTGGGCATCCATCATTTGGTACA
isotig12565 CTCCAACATCTGTCAGATGCCAAATGCCTGGGCATCCATCCTGTGGTATA
isotig12566 CTCCAACATCTGTCAGATGCCAAATGCCTGGGCATCCATCCTGTGGTATA
ENSG00000166888:ENST0000030013 ATGCCTTCTCTGAG------ATGGACCGCGTGCCCTTTGTGGTGGCTGAG
ENSG00000166888:ENST0000054387 ATGCCTTCTCTGAG------ATGGACCGCGTGCCCTTTGTGGTGGCTGAG
ENSG00000166888:ENST0000055615 ATGCCTTCTCTGAG------ATGGACCGCGTGCCCTTTGTGGTGGCTGAG
ENSG00000166888:ENST0000045407 ATGCCTTCTCTGAG------ATGGACCGCGTGCCCTTTGTGGTGGCTGAG
ENSG00000166888:ENST0000053891 ATGCCTTCTCTGAG------ATGGACCGCGTGCCCTTTGTGGTGGCTGAG
ENSG00000166888:ENST0000053721 ATGCCTTCTCTGAG------ATGGACCGCGTGCCCTTTGTGGTGGCTGAG
ENSG00000166888:ENST0000053520 ATGCCTTCTCTGAG------ATGGACCGCGTGCCCTTTGTGGTGGCTGAG
isotig46679 ATGTGTCAACCAACGATTGCCAGAACTTGGTTTTCTTTAATAATCCTCCG
isotig12565 ACATGCTGACCAACAACCCCAAGAACGTGAACTTCTTCACCAAGCCACCA
isotig12566 ACATGCTGACCAACAACCCCAAGAACGTGAACTTCTTCACCAAGCCACCA
ENSG00000166888:ENST0000030013 CGGGTGCCCTGGGAGAAGATGTGTGAAACTCTGAACCTGAAGTTCATGGC
ENSG00000166888:ENST0000054387 CGGGTGCCCTGGGAGAAGATGTGTGAAACTCTGAACCTGAAGTTCATGGC
ENSG00000166888:ENST0000055615 CGGGTGCCCTGGGAGAAGATGTGTGAAACTCTGAACCTGAAGTTCATGGC
ENSG00000166888:ENST0000045407 CGGGTGCCCTGGGAGAAGATGTGTGAAACTCTGAACCTGAAGTTCATGGC
ENSG00000166888:ENST0000053891 CGGGTGCCCTGGGAGAAGATGTGTGAAACTCTGAACCTGAAGTTCATGGC
ENSG00000166888:ENST0000053721 CGGGTGCCCTGGGAGAAGATGTGTGAAACTCTGAACCTGAAGTTCATGGC
ENSG00000166888:ENST0000053520 CGGGTGCCCTGGGAGAAGATGTGTGAAACTCTGAACCTGAAGTTCATGGC
isotig46679 CCTGTCACTTTGAGTCAACTCCTGGAAGTGATGAGCTGGCAGTTTTCATC
isotig12565 ATCGGAACCTGGGACCAGGTGGCCGAGGTGCTCAGCTGGCAGTTCTCATC
isotig12566 ATCGGAACCTGGGACCAGGTGGCCGAGGTGCTCAGCTGGCAGTTCTCATC
ENSG00000166888:ENST0000030013 TGAGGTGGGGACCAACCGGGGGCTGCTCCCAGAGCACTTCCTCTTCCTGG
ENSG00000166888:ENST0000054387 TGAGGTGGGGACCAACCGGGGGCTGCTCCCAGAGCACTTCCTCTTCCTGG
ENSG00000166888:ENST0000055615 TGAGGTGGGGACCAACCGGGGGCTGCTCCCAGAGCACTTCCTCTTCCTGG
ENSG00000166888:ENST0000045407 TGAGGTGGGGACCAACCGGGGGCTGCTCCCAGAGCACTTCCTCTTCCTGG
ENSG00000166888:ENST0000053891 TGAGGTGGGGACCAACCGGGGGCTGCTCCCAGAGCACTTCCTCTTCCTGG
ENSG00000166888:ENST0000053721 TGAGGTGGGGACCAACCGGGGGCTGCTCCCAGAGCACTTCCTCTTCCTGG
ENSG00000166888:ENST0000053520 TGAGGTGGGGACCAACCGGGGGCTGCTCCCAGAGCACTTCCTCTTCCTGG
isotig46679 CTATGTTGGT------CGTGGCCTTAATTCAGACCAGCTCAACATGCTGG
isotig12565 CACCACAAAG------CGAGGGCTGAGCATCGAGCAGCTGACTACGCTGG
isotig12566 CACCACAAAG------CGAGGGCTGAGCATCGAGCAGCTGACTACGCTGG
ENSG00000166888:ENST0000030013 CCCAGAAGATCTTCAATGACAACAGCCTCAGTATGGAGGCCTTCCAGCAC
ENSG00000166888:ENST0000054387 CCCAGAAGATCTTCAATGACAACAGCCTCAGTATGGAGGCCTTCCAGCAC
ENSG00000166888:ENST0000055615 CCCAGAAGATCTTCAATGACAACAGCCTCAGTATGGAGGCCTTCCAGCAC
ENSG00000166888:ENST0000045407 CCCAGAAGATCTTCAATGACAACAGCCTCAGTATGGAGGCCTTCCAGCAC
ENSG00000166888:ENST0000053891 CCCAGAAGATCTTCAATGACAACAGCCTCAGTATGGAGGCCTTCCAGCAC
ENSG00000166888:ENST0000053721 CCCAGAAGATCTTCAATGACAACAGCCTCAGTATGGAGGCCTTCCAGCAC
ENSG00000166888:ENST0000053520 CCCAGAAGATCTTCAATGACAACAGCCTCAGTATGGAGGCCTTCCAGCAC
isotig46679 CAGAGAAGCTCACAGTTCAGTCT---------------AACTACAGCGAT
isotig12565 CCGAGAAGCTCCTAGGACCTGGTGTC------------AACTACTCCGGG
isotig12566 CCGAGAAGCTCCTAGGACCTGGTGTC------------AACTACTCCGGG
ENSG00000166888:ENST0000030013 CGTTCTGTGTCCTGGTCGCAGTTCAACAAGGAGATCCTGCTGGGCCGTGG
ENSG00000166888:ENST0000054387 CGTTCTGTGTCCTGGTCGCAGTTCAACAAGGAGATCCTGCTGGGCCGTGG
ENSG00000166888:ENST0000055615 CGTTCTGTGTCCTGGTCGCAGTTCAACAAGGAGATCCTGCTGGGCCGTGG
ENSG00000166888:ENST0000045407 CGTTCTGTGTCCTGGTCGCAGTTCAACAAGGAGATCCTGCTGGGCCGTGG
ENSG00000166888:ENST0000053891 CGTTCTGTGTCCTGGTCGCAGTTCAACAAGGAGATCCTGCTGGGCCGTGG
ENSG00000166888:ENST0000053721 CGTTCTGTGTCCTGGTCGCAGTTCAACAAGGAGATCCTGCTGGGCCGTGG
ENSG00000166888:ENST0000053520 CGTTCTGTGTCCTGGTCGCAGTTCAACAAGGAGATCCTGCTGGGCCGTGG
isotig46679 GGTCACCTCACCTGGGCCAAGTTCTGCAAGGAACACTTGCCTGGCAAACC
isotig12565 TGTCAGATCACATGGGCTAAATTTTGCAAAGAAAACATGGCTGGCAAGGG
isotig12566 TGTCAGATCACATGGGCTAAATTTTGCAAAGAAAACATGGCTGGCAAGGG
ENSG00000166888:ENST0000030013 CTTCACCTTTTGGCAGTGGTTTGATGGTGTCCTGGACCTCACCAAACGCT
ENSG00000166888:ENST0000054387 CTTCACCTTTTGGCAGTGGTTTGATGGTGTCCTGGACCTCACCAAACGCT
ENSG00000166888:ENST0000055615 CTTCACCTTTTGGCAGTGGTTTGATGGTGTCCTGGACCTCACCAAACGCT
ENSG00000166888:ENST0000045407 CTTCACCTTTTGGCAGTGGTTTGATGGTGTCCTGGACCTCACCAAACGCT
ENSG00000166888:ENST0000053891 CTTCACCTTTTGGCAGTGGTTTGATGGTGTCCTGGACCTCACCAAACGCT
ENSG00000166888:ENST0000053721 CTTCACCTTTTGGCAGTGGTTTGATGGTGTCCTGGACCTCACCAAACGCT
ENSG00000166888:ENST0000053520 CTTCACCTTTTGGCAGTGGTTTGATGGTGTCCTGGACCTCACCAAACGCT
isotig46679 ATTTACCTTCTGGACCTGGCTTGAAGCAATATTGGACCTAATTAAAAAAC
isotig12565 CTTCTCCTTCTGGGTGTGGCTAGACAATATCATTGACCTTGTGAAAAAGT
isotig12566 CTTCTCCTTCTGGGTGTGGCTAGACAATATCATTGACCTTGTGAAAAAGT
ENSG00000166888:ENST0000030013 GTCTCCGGAGCTACTGGTCTGACCGGCTGATCATTGGCTTCATCAGCAAA
ENSG00000166888:ENST0000054387 GTCTCCGGAGCTACTGGTCTGACCGGCTGATCATTGGCTTCATCAGCAAA
ENSG00000166888:ENST0000055615 GTCTCCGGAGCTACTGGTCTGACCGGCTGATCATTGGCTTCATCAGCAAA
ENSG00000166888:ENST0000045407 GTCTCCGGAGCTACTGGTCTGACCGGCTGATCATTGGCTTCATCAGCAAA
ENSG00000166888:ENST0000053891 GTCTCCGGAGCTACTGGTCTGACCGGCTGATCATTGGCTTCATCAGCAAA
ENSG00000166888:ENST0000053721 GTCTCCGGAGCTACTGGTCTGACCGGCTGATCATTGGCTTCATCAGCAAA
ENSG00000166888:ENST0000053520 GTCTCCGGAGCTACTGGTCTGACCGGCTGATCATTGGCTTCATCAGCAAA
isotig46679 ACATTCTTCCCCTCTGGATTGATGGGTACATCATGGGCTTCGTGAGCAAA
isotig12565 ATATCTTGGCCCTCTGGAATGAAGGGTACATCATGGGCTTCATTAGCAAG
isotig12566 ATATCTTGGCCCTCTGGAATGAAGGGTACATCATGGGCTTCATTAGCAAG
ENSG00000166888:ENST0000030013 CAGTACGTTACTAGCCTTCTTCTCAATGAGCCCGACGGAACCTTTCTCCT
ENSG00000166888:ENST0000054387 CAGTACGTTACTAGCCTTCTTCTCAATGAGCCCGACGGAACCTTTCTCCT
ENSG00000166888:ENST0000055615 CAGTACGTTACTAGCCTTCTTCTCAATGAGCCCGACGGAACCTTTCTCCT
ENSG00000166888:ENST0000045407 CAGTACGTTACTAGCCTTCTTCTCAATGAGCCCGACGGAACCTTTCTCCT
ENSG00000166888:ENST0000053891 CAGTACGTTACTAGCCTTCTTCTCAATGAGCCCGACGGAACCTTTCTCCT
ENSG00000166888:ENST0000053721 CAGTACGTTACTAGCCTTCTTCTCAATGAGCCCGACGGAACCTTTCTCCT
ENSG00000166888:ENST0000053520 CAGTACGTTACTAGCCTTCTTCTCAATGAGCCCGACGGAACCTTTCTCCT
isotig46679 GAGAAGGAGAGGTTTCTGCTCAAGGATAAAATGCCCGGGACATTTTTGTT
isotig12565 GAGCGGGAGCGGGCGATCCTGAGCACGAAACCCCCGGGCACCTTCCTGCT
isotig12566 GAGCGGGAGCGGGCGATCCTGAGCACGAAACCCCCGGGCACCTTCCTGCT
ENSG00000166888:ENST0000030013 CCGCTTCAGCGAC---TCAGAGATTGGGGGCATCACCATTGCCCATGTCA
ENSG00000166888:ENST0000054387 CCGCTTCAGCGAC---TCAGAGATTGGGGGCATCACCATTGCCCATGTCA
ENSG00000166888:ENST0000055615 CCGCTTCAGCGAC---TCAGAGATTGGGGGCATCACCATTGCCCATGTCA
ENSG00000166888:ENST0000045407 CCGCTTCAGCGAC---TCAGAGATTGGGGGCATCACCATTGCCCATGTCA
ENSG00000166888:ENST0000053891 CCGCTTCAGCGAC---TCAGAGATTGGGGGCATCACCATTGCCCATGTCA
ENSG00000166888:ENST0000053721 CCGCTTCAGCGAC---TCAGAGATTGGGGGCATCACCATTGCCCATGTCA
ENSG00000166888:ENST0000053520 CCGCTTCAGCGAC---TCAGAGATTGGGGGCATCACCATTGCCCATGTCA
isotig46679 ACGATTCAGTGAG---AGCCATCTCGGAGGGATCACCTTCACCTGGGTGG
isotig12565 GAGATTCAGCGAGAGCAGCAAAGAAGGAGGGGTCACTTTCACTTGGGTGG
isotig12566 GAGATTCAGCGAGAGCAGCAAAGAAGGAGGGGTCACTTTCACTTGGGTGG
ENSG00000166888:ENST0000030013 TCCGGGGCCAGGATGGCTCTCCACAGATAGAGAACATCCAGCCATTCTCT
ENSG00000166888:ENST0000054387 TCCGGGGCCAGGATGGCTCTCCACAGATAGAGAACATCCAGCCATTCTCT
ENSG00000166888:ENST0000055615 TCCGGGGCCAGGATGGCTCTCCACAGATAGAGAACATCCAGCCATTCTCT
ENSG00000166888:ENST0000045407 TCCGGGGCCAGGATGGCTCTCCACAGATAGAGAACATCCAGCCATTCTCT
ENSG00000166888:ENST0000053891 TCCGGGGCCAGGATGGCTCTCCACAGATAGAGAACATCCAGCCATTCTCT
ENSG00000166888:ENST0000053721 TCCGGGGCCAGGATGGCTCTCCACAGATAGAGAACATCCAGCCATTCTCT
ENSG00000166888:ENST0000053520 TCCGGGGCCAGGATGGCTCTCCACAGATAGAGAACATCCAGCCATTCTCT
isotig46679 ACCACTCTGAAAACGGAGAAGTGAGATTCCACTCCGTAGAACCCTACAAC
isotig12565 AAAAGGACATCAGTGGCAAGACCCAGATCCAGTCTGTAGAGCCGTACACC
isotig12566 AAAAGGACATCAGTGGCAAGACCCAGATCCAGTCTGTAGAGCCGTACACC
ENSG00000166888:ENST0000030013 GCCAAAGACCTGTCCATTCGCTCACTGGGGGACCGAATCCGGGAT-----
ENSG00000166888:ENST0000054387 GCCAAAGACCTGTCCATTCGCTCACTGGGGGACCGAATCCGGGAT-----
ENSG00000166888:ENST0000055615 GCCAAAGACCTGTCCATTCGCTCACTGGGGGACCGAATCCGGGAT-----
ENSG00000166888:ENST0000045407 GCCAAAGACCTGTCCATTCGCTCACTGGGGGACCGAATCCGGGAT-----
ENSG00000166888:ENST0000053891 GCCAAAGACCTGTCCATTCGCTCACTGGGGGACCGAATCCGGGAT-----
ENSG00000166888:ENST0000053721 GCCAAAGACCTGTCCATTCGCTCACTGGGGGACCGAATCCGGGAT-----
ENSG00000166888:ENST0000053520 GCCAAAGACCTGTCCATTCGCTCACTGGGGGACCGAATCCGGGAT-----
isotig46679 AAAGGGCGTCTGTCGGCCCTGCCATTTGCTGACATCCTGCGGGACTACAA
isotig12565 AAGCAGCAGCTGAACAACATGTCCTTTGCTGAAATCATCATGGGCTACAA
isotig12566 AAGCAGCAGCTGAACAACATGTCCTTTGCTGAAATCATCATGGGCTACAA
ENSG00000166888:ENST0000030013 -------------------------CTTGCTCAGCTCAAAAATCTCTATC
ENSG00000166888:ENST0000054387 -------------------------CTTGCTCAGCTCAAAAATCTCTATC
ENSG00000166888:ENST0000055615 -------------------------CTTGCTCAGCTCAAAAATCTCTATC
ENSG00000166888:ENST0000045407 -------------------------CTTGCTCAGCTCAAAAATCTCTATC
ENSG00000166888:ENST0000053891 -------------------------CTTGCTCAGCTCAAAAATCTCTATC
ENSG00000166888:ENST0000053721 -------------------------CTTGCTCAGCTCAAAAATCTCTATC
ENSG00000166888:ENST0000053520 -------------------------CTTGCTCAGCTCAAAAATCTCTATC
isotig46679 GGTCATCATGGCTGAGAACATTCCCGAGAACCCTCTCAAGTACCTCTACC
isotig12565 GATCATGGATGCCACCAACATCCTGGTGTCCCCATTGGTCTACCTCTACC
isotig12566 GATCATGGATGCCACCAACATCCTGGTGTCCCCATTGGTCTACCTCTACC
ENSG00000166888:ENST0000030013 CCAAGAAGCCCAAGGATGAGGCTTTCCGGAGCCACTAC------------
ENSG00000166888:ENST0000054387 CCAAGAAGCCCAAGGATGAGGCTTTCCGGAGCCACTAC------------
ENSG00000166888:ENST0000055615 CCAAGAAGCCCAAGGATGAGGCTTTCCGGAGCCACTAC------------
ENSG00000166888:ENST0000045407 CCAAGAAGCCCAAGGATGAGGCTTTCCGGAGCCACTAC------------
ENSG00000166888:ENST0000053891 CCAAGAAGCCCAAGGATGAGGCTTTCCGGAGCCACTAC------------
ENSG00000166888:ENST0000053721 CCAAGAAGCCCAAGGATGAGGCTTTCCGGAGCCACTAC------------
ENSG00000166888:ENST0000053520 CCAAGAAGCCCAAGGATGAGGCTTTCCGGAGCCACTAC------------
isotig46679 CCGACATCCCCAAAGACAAAGCCTTCGGTAAACACTACAGCTCCCAGCCT
isotig12565 CTGACATTCCCAAGGAGGAGGCGTTCGGGAAGTACTGT------------
isotig12566 CTGACATTCCCAAGGAGGAGGCGTTCGGGAAGTACTGT------------
ENSG00000166888:ENST0000030013 ------------AAGCCTGAACAGATGGGTAAGGATGGCAGGGGTTATGT
ENSG00000166888:ENST0000054387 ------------AAGCCTGAACAGATGGGTAAGGATGGCAGGGGTTATGT
ENSG00000166888:ENST0000055615 ------------AAGCCTGAACAGATGGGTAAGGATGGCAGGGGTTATGT
ENSG00000166888:ENST0000045407 ------------AAGCCTGAACAGATGGGTAAGGATGGCAGGGGTTATGT
ENSG00000166888:ENST0000053891 ------------AAGCCTGAACAGATGGGTAAGGATGGCAGGGGTTATGT
ENSG00000166888:ENST0000053721 ------------AAGCCTGAACAGATGGGTAAGGATGGCAGGGGTTATGT
ENSG00000166888:ENST0000053520 ------------AAGCCTGAACAGATGGGTAAGGATGGCAGGGGTTATGT
isotig46679 TGCGAAGTTTCAAGGCCAACA------GAACGGGGAGACAAAGGTTATGT
isotig12565 ------------CGACCAGAG-----------------------------
isotig12566 ------------CGACCAGAG-----------------------------
ENSG00000166888:ENST0000030013 CCCAGCTACCATCAAGATGACCGTGGAAAGGGACCAACCACTTCCTACCC
ENSG00000166888:ENST0000054387 CCCAGCTACCATCAAGATGACCGTGGAAAGGGACCAACCACTTCCTACCC
ENSG00000166888:ENST0000055615 CCCAGCTACCATCAAGATGACCGTGGAAAGGGACCAACCACTTCCTACCC
ENSG00000166888:ENST0000045407 CCCAGCTACCATCAAGATGACCGTGGAAAGGGACCAACCACTTCCTACCC
ENSG00000166888:ENST0000053891 CCCAGCTACCATCAAGATGACCGTGGAAAGGGACCAACCACTTCCTACCC
ENSG00000166888:ENST0000053721 CCCAGCTACCATCAAGATGACCGTGGAAAGGGACCAACCACTTCCTACCC
ENSG00000166888:ENST0000053520 CCCAGCTACCATCAAGATGACCGTGGAAAGGGACCAACCACTTCCTACCC
isotig46679 TCCTTCAGTTTTTATCCCTATTTCAACAATCCGCAGCGACGCCATGGAGC
isotig12565 -------------------------------AGCCAGGAGCATCCTGAAG
isotig12566 -------------------------------AGCCAGGAGCATCCTGAAG
ENSG00000166888:ENST0000030013 CAGAGCTCCAGATGCCTACCATGGTGCCTTCTTATGACCTTGGAATGGCC
ENSG00000166888:ENST0000054387 CAGAGCTCCAGATGCCTACCATGGTGCCTTCTTATGACCTTGGAATGGCC
ENSG00000166888:ENST0000055615 CAGAGCTCCAGATGCCTACCATGGTGCCTTCTTATGACCTTGGAATGGCC
ENSG00000166888:ENST0000045407 CAGAGCTCCAGATGCCTACCATGGTGCCTTCTTATGACCTTGGAATGGCC
ENSG00000166888:ENST0000053891 CAGAGCTCCAGATGCCTACCATGGTGCCTTCTTATGACCTTGGAATGGCC
ENSG00000166888:ENST0000053721 CAGAGCTCCAGATGCCTACCATGGTGCCTTCTTATGACCTTGGAATGGCC
ENSG00000166888:ENST0000053520 CAGAGCTCCAGATGCCTACCATGGTGCCTTCTTATGACCTTGGAATGGCC
isotig46679 CGCAG------------------------------------------TCT
isotig12565 CTGAC---------------------------------------------
isotig12566 CTGAC---------------------------------------------
ENSG00000166888:ENST0000030013 CCTGATTCCTCCATGAGCATGCAGCTTGGCCCAGATATGGTGCCCCAGGT
ENSG00000166888:ENST0000054387 CCTGATTCCTCCATGAGCATGCAGCTTGGCCCAGATATGGTGCCCCAGGT
ENSG00000166888:ENST0000055615 CCTGATTCCTCCATGAGCATGCAGCTTGGCCCAGATATGGTGCCCCAGGT
ENSG00000166888:ENST0000045407 CCTGATTCCTCCATGAGCATGCAGCTTGGCCCAGATATGGTGCCCCAGGT
ENSG00000166888:ENST0000053891 CCTGATTCCTCCATGAGCATGCAGCTTGGCCCAGATATGGTGCCCCAGGT
ENSG00000166888:ENST0000053721 CCTGATTCCTCCATGAGCATGCAGCTTGGCCCAGATATGGTGCCCCAGGT
ENSG00000166888:ENST0000053520 CCTGATTCCTCCATGAGCATGCAGCTTGGCCCAGATATGGTGCCCCAGGT
isotig46679 CCTTCAGACCTTCTCCCC------------------ATGTCTCCGAGTGT
isotig12565 CCCGGTAGTGCCGCCCCT------------------TACCTGAAGACCAA
isotig12566 CCCGGTAGTTGTTTTTCCATG-----------------------------
ENSG00000166888:ENST0000030013 GTACCCACCACACTCTCACTCCATCCCCCCGTATCAAGGCCTCTCCCCAG
ENSG00000166888:ENST0000054387 GTACCCACCACACTCTCACTCCATCCCCCCGTATCAAGGCCTCTCCCCAG
ENSG00000166888:ENST0000055615 GTACCCACCACACTCTCACTCCATCCCCCCGTATCAAGGCCTCTCCCCAG
ENSG00000166888:ENST0000045407 GTACCCACCACACTCTCACTCCATCCCCCCGTATCAAGGCCTCTCCCCAG
ENSG00000166888:ENST0000053891 GTACCCACCACACTCTCACTCCATCCCCCCGTATCAAGGCCTCTCCCCAG
ENSG00000166888:ENST0000053721 GTACCCACCACACTCTCACTCCATCCCCCCGTATCAAGGCCTCTCCCCAG
ENSG00000166888:ENST0000053520 GTACCCACCACACTCTCACTCCATCCCCCCGTATCAAGGCCTCTCCCCAG
isotig46679 ATACGCTGTGCTGAGAGAAAACCTGAGCCCT-------------------
isotig12565 GTTCATCTGTGTGACACCAACGACCTGCAGC-------------------
isotig12566 --------------------------------------------------
ENSG00000166888:ENST0000030013 AAGAATCAGTCAACGTGTTGTCAGCCTTCCAGGAGCCTCACCTGCAGATG
ENSG00000166888:ENST0000054387 AAGAATCAGTCAACGTGTTGTCAGCCTTCCAGGAGCCTCACCTGCAGATG
ENSG00000166888:ENST0000055615 AAGAATCAGTCAACGTGTTGTCAGCCTTCCAGGAGCCTCACCTGCAGATG
ENSG00000166888:ENST0000045407 AAGAATCAGTCAACGTGTTGTCAGCCTTCCAGGAGCCTCACCTGCAGATG
ENSG00000166888:ENST0000053891 AAGAATCAGTCAACGTGTTGTCAGCCTTCCAGGAGCCTCACCTGCAGATG
ENSG00000166888:ENST0000053721 AAGAATCAGTCAACGTGTTGTCAGCCTTCCAGGAGCCTCACCTGCAGATG
ENSG00000166888:ENST0000053520 AAGAATCAGTCAACGTGTTGTCAGCCTTCCAGGAGCCTCACCTGCAGATG
isotig46679 --------------------------------------------------
isotig12565 --------------------------------------------------
isotig12566 --------------------------------------------------
ENSG00000166888:ENST0000030013 CCCCCCAGCCTGGGCCAGATGAGCCTGCCCTTTGACCAGCCTCACCCCCA
ENSG00000166888:ENST0000054387 CCCCCCAGCCTGGGCCAGATGAGCCTGCCCTTTGACCAGCCTCACCCCCA
ENSG00000166888:ENST0000055615 CCCCCCAGCCTGGGCCAGATGAGCCTGCCCTTTGACCAGCCTCACCCCCA
ENSG00000166888:ENST0000045407 CCCCCCAGCCTGGGCCAGATGAGCCTGCCCTTTGACCAGCCTCACCCCCA
ENSG00000166888:ENST0000053891 CCCCCCAGCCTGGGCCAGATGAGCCTGCCCTTTGACCAGCCTCACCCCCA
ENSG00000166888:ENST0000053721 CCCCCCAGCCTGGGCCAGATGAGCCTGCCCTTTGACCAGCCTCACCCCCA
ENSG00000166888:ENST0000053520 CCCCCCAGCCTGGGCCAGATGAGCCTGCCCTTTGACCAGCCTCACCCCCA
isotig46679 ------------ACCACAATTGAAACAGCAATGAAGTCTCCATATTCTGA
isotig12565 ------------AATACCATTGACCTGCCGATGTCCCCCCCGCAC-----
isotig12566 ------------GTTCTGGTTTCGCTGTTAGGGAAAGGGGGACAGTGCAG
ENSG00000166888:ENST0000030013 GGGCCTGCTGCCGTGCCAGCCTCAGGAGCATGCTGTGTCCAGCCCTGACC
ENSG00000166888:ENST0000054387 GGGCCTGCTGCCGTGCCAGCCTCAGGAGCATGCTGTGTCCAGCCCTGACC
ENSG00000166888:ENST0000055615 GGGCCTGCTGCCGTGCCAGCCTCAGGAGCATGCTGTGTCCAGCCCTGACC
ENSG00000166888:ENST0000045407 GGGCCTGCTGCCGTGCCAGCCTCAGGAGCATGCTGTGTCCAGCCCTGACC
ENSG00000166888:ENST0000053891 GGGCCTGCTGCCGTGCCAGCCTCAGGAGCATGCTGTGTCCAGCCCTGACC
ENSG00000166888:ENST0000053721 GGGCCTGCTGCCGTGCCAGCCTCAGGAGCATGCTGTGTCCAGCCCTGACC
ENSG00000166888:ENST0000053520 GGGCCTGCTGCCGTGCCAGCCTCAGGAGCATGCTGTGTCCAGCCCTGACC
isotig46679 GCGGTAC---------------------AAAGCGACTCTTCAAGGAAGAG
isotig12565 --------------------------------------------------
isotig12566 GTCCTTG---------------------------------------GAGG
ENSG00000166888:ENST0000030013 CCCTGCTCTGCTCAGATGTGACCATGGTGGAAGACAGCTGCCTGAGCCAG
ENSG00000166888:ENST0000054387 CCCTGCTCTGCTCAGATGTGACCATGGTGGAAGACAGCTGCCTGAGCCAG
ENSG00000166888:ENST0000055615 CCCTGCTCTGCTCAGATGTGACCATGGTGGAAGACAGCTGCCTGAGCCAG
ENSG00000166888:ENST0000045407 CCCTGCTCTGCTCAGATGTGACCATGGTGGAAGACAGCTGCCTGAGCCAG
ENSG00000166888:ENST0000053891 CCCTGCTCTGCTCAGATGTGACCATGGTGGAAGACAGCTGCCTGAGCCAG
ENSG00000166888:ENST0000053721 CCCTGCTCTGCTCAGATGTGACCATGGTGGAAGACAGCTGCCTGAGCCAG
ENSG00000166888:ENST0000053520 CCCTGCTCTGCTCAGATGTGACCATGGTGGAAGACAGCTGCCTGAGCCAG
isotig46679 AGCAGATGAAAACGGAGACTGCTCTTTGCCAAAGTCCACAATTCATTTCT
isotig12565 --------------------------------------------------
isotig12566 AGAGACAAGGACATGACCGGGTGTCTGGTGGTGAGTCCTGCTATGGAAGA
ENSG00000166888:ENST0000030013 CCAGTGACAGCGTTTCCTCAGGGCACTTGGATTGGTGAAGACATATTCCC
ENSG00000166888:ENST0000054387 CCAGTGACAGCGTTTCCTCAGGGCACTTGGATTGGTGAAGACATATTCCC
ENSG00000166888:ENST0000055615 CCAGTGACAGCGTTTCCTCAGGGCACTTGGATTGGTGAAGACATATTCCC
ENSG00000166888:ENST0000045407 CCAGTGACAGCGTTTCCTCAGGGCACTTGGATTGGTGAAGACATATTCCC
ENSG00000166888:ENST0000053891 CCAGTGACAGCGTTTCCTCAGGGCACTTGGATTGGTGAAGACATATTCCC
ENSG00000166888:ENST0000053721 CCAGTGACAGCGTTTCCTCAGGGCACTTGGATTGGTGAAGACATATTCCC
ENSG00000166888:ENST0000053520 CCAGTGACAGCGTTTCCTCAGGGCACTTGGATTGGTGAAGACATATTCCC
isotig46679 TCAGCTTTGATACTGGTTTCTAGAAAATGGCACAAATCCGAAGCTTTCCT
isotig12565 ------TTTAGATTCATTGATGCAGTTTGGAAACGGAGGTGCGCCCTC--
isotig12566 GCTGTTTAT------------------TGGGTACTTCAG-----------
ENSG00000166888:ENST0000030013 TCCTCTGCTGCCTCCCACTGAACAGGACCTCACTAAGCTTCTCCTGGAGG
ENSG00000166888:ENST0000054387 TCCTCTGCTGCCTCCCACTGAACAGGACCTCACTAAGCTTCTCCTGGAGG
ENSG00000166888:ENST0000055615 TCCTCTGCTGCCTCCCACTGAACAGGACCTCACTAAGCTTCTCCTGGAGG
ENSG00000166888:ENST0000045407 TCCTCTGCTGCCTCCCACTGAACAGGACCTCACTAAGCTTCTCCTGGAGG
ENSG00000166888:ENST0000053891 TCCTCTGCTGCCTCCCACTGAACAGGACCTCACTAAGCTTCTCCTGGAGG
ENSG00000166888:ENST0000053721 TCCTCTGCTGCCTCCCACTGAACAGGACCTCACTAAGCTTCTCCTGGAGG
ENSG00000166888:ENST0000053520 TCCTCTGCTGCCTCCCACTGAACAGGACCTCACTAAGCTTCTCCTGGAGG
isotig46679 CTCACTA------------------------------------------G
isotig12565 -------------------------------------------------G
isotig12566 -------------------------------------------------G
ENSG00000166888:ENST0000030013 GGCAAGGGGAGTCGGGGGGAGGGTCCTTGGGGGCACAGCCCCTCCTGCAG
ENSG00000166888:ENST0000054387 GGCAAGGGGAGTCGGGGGGAGGGTCCTTGGGGGCACAGCCCCTCCTGCAG
ENSG00000166888:ENST0000055615 GGCAAGGGGAGTCGGGGGGAGGGTCCTTGGGGGCACAGCCCCTCCTGCAG
ENSG00000166888:ENST0000045407 GGCAAGGGGAGTCGGGGGGAGGGTCCTTGGGGGCACAGCCCCTCCTGCAG
ENSG00000166888:ENST0000053891 GGCAAGGGGAGTCGGGGGGAGGGTCCTTGGGGGCACAGCCCCTCCTGCAG
ENSG00000166888:ENST0000053721 GGCAAGGGGAGTCGGGGGGAGGGTCCTTGGGGGCACAGCCCCTCCTGCAG
ENSG00000166888:ENST0000053520 GGCAAGGGGAGTCGGGGGGAGGGTCCTTGGGGGCACAGCCCCTCCTGCAG
isotig46679 GTGACATTCCCCAACTGGGAGTGCTGCTGAAATGCAAACCAAAGCTTCAG
isotig12565 GCAGGAGGGCAGTTGTCACTCACGTTCATGGATCTGAC------------
isotig12566 GTGACCGGGATTCAAGAGAAGACCAGAATCAGGCCTCA------------
ENSG00000166888:ENST0000030013 CCCTCCCACTATGGGCAATCTGGGATCTCAATGTCCCACATGGACCTAAG
ENSG00000166888:ENST0000054387 CCCTCCCACTATGGGCAATCTGGGATCTCAATGTCCCACATGGACCTAAG
ENSG00000166888:ENST0000055615 CCCTCCCACTATGGGCAATCTGGGATCTCAATGTCCCACATGGACCTAAG
ENSG00000166888:ENST0000045407 CCCTCCCACTATGGGCAATCTGGGATCTCAATGTCCCACATGGACCTAAG
ENSG00000166888:ENST0000053891 CCCTCCCACTATGGGCAATCTGGGATCTCAATGTCCCACATGGACCTAAG
ENSG00000166888:ENST0000053721 CCCTCCCACTATGGGCAATCTGGGATCTCAATGTCCCACATGGACCTAAG
ENSG00000166888:ENST0000053520 CCCTCCCACTATGGGCAATCTGGGATCTCAATGTCCCACATGGACCTAAG
isotig46679 ATAAACACGCAGGAAAAGACAGCTTCGAGAAACCTATGTTCGCAATATAA
isotig12565 ---------TTCGGAGTGCGCTACCTCCCCCATGTGAGGAGC--------
isotig12566 --------------------------------------------------
ENSG00000166888:ENST0000030013 GGCCAACCCCAGTTGG
ENSG00000166888:ENST0000054387 GGCCAACCCCAGTTGG
ENSG00000166888:ENST0000055615 GGCCAACCCCAGTTGG
ENSG00000166888:ENST0000045407 GGCCAACCCCAGTTGG
ENSG00000166888:ENST0000053891 GGCCAACCCCAGTTGG
ENSG00000166888:ENST0000053721 GGCCAACCCCAGTTGG
ENSG00000166888:ENST0000053520 GGCCAACCCCAGTTGG
isotig46679 CAGAAGGCTGCTTTGC
isotig12565 ----------------
isotig12566 ----------------
""",
)
def test4(self):
aligner = CodonAligner()
nucleotide_records = SeqIO.index("codonalign/nucl4.fa", "fasta")
protein_alignment = Align.read("codonalign/pro4.aln", "clustal")
self.assertEqual(len(protein_alignment.sequences), 10)
codon_alignments = []
protein_record = protein_alignment.sequences[0]
nucleotide_record = nucleotide_records[protein_record.id]
self.assertEqual(nucleotide_record.id, protein_record.id)
alignments = aligner.align(protein_record, nucleotide_record)
self.assertEqual(len(alignments), 1)
alignment = next(alignments)
codon_alignments.append(alignment)
self.assertTrue(
np.array_equal(alignment.coordinates, np.array([[0, 847], [0, 2541]]))
)
self.assertEqual(
str(alignment),
"""\
ENSG00000 0 M S L W G L V S K M P P E K V Q R L Y V
ENSG00000 0 ATGTCTCTGTGGGGTCTGGTCTCCAAGATGCCCCCAGAAAAAGTGCAGCGGCTCTATGTC
ENSG00000 20 D F P Q H L R H L L G D W L E S Q P W E
ENSG00000 60 GACTTTCCCCAACACCTGCGGCATCTTCTGGGTGACTGGCTGGAGAGCCAGCCCTGGGAG
ENSG00000 40 F L V G S D A F C C N L A S A L L S D T
ENSG00000 120 TTCCTGGTCGGCTCCGACGCCTTCTGCTGCAACTTGGCTAGTGCCCTACTTTCAGACACT
ENSG00000 60 V Q H L Q A S V G E Q G E G S T I L Q H
ENSG00000 180 GTCCAGCACCTTCAGGCCTCGGTGGGAGAGCAGGGGGAGGGGAGCACCATCTTGCAACAC
ENSG00000 80 I S T L E S I Y Q R D P L K L V A T F R
ENSG00000 240 ATCAGCACCCTTGAGAGCATATATCAGAGGGACCCCCTGAAGCTGGTGGCCACTTTCAGA
ENSG00000 100 Q I L Q G E K K A V M E Q F R H L P M P
ENSG00000 300 CAAATACTTCAAGGAGAGAAAAAAGCTGTTATGGAACAGTTCCGCCACTTGCCAATGCCT
ENSG00000 120 F H W K Q E E L K F K T G L R R L Q H R
ENSG00000 360 TTCCACTGGAAGCAGGAAGAACTCAAGTTTAAGACAGGCTTGCGGAGGCTGCAGCACCGA
ENSG00000 140 V G E I H L L R E A L Q K G A E A G Q V
ENSG00000 420 GTAGGGGAGATCCACCTTCTCCGAGAAGCCCTGCAGAAGGGGGCTGAGGCTGGCCAAGTG
ENSG00000 160 S L H S L I E T P A N G T G P S E A L A
ENSG00000 480 TCTCTGCACAGCTTGATAGAAACTCCTGCTAATGGGACTGGGCCAAGTGAGGCCCTGGCC
ENSG00000 180 M L L Q E T T G E L E A A K A L V L K R
ENSG00000 540 ATGCTACTGCAGGAGACCACTGGAGAGCTAGAGGCAGCCAAAGCCCTAGTGCTGAAGAGG
ENSG00000 200 I Q I W K R Q Q Q L A G N G A P F E E S
ENSG00000 600 ATCCAGATTTGGAAACGGCAGCAGCAGCTGGCAGGGAATGGCGCACCGTTTGAGGAGAGC
ENSG00000 220 L A P L Q E R C E S L V D I Y S Q L Q Q
ENSG00000 660 CTGGCCCCACTCCAGGAGAGGTGTGAAAGCCTGGTGGACATTTATTCCCAGCTACAGCAG
ENSG00000 240 E V G A A G G E L E P K T R A S L T G R
ENSG00000 720 GAGGTAGGGGCGGCTGGTGGGGAGCTTGAGCCCAAGACCCGGGCATCGCTGACTGGCCGG
ENSG00000 260 L D E V L R T L V T S C F L V E K Q P P
ENSG00000 780 CTGGATGAAGTCCTGAGAACCCTCGTCACCAGTTGCTTCCTGGTGGAGAAGCAGCCCCCC
ENSG00000 280 Q V L K T Q T K F Q A G V R F L L G L R
ENSG00000 840 CAGGTACTGAAGACTCAGACCAAGTTCCAGGCTGGAGTTCGATTCCTGTTGGGCTTGAGG
ENSG00000 300 F L G A P A K P P L V R A D M V T E K Q
ENSG00000 900 TTCCTGGGGGCCCCAGCCAAGCCTCCGCTGGTCAGGGCCGACATGGTGACAGAGAAGCAG
ENSG00000 320 A R E L S V P Q G P G A G A E S T G E I
ENSG00000 960 GCGCGGGAGCTGAGTGTGCCTCAGGGTCCTGGGGCTGGAGCAGAAAGCACTGGAGAAATC
ENSG00000 340 I N N T V P L E N S I P G N C C S A L F
ENSG00000 1020 ATCAACAACACTGTGCCCTTGGAGAACAGCATTCCTGGGAACTGCTGCTCTGCCCTGTTC
ENSG00000 360 K N L L L K K I K R C E R K G T E S V T
ENSG00000 1080 AAGAACCTGCTTCTCAAGAAGATCAAGCGGTGTGAGCGGAAGGGCACTGAGTCTGTCACA
ENSG00000 380 E E K C A V L F S A S F T L G P G K L P
ENSG00000 1140 GAGGAGAAGTGCGCTGTGCTCTTCTCTGCCAGCTTCACACTTGGCCCCGGCAAACTCCCC
ENSG00000 400 I Q L Q A L S L P L V V I V H G N Q D N
ENSG00000 1200 ATCCAGCTCCAGGCCCTGTCTCTGCCCCTGGTGGTCATCGTCCATGGCAACCAAGACAAC
ENSG00000 420 N A K A T I L W D N A F S E M D R V P F
ENSG00000 1260 AATGCCAAAGCCACTATCCTGTGGGACAATGCCTTCTCTGAGATGGACCGCGTGCCCTTT
ENSG00000 440 V V A E R V P W E K M C E T L N L K F M
ENSG00000 1320 GTGGTGGCTGAGCGGGTGCCCTGGGAGAAGATGTGTGAAACTCTGAACCTGAAGTTCATG
ENSG00000 460 A E V G T N R G L L P E H F L F L A Q K
ENSG00000 1380 GCTGAGGTGGGGACCAACCGGGGGCTGCTCCCAGAGCACTTCCTCTTCCTGGCCCAGAAG
ENSG00000 480 I F N D N S L S M E A F Q H R S V S W S
ENSG00000 1440 ATCTTCAATGACAACAGCCTCAGTATGGAGGCCTTCCAGCACCGTTCTGTGTCCTGGTCG
ENSG00000 500 Q F N K E I L L G R G F T F W Q W F D G
ENSG00000 1500 CAGTTCAACAAGGAGATCCTGCTGGGCCGTGGCTTCACCTTTTGGCAGTGGTTTGATGGT
ENSG00000 520 V L D L T K R C L R S Y W S D R L I I G
ENSG00000 1560 GTCCTGGACCTCACCAAACGCTGTCTCCGGAGCTACTGGTCTGACCGGCTGATCATTGGC
ENSG00000 540 F I S K Q Y V T S L L L N E P D G T F L
ENSG00000 1620 TTCATCAGCAAACAGTACGTTACTAGCCTTCTTCTCAATGAGCCCGACGGAACCTTTCTC
ENSG00000 560 L R F S D S E I G G I T I A H V I R G Q
ENSG00000 1680 CTCCGCTTCAGCGACTCAGAGATTGGGGGCATCACCATTGCCCATGTCATCCGGGGCCAG
ENSG00000 580 D G S P Q I E N I Q P F S A K D L S I R
ENSG00000 1740 GATGGCTCTCCACAGATAGAGAACATCCAGCCATTCTCTGCCAAAGACCTGTCCATTCGC
ENSG00000 600 S L G D R I R D L A Q L K N L Y P K K P
ENSG00000 1800 TCACTGGGGGACCGAATCCGGGATCTTGCTCAGCTCAAAAATCTCTATCCCAAGAAGCCC
ENSG00000 620 K D E A F R S H Y K P E Q M G K E G R G
ENSG00000 1860 AAGGATGAGGCTTTCCGGAGCCACTACAAGCCTGAACAGATGGGTAAGGATGGCAGGGGT
ENSG00000 640 Y V P A T I K M T V E R D Q P L P T P E
ENSG00000 1920 TATGTCCCAGCTACCATCAAGATGACCGTGGAAAGGGACCAACCACTTCCTACCCCAGAG
ENSG00000 660 L Q M P T M V P S Y D L G M A P D S S M
ENSG00000 1980 CTCCAGATGCCTACCATGGTGCCTTCTTATGACCTTGGAATGGCCCCTGATTCCTCCATG
ENSG00000 680 S M Q L G P D M V P Q V Y P P H S H S I
ENSG00000 2040 AGCATGCAGCTTGGCCCAGATATGGTGCCCCAGGTGTACCCACCACACTCTCACTCCATC
ENSG00000 700 P P Y Q G L S P E E S V N V L S A F Q E
ENSG00000 2100 CCCCCGTATCAAGGCCTCTCCCCAGAAGAATCAGTCAACGTGTTGTCAGCCTTCCAGGAG
ENSG00000 720 P H L Q M P P S L G Q M S L P F D Q P H
ENSG00000 2160 CCTCACCTGCAGATGCCCCCCAGCCTGGGCCAGATGAGCCTGCCCTTTGACCAGCCTCAC
ENSG00000 740 P Q G L L P C Q P Q E H A V S S P D P L
ENSG00000 2220 CCCCAGGGCCTGCTGCCGTGCCAGCCTCAGGAGCATGCTGTGTCCAGCCCTGACCCCCTG
ENSG00000 760 L C S D V T M V E D S C L S Q P V T A F
ENSG00000 2280 CTCTGCTCAGATGTGACCATGGTGGAAGACAGCTGCCTGAGCCAGCCAGTGACAGCGTTT
ENSG00000 780 P Q G T W I G E D I F P P L L P P T E Q
ENSG00000 2340 CCTCAGGGCACTTGGATTGGTGAAGACATATTCCCTCCTCTGCTGCCTCCCACTGAACAG
ENSG00000 800 D L T K L L L E G Q G E S G G G S L G A
ENSG00000 2400 GACCTCACTAAGCTTCTCCTGGAGGGGCAAGGGGAGTCGGGGGGAGGGTCCTTGGGGGCA
ENSG00000 820 Q P L L Q P S H Y G Q S G I S M S H M D
ENSG00000 2460 CAGCCCCTCCTGCAGCCCTCCCACTATGGGCAATCTGGGATCTCAATGTCCCACATGGAC
ENSG00000 840 L R A N P S W 847
ENSG00000 2520 CTAAGGGCCAACCCCAGTTGG 2541
""",
)
protein_record = protein_alignment.sequences[1]
nucleotide_record = nucleotide_records[protein_record.id]
self.assertEqual(nucleotide_record.id, protein_record.id)
alignments = aligner.align(protein_record, nucleotide_record)
self.assertEqual(len(alignments), 1)
alignment = next(alignments)
codon_alignments.append(alignment)
self.assertTrue(
np.array_equal(alignment.coordinates, np.array([[0, 847], [0, 2541]]))
)
self.assertEqual(
str(alignment),
"""\
ENSG00000 0 M S L W G L V S K M P P E K V Q R L Y V
ENSG00000 0 ATGTCTCTGTGGGGTCTGGTCTCCAAGATGCCCCCAGAAAAAGTGCAGCGGCTCTATGTC
ENSG00000 20 D F P Q H L R H L L G D W L E S Q P W E
ENSG00000 60 GACTTTCCCCAACACCTGCGGCATCTTCTGGGTGACTGGCTGGAGAGCCAGCCCTGGGAG
ENSG00000 40 F L V G S D A F C C N L A S A L L S D T
ENSG00000 120 TTCCTGGTCGGCTCCGACGCCTTCTGCTGCAACTTGGCTAGTGCCCTACTTTCAGACACT
ENSG00000 60 V Q H L Q A S V G E Q G E G S T I L Q H
ENSG00000 180 GTCCAGCACCTTCAGGCCTCGGTGGGAGAGCAGGGGGAGGGGAGCACCATCTTGCAACAC
ENSG00000 80 I S T L E S I Y Q R D P L K L V A T F R
ENSG00000 240 ATCAGCACCCTTGAGAGCATATATCAGAGGGACCCCCTGAAGCTGGTGGCCACTTTCAGA
ENSG00000 100 Q I L Q G E K K A V M E Q F R H L P M P
ENSG00000 300 CAAATACTTCAAGGAGAGAAAAAAGCTGTTATGGAACAGTTCCGCCACTTGCCAATGCCT
ENSG00000 120 F H W K Q E E L K F K T G L R R L Q H R
ENSG00000 360 TTCCACTGGAAGCAGGAAGAACTCAAGTTTAAGACAGGCTTGCGGAGGCTGCAGCACCGA
ENSG00000 140 V G E I H L L R E A L Q K G A E A G Q V
ENSG00000 420 GTAGGGGAGATCCACCTTCTCCGAGAAGCCCTGCAGAAGGGGGCTGAGGCTGGCCAAGTG
ENSG00000 160 S L H S L I E T P A N G T G P S E A L A
ENSG00000 480 TCTCTGCACAGCTTGATAGAAACTCCTGCTAATGGGACTGGGCCAAGTGAGGCCCTGGCC
ENSG00000 180 M L L Q E T T G E L E A A K A L V L K R
ENSG00000 540 ATGCTACTGCAGGAGACCACTGGAGAGCTAGAGGCAGCCAAAGCCCTAGTGCTGAAGAGG
ENSG00000 200 I Q I W K R Q Q Q L A G N G A P F E E S
ENSG00000 600 ATCCAGATTTGGAAACGGCAGCAGCAGCTGGCAGGGAATGGCGCACCGTTTGAGGAGAGC
ENSG00000 220 L A P L Q E R C E S L V D I Y S Q L Q Q
ENSG00000 660 CTGGCCCCACTCCAGGAGAGGTGTGAAAGCCTGGTGGACATTTATTCCCAGCTACAGCAG
ENSG00000 240 E V G A A G G E L E P K T R A S L T G R
ENSG00000 720 GAGGTAGGGGCGGCTGGTGGGGAGCTTGAGCCCAAGACCCGGGCATCGCTGACTGGCCGG
ENSG00000 260 L D E V L R T L V T S C F L V E K Q P P
ENSG00000 780 CTGGATGAAGTCCTGAGAACCCTCGTCACCAGTTGCTTCCTGGTGGAGAAGCAGCCCCCC
ENSG00000 280 Q V L K T Q T K F Q A G V R F L L G L R
ENSG00000 840 CAGGTACTGAAGACTCAGACCAAGTTCCAGGCTGGAGTTCGATTCCTGTTGGGCTTGAGG
ENSG00000 300 F L G A P A K P P L V R A D M V T E K Q
ENSG00000 900 TTCCTGGGGGCCCCAGCCAAGCCTCCGCTGGTCAGGGCCGACATGGTGACAGAGAAGCAG
ENSG00000 320 A R E L S V P Q G P G A G A E S T G E I
ENSG00000 960 GCGCGGGAGCTGAGTGTGCCTCAGGGTCCTGGGGCTGGAGCAGAAAGCACTGGAGAAATC
ENSG00000 340 I N N T V P L E N S I P G N C C S A L F
ENSG00000 1020 ATCAACAACACTGTGCCCTTGGAGAACAGCATTCCTGGGAACTGCTGCTCTGCCCTGTTC
ENSG00000 360 K N L L L K K I K R C E R K G T E S V T
ENSG00000 1080 AAGAACCTGCTTCTCAAGAAGATCAAGCGGTGTGAGCGGAAGGGCACTGAGTCTGTCACA
ENSG00000 380 E E K C A V L F S A S F T L G P G K L P
ENSG00000 1140 GAGGAGAAGTGCGCTGTGCTCTTCTCTGCCAGCTTCACACTTGGCCCCGGCAAACTCCCC
ENSG00000 400 I Q L Q A L S L P L V V I V H G N Q D N
ENSG00000 1200 ATCCAGCTCCAGGCCCTGTCTCTGCCCCTGGTGGTCATCGTCCATGGCAACCAAGACAAC
ENSG00000 420 N A K A T I L W D N A F S E M D R V P F
ENSG00000 1260 AATGCCAAAGCCACTATCCTGTGGGACAATGCCTTCTCTGAGATGGACCGCGTGCCCTTT
ENSG00000 440 V V A E R V P W E K M C E T L N L K F M
ENSG00000 1320 GTGGTGGCTGAGCGGGTGCCCTGGGAGAAGATGTGTGAAACTCTGAACCTGAAGTTCATG
ENSG00000 460 A E V G T N R G L L P E H F L F L A Q K
ENSG00000 1380 GCTGAGGTGGGGACCAACCGGGGGCTGCTCCCAGAGCACTTCCTCTTCCTGGCCCAGAAG
ENSG00000 480 I F N D N S L S M E A F Q H R S V S W S
ENSG00000 1440 ATCTTCAATGACAACAGCCTCAGTATGGAGGCCTTCCAGCACCGTTCTGTGTCCTGGTCG
ENSG00000 500 Q F N K E I L L G R G F T F W Q W F D G
ENSG00000 1500 CAGTTCAACAAGGAGATCCTGCTGGGCCGTGGCTTCACCTTTTGGCAGTGGTTTGATGGT
ENSG00000 520 V L D L T K R C L R S Y W S D R L I I G
ENSG00000 1560 GTCCTGGACCTCACCAAACGCTGTCTCCGGAGCTACTGGTCTGACCGGCTGATCATTGGC
ENSG00000 540 F I S K Q Y V T S L L L N E P D G T F L
ENSG00000 1620 TTCATCAGCAAACAGTACGTTACTAGCCTTCTTCTCAATGAGCCCGACGGAACCTTTCTC
ENSG00000 560 L R F S D S E I G G I T I A H V I R G Q
ENSG00000 1680 CTCCGCTTCAGCGACTCAGAGATTGGGGGCATCACCATTGCCCATGTCATCCGGGGCCAG
ENSG00000 580 D G S P Q I E N I Q P F S A K D L S I R
ENSG00000 1740 GATGGCTCTCCACAGATAGAGAACATCCAGCCATTCTCTGCCAAAGACCTGTCCATTCGC
ENSG00000 600 S L G D R I R D L A Q L K N L Y P K K P
ENSG00000 1800 TCACTGGGGGACCGAATCCGGGATCTTGCTCAGCTCAAAAATCTCTATCCCAAGAAGCCC
ENSG00000 620 K D E A F R S H Y K P E Q M G K D G R G
ENSG00000 1860 AAGGATGAGGCTTTCCGGAGCCACTACAAGCCTGAACAGATGGGTAAGGATGGCAGGGGT
ENSG00000 640 Y V P A T I K M T V E R D Q P L P T P E
ENSG00000 1920 TATGTCCCAGCTACCATCAAGATGACCGTGGAAAGGGACCAACCACTTCCTACCCCAGAG
ENSG00000 660 L Q M P T M V P S Y D L G M A P D S S M
ENSG00000 1980 CTCCAGATGCCTACCATGGTGCCTTCTTATGACCTTGGAATGGCCCCTGATTCCTCCATG
ENSG00000 680 S M Q L G P D M V P Q V Y P P H S H S I
ENSG00000 2040 AGCATGCAGCTTGGCCCAGATATGGTGCCCCAGGTGTACCCACCACACTCTCACTCCATC
ENSG00000 700 P P Y Q G L S P E E S V N V L S A F Q E
ENSG00000 2100 CCCCCGTATCAAGGCCTCTCCCCAGAAGAATCAGTCAACGTGTTGTCAGCCTTCCAGGAG
ENSG00000 720 P H L Q M P P S L G Q M S L P F D Q P H
ENSG00000 2160 CCTCACCTGCAGATGCCCCCCAGCCTGGGCCAGATGAGCCTGCCCTTTGACCAGCCTCAC
ENSG00000 740 P Q G L L P C Q P Q E H A V S S P D P L
ENSG00000 2220 CCCCAGGGCCTGCTGCCGTGCCAGCCTCAGGAGCATGCTGTGTCCAGCCCTGACCCCCTG
ENSG00000 760 L C S D V T M V E D S C L S Q P V T A F
ENSG00000 2280 CTCTGCTCAGATGTGACCATGGTGGAAGACAGCTGCCTGAGCCAGCCAGTGACAGCGTTT
ENSG00000 780 P Q G T W I G E D I F P P L L P P T E Q
ENSG00000 2340 CCTCAGGGCACTTGGATTGGTGAAGACATATTCCCTCCTCTGCTGCCTCCCACTGAACAG
ENSG00000 800 D L T K L L L E G Q G E S G G G S L G A
ENSG00000 2400 GACCTCACTAAGCTTCTCCTGGAGGGGCAAGGGGAGTCGGGGGGAGGGTCCTTGGGGGCA
ENSG00000 820 Q P L L Q P S H Y G Q S G I S M S H M D
ENSG00000 2460 CAGCCCCTCCTGCAGCCCTCCCACTATGGGCAATCTGGGATCTCAATGTCCCACATGGAC
ENSG00000 840 L R A N P S W 847
ENSG00000 2520 CTAAGGGCCAACCCCAGTTGG 2541
""",
)
protein_record = protein_alignment.sequences[2]
nucleotide_record = nucleotide_records[protein_record.id]
self.assertEqual(nucleotide_record.id, protein_record.id)
alignments = aligner.align(protein_record, nucleotide_record)
self.assertEqual(len(alignments), 1)
alignment = next(alignments)
codon_alignments.append(alignment)
self.assertTrue(
np.array_equal(alignment.coordinates, np.array([[0, 847], [0, 2541]]))
)
self.assertEqual(
str(alignment),
"""\
ENSG00000 0 M S L W G L V S K M P P E K V Q R L Y V
ENSG00000 0 ATGTCTCTGTGGGGTCTGGTCTCCAAGATGCCCCCAGAAAAAGTGCAGCGGCTCTATGTC
ENSG00000 20 D F P Q H L R H L L G D W L E S Q P W E
ENSG00000 60 GACTTTCCCCAACACCTGCGGCATCTTCTGGGTGACTGGCTGGAGAGCCAGCCCTGGGAG
ENSG00000 40 F L V G S D A F C C N L A S A L L S D T
ENSG00000 120 TTCCTGGTCGGCTCCGACGCCTTCTGCTGCAACTTGGCTAGTGCCCTACTTTCAGACACT
ENSG00000 60 V Q H L Q A S V G E Q G E G S T I L Q H
ENSG00000 180 GTCCAGCACCTTCAGGCCTCGGTGGGAGAGCAGGGGGAGGGGAGCACCATCTTGCAACAC
ENSG00000 80 I S T L E S I Y Q R D P L K L V A T F R
ENSG00000 240 ATCAGCACCCTTGAGAGCATATATCAGAGGGACCCCCTGAAGCTGGTGGCCACTTTCAGA
ENSG00000 100 Q I L Q G E K K A V M E Q F R H L P M P
ENSG00000 300 CAAATACTTCAAGGAGAGAAAAAAGCTGTTATGGAACAGTTCCGCCACTTGCCAATGCCT
ENSG00000 120 F H W K Q E E L K F K T G L R R L Q H R
ENSG00000 360 TTCCACTGGAAGCAGGAAGAACTCAAGTTTAAGACAGGCTTGCGGAGGCTGCAGCACCGA
ENSG00000 140 V G E I H L L R E A L Q K G A E A G Q V
ENSG00000 420 GTAGGGGAGATCCACCTTCTCCGAGAAGCCCTGCAGAAGGGGGCTGAGGCTGGCCAAGTG
ENSG00000 160 S L H S L I E T P A N G T G P S E A L A
ENSG00000 480 TCTCTGCACAGCTTGATAGAAACTCCTGCTAATGGGACTGGGCCAAGTGAGGCCCTGGCC
ENSG00000 180 M L L Q E T T G E L E A A K A L V L K R
ENSG00000 540 ATGCTACTGCAGGAGACCACTGGAGAGCTAGAGGCAGCCAAAGCCCTAGTGCTGAAGAGG
ENSG00000 200 I Q I W K R Q Q Q L A G N G A P F E E S
ENSG00000 600 ATCCAGATTTGGAAACGGCAGCAGCAGCTGGCAGGGAATGGCGCACCGTTTGAGGAGAGC
ENSG00000 220 L A P L Q E R C E S L V D I Y S Q L Q Q
ENSG00000 660 CTGGCCCCACTCCAGGAGAGGTGTGAAAGCCTGGTGGACATTTATTCCCAGCTACAGCAG
ENSG00000 240 E V G A A G G E L E P K T R A S L T G R
ENSG00000 720 GAGGTAGGGGCGGCTGGTGGGGAGCTTGAGCCCAAGACCCGGGCATCGCTGACTGGCCGG
ENSG00000 260 L D E V L R T L V T S C F L V E K Q P P
ENSG00000 780 CTGGATGAAGTCCTGAGAACCCTCGTCACCAGTTGCTTCCTGGTGGAGAAGCAGCCCCCC
ENSG00000 280 Q V L K T Q T K F Q A G V R F L L G L R
ENSG00000 840 CAGGTACTGAAGACTCAGACCAAGTTCCAGGCTGGAGTTCGATTCCTGTTGGGCTTGAGG
ENSG00000 300 F L G A P A K P P L V R A D M V T E K Q
ENSG00000 900 TTCCTGGGGGCCCCAGCCAAGCCTCCGCTGGTCAGGGCCGACATGGTGACAGAGAAGCAG
ENSG00000 320 A R E L S V P Q G P G A G A E S T G E I
ENSG00000 960 GCGCGGGAGCTGAGTGTGCCTCAGGGTCCTGGGGCTGGAGCAGAAAGCACTGGAGAAATC
ENSG00000 340 I N N T V P L E N S I P G N C C S A L F
ENSG00000 1020 ATCAACAACACTGTGCCCTTGGAGAACAGCATTCCTGGGAACTGCTGCTCTGCCCTGTTC
ENSG00000 360 K N L L L K K I K R C E R K G T E S V T
ENSG00000 1080 AAGAACCTGCTTCTCAAGAAGATCAAGCGGTGTGAGCGGAAGGGCACTGAGTCTGTCACA
ENSG00000 380 E E K C A V L F S A S F T L G P G K L P
ENSG00000 1140 GAGGAGAAGTGCGCTGTGCTCTTCTCTGCCAGCTTCACACTTGGCCCCGGCAAACTCCCC
ENSG00000 400 I Q L Q A L S L P L V V I V H G N Q D N
ENSG00000 1200 ATCCAGCTCCAGGCCCTGTCTCTGCCCCTGGTGGTCATCGTCCATGGCAACCAAGACAAC
ENSG00000 420 N A K A T I L W D N A F S E M D R V P F
ENSG00000 1260 AATGCCAAAGCCACTATCCTGTGGGACAATGCCTTCTCTGAGATGGACCGCGTGCCCTTT
ENSG00000 440 V V A E R V P W E K M C E T L N L K F M
ENSG00000 1320 GTGGTGGCTGAGCGGGTGCCCTGGGAGAAGATGTGTGAAACTCTGAACCTGAAGTTCATG
ENSG00000 460 A E V G T N R G L L P E H F L F L A Q K
ENSG00000 1380 GCTGAGGTGGGGACCAACCGGGGGCTGCTCCCAGAGCACTTCCTCTTCCTGGCCCAGAAG
ENSG00000 480 I F N D N S L S M E A F Q H R S V S W S
ENSG00000 1440 ATCTTCAATGACAACAGCCTCAGTATGGAGGCCTTCCAGCACCGTTCTGTGTCCTGGTCG
ENSG00000 500 Q F N K E I L L G R G F T F W Q W F D G
ENSG00000 1500 CAGTTCAACAAGGAGATCCTGCTGGGCCGTGGCTTCACCTTTTGGCAGTGGTTTGATGGT
ENSG00000 520 V L D L T K R C L R S Y W S D R L I I G
ENSG00000 1560 GTCCTGGACCTCACCAAACGCTGTCTCCGGAGCTACTGGTCTGACCGGCTGATCATTGGC
ENSG00000 540 F I S K Q Y V T S L L L N E P D G T F L
ENSG00000 1620 TTCATCAGCAAACAGTACGTTACTAGCCTTCTTCTCAATGAGCCCGACGGAACCTTTCTC
ENSG00000 560 L R F S D S E I G G I T I A H V I R G Q
ENSG00000 1680 CTCCGCTTCAGCGACTCAGAGATTGGGGGCATCACCATTGCCCATGTCATCCGGGGCCAG
ENSG00000 580 D G S P Q I E N I Q P F S A K D L S I R
ENSG00000 1740 GATGGCTCTCCACAGATAGAGAACATCCAGCCATTCTCTGCCAAAGACCTGTCCATTCGC
ENSG00000 600 S L G D R I R D L A Q L K N L Y P K K P
ENSG00000 1800 TCACTGGGGGACCGAATCCGGGATCTTGCTCAGCTCAAAAATCTCTATCCCAAGAAGCCC
ENSG00000 620 K D E A F R S H Y K P E Q M G K D G R G
ENSG00000 1860 AAGGATGAGGCTTTCCGGAGCCACTACAAGCCTGAACAGATGGGTAAGGATGGCAGGGGT
ENSG00000 640 Y V P A T I K M T V E R D Q P L P T P E
ENSG00000 1920 TATGTCCCAGCTACCATCAAGATGACCGTGGAAAGGGACCAACCACTTCCTACCCCAGAG
ENSG00000 660 L Q M P T M V P S Y D L G M A P D S S M
ENSG00000 1980 CTCCAGATGCCTACCATGGTGCCTTCTTATGACCTTGGAATGGCCCCTGATTCCTCCATG
ENSG00000 680 S M Q L G P D M V P Q V Y P P H S H S I
ENSG00000 2040 AGCATGCAGCTTGGCCCAGATATGGTGCCCCAGGTGTACCCACCACACTCTCACTCCATC
ENSG00000 700 P P Y Q G L S P E E S V N V L S A F Q E
ENSG00000 2100 CCCCCGTATCAAGGCCTCTCCCCAGAAGAATCAGTCAACGTGTTGTCAGCCTTCCAGGAG
ENSG00000 720 P H L Q M P P S L G Q M S L P F D Q P H
ENSG00000 2160 CCTCACCTGCAGATGCCCCCCAGCCTGGGCCAGATGAGCCTGCCCTTTGACCAGCCTCAC
ENSG00000 740 P Q G L L P C Q P Q E H A V S S P D P L
ENSG00000 2220 CCCCAGGGCCTGCTGCCGTGCCAGCCTCAGGAGCATGCTGTGTCCAGCCCTGACCCCCTG
ENSG00000 760 L C S D V T M V E D S C L S Q P V T A F
ENSG00000 2280 CTCTGCTCAGATGTGACCATGGTGGAAGACAGCTGCCTGAGCCAGCCAGTGACAGCGTTT
ENSG00000 780 P Q G T W I G E D I F P P L L P P T E Q
ENSG00000 2340 CCTCAGGGCACTTGGATTGGTGAAGACATATTCCCTCCTCTGCTGCCTCCCACTGAACAG
ENSG00000 800 D L T K L L L E G Q G E S G G G S L G A
ENSG00000 2400 GACCTCACTAAGCTTCTCCTGGAGGGGCAAGGGGAGTCGGGGGGAGGGTCCTTGGGGGCA
ENSG00000 820 Q P L L Q P S H Y G Q S G I S M S H M D
ENSG00000 2460 CAGCCCCTCCTGCAGCCCTCCCACTATGGGCAATCTGGGATCTCAATGTCCCACATGGAC
ENSG00000 840 L R A N P S W 847
ENSG00000 2520 CTAAGGGCCAACCCCAGTTGG 2541
""",
)
protein_record = protein_alignment.sequences[3]
nucleotide_record = nucleotide_records[protein_record.id]
self.assertEqual(nucleotide_record.id, protein_record.id)
alignments = aligner.align(protein_record, nucleotide_record)
self.assertEqual(len(alignments), 1)
alignment = next(alignments)
codon_alignments.append(alignment)
self.assertTrue(
np.array_equal(alignment.coordinates, np.array([[0, 847], [0, 2541]]))
)
self.assertEqual(
str(alignment),
"""\
ENSG00000 0 M S L W G L V S K M P P E K V Q R L Y V
ENSG00000 0 ATGTCTCTGTGGGGTCTGGTCTCCAAGATGCCCCCAGAAAAAGTGCAGCGGCTCTATGTC
ENSG00000 20 D F P Q H L R H L L G D W L E S Q P W E
ENSG00000 60 GACTTTCCCCAACACCTGCGGCATCTTCTGGGTGACTGGCTGGAGAGCCAGCCCTGGGAG
ENSG00000 40 F L V G S D A F C C N L A S A L L S D T
ENSG00000 120 TTCCTGGTCGGCTCCGACGCCTTCTGCTGCAACTTGGCTAGTGCCCTACTTTCAGACACT
ENSG00000 60 V Q H L Q A S V G E Q G E G S T I L Q H
ENSG00000 180 GTCCAGCACCTTCAGGCCTCGGTGGGAGAGCAGGGGGAGGGGAGCACCATCTTGCAACAC
ENSG00000 80 I S T L E S I Y Q R D P L K L V A T F R
ENSG00000 240 ATCAGCACCCTTGAGAGCATATATCAGAGGGACCCCCTGAAGCTGGTGGCCACTTTCAGA
ENSG00000 100 Q I L Q G E K K A V M E Q F R H L P M P
ENSG00000 300 CAAATACTTCAAGGAGAGAAAAAAGCTGTTATGGAACAGTTCCGCCACTTGCCAATGCCT
ENSG00000 120 F H W K Q E E L K F K T G L R R L Q H R
ENSG00000 360 TTCCACTGGAAGCAGGAAGAACTCAAGTTTAAGACAGGCTTGCGGAGGCTGCAGCACCGA
ENSG00000 140 V G E I H L L R E A L Q K G A E A G Q V
ENSG00000 420 GTAGGGGAGATCCACCTTCTCCGAGAAGCCCTGCAGAAGGGGGCTGAGGCTGGCCAAGTG
ENSG00000 160 S L H S L I E T P A N G T G P S E A L A
ENSG00000 480 TCTCTGCACAGCTTGATAGAAACTCCTGCTAATGGGACTGGGCCAAGTGAGGCCCTGGCC
ENSG00000 180 M L L Q E T T G E L E A A K A L V L K R
ENSG00000 540 ATGCTACTGCAGGAGACCACTGGAGAGCTAGAGGCAGCCAAAGCCCTAGTGCTGAAGAGG
ENSG00000 200 I Q I W K R Q Q Q L A G N G A P F E E S
ENSG00000 600 ATCCAGATTTGGAAACGGCAGCAGCAGCTGGCAGGGAATGGCGCACCGTTTGAGGAGAGC
ENSG00000 220 L A P L Q E R C E S L V D I Y S Q L Q Q
ENSG00000 660 CTGGCCCCACTCCAGGAGAGGTGTGAAAGCCTGGTGGACATTTATTCCCAGCTACAGCAG
ENSG00000 240 E V G A A G G E L E P K T R A S L T G R
ENSG00000 720 GAGGTAGGGGCGGCTGGTGGGGAGCTTGAGCCCAAGACCCGGGCATCGCTGACTGGCCGG
ENSG00000 260 L D E V L R T L V T S C F L V E K Q P P
ENSG00000 780 CTGGATGAAGTCCTGAGAACCCTCGTCACCAGTTGCTTCCTGGTGGAGAAGCAGCCCCCC
ENSG00000 280 Q V L K T Q T K F Q A G V R F L L G L R
ENSG00000 840 CAGGTACTGAAGACTCAGACCAAGTTCCAGGCTGGAGTTCGATTCCTGTTGGGCTTGAGG
ENSG00000 300 F L G A P A K P P L V R A D M V T E K Q
ENSG00000 900 TTCCTGGGGGCCCCAGCCAAGCCTCCGCTGGTCAGGGCCGACATGGTGACAGAGAAGCAG
ENSG00000 320 A R E L S V P Q G P G A G A E S T G E I
ENSG00000 960 GCGCGGGAGCTGAGTGTGCCTCAGGGTCCTGGGGCTGGAGCAGAAAGCACTGGAGAAATC
ENSG00000 340 I N N T V P L E N S I P G N C C S A L F
ENSG00000 1020 ATCAACAACACTGTGCCCTTGGAGAACAGCATTCCTGGGAACTGCTGCTCTGCCCTGTTC
ENSG00000 360 K N L L L K K I K R C E R K G T E S V T
ENSG00000 1080 AAGAACCTGCTTCTCAAGAAGATCAAGCGGTGTGAGCGGAAGGGCACTGAGTCTGTCACA
ENSG00000 380 E E K C A V L F S A S F T L G P G K L P
ENSG00000 1140 GAGGAGAAGTGCGCTGTGCTCTTCTCTGCCAGCTTCACACTTGGCCCCGGCAAACTCCCC
ENSG00000 400 I Q L Q A L S L P L V V I V H G N Q D N
ENSG00000 1200 ATCCAGCTCCAGGCCCTGTCTCTGCCCCTGGTGGTCATCGTCCATGGCAACCAAGACAAC
ENSG00000 420 N A K A T I L W D N A F S E M D R V P F
ENSG00000 1260 AATGCCAAAGCCACTATCCTGTGGGACAATGCCTTCTCTGAGATGGACCGCGTGCCCTTT
ENSG00000 440 V V A E R V P W E K M C E T L N L K F M
ENSG00000 1320 GTGGTGGCTGAGCGGGTGCCCTGGGAGAAGATGTGTGAAACTCTGAACCTGAAGTTCATG
ENSG00000 460 A E V G T N R G L L P E H F L F L A Q K
ENSG00000 1380 GCTGAGGTGGGGACCAACCGGGGGCTGCTCCCAGAGCACTTCCTCTTCCTGGCCCAGAAG
ENSG00000 480 I F N D N S L S M E A F Q H R S V S W S
ENSG00000 1440 ATCTTCAATGACAACAGCCTCAGTATGGAGGCCTTCCAGCACCGTTCTGTGTCCTGGTCG
ENSG00000 500 Q F N K E I L L G R G F T F W Q W F D G
ENSG00000 1500 CAGTTCAACAAGGAGATCCTGCTGGGCCGTGGCTTCACCTTTTGGCAGTGGTTTGATGGT
ENSG00000 520 V L D L T K R C L R S Y W S D R L I I G
ENSG00000 1560 GTCCTGGACCTCACCAAACGCTGTCTCCGGAGCTACTGGTCTGACCGGCTGATCATTGGC
ENSG00000 540 F I S K Q Y V T S L L L N E P D G T F L
ENSG00000 1620 TTCATCAGCAAACAGTACGTTACTAGCCTTCTTCTCAATGAGCCCGACGGAACCTTTCTC
ENSG00000 560 L R F S D S E I G G I T I A H V I R G Q
ENSG00000 1680 CTCCGCTTCAGCGACTCAGAGATTGGGGGCATCACCATTGCCCATGTCATCCGGGGCCAG
ENSG00000 580 D G S P Q I E N I Q P F S A K D L S I R
ENSG00000 1740 GATGGCTCTCCACAGATAGAGAACATCCAGCCATTCTCTGCCAAAGACCTGTCCATTCGC
ENSG00000 600 S L G D R I R D L A Q L K N L Y P K K P
ENSG00000 1800 TCACTGGGGGACCGAATCCGGGATCTTGCTCAGCTCAAAAATCTCTATCCCAAGAAGCCC
ENSG00000 620 K D E A F R S H Y K P E Q M G K D G R G
ENSG00000 1860 AAGGATGAGGCTTTCCGGAGCCACTACAAGCCTGAACAGATGGGTAAGGATGGCAGGGGT
ENSG00000 640 Y V P A T I K M T V E R D Q P L P T P E
ENSG00000 1920 TATGTCCCAGCTACCATCAAGATGACCGTGGAAAGGGACCAACCACTTCCTACCCCAGAG
ENSG00000 660 L Q M P T M V P S Y D L G M A P D S S M
ENSG00000 1980 CTCCAGATGCCTACCATGGTGCCTTCTTATGACCTTGGAATGGCCCCTGATTCCTCCATG
ENSG00000 680 S M Q L G P D M V P Q V Y P P H S H S I
ENSG00000 2040 AGCATGCAGCTTGGCCCAGATATGGTGCCCCAGGTGTACCCACCACACTCTCACTCCATC
ENSG00000 700 P P Y Q G L S P E E S V N V L S A F Q E
ENSG00000 2100 CCCCCGTATCAAGGCCTCTCCCCAGAAGAATCAGTCAACGTGTTGTCAGCCTTCCAGGAG
ENSG00000 720 P H L Q M P P S L G Q M S L P F D Q P H
ENSG00000 2160 CCTCACCTGCAGATGCCCCCCAGCCTGGGCCAGATGAGCCTGCCCTTTGACCAGCCTCAC
ENSG00000 740 P Q G L L P C Q P Q E H A V S S P D P L
ENSG00000 2220 CCCCAGGGCCTGCTGCCGTGCCAGCCTCAGGAGCATGCTGTGTCCAGCCCTGACCCCCTG
ENSG00000 760 L C S D V T M V E D S C L S Q P V T A F
ENSG00000 2280 CTCTGCTCAGATGTGACCATGGTGGAAGACAGCTGCCTGAGCCAGCCAGTGACAGCGTTT
ENSG00000 780 P Q G T W I G E D I F P P L L P P T E Q
ENSG00000 2340 CCTCAGGGCACTTGGATTGGTGAAGACATATTCCCTCCTCTGCTGCCTCCCACTGAACAG
ENSG00000 800 D L T K L L L E G Q G E S G G G S L G A
ENSG00000 2400 GACCTCACTAAGCTTCTCCTGGAGGGGCAAGGGGAGTCGGGGGGAGGGTCCTTGGGGGCA
ENSG00000 820 Q P L L Q P S H Y G Q S G I S M S H M D
ENSG00000 2460 CAGCCCCTCCTGCAGCCCTCCCACTATGGGCAATCTGGGATCTCAATGTCCCACATGGAC
ENSG00000 840 L R A N P S W 847
ENSG00000 2520 CTAAGGGCCAACCCCAGTTGG 2541
""",
)
protein_record = protein_alignment.sequences[4]
nucleotide_record = nucleotide_records[protein_record.id]
self.assertEqual(nucleotide_record.id, protein_record.id)
alignments = aligner.align(protein_record, nucleotide_record)
self.assertEqual(len(alignments), 1)
alignment = next(alignments)
codon_alignments.append(alignment)
self.assertTrue(
np.array_equal(alignment.coordinates, np.array([[0, 737], [0, 2211]]))
)
self.assertEqual(
str(alignment),
"""\
ENSG00000 0 M E Q F R H L P M P F H W K Q E E L K F
ENSG00000 0 ATGGAACAGTTCCGCCACTTGCCAATGCCTTTCCACTGGAAGCAGGAAGAACTCAAGTTT
ENSG00000 20 K T G L R R L Q H R V G E I H L L R E A
ENSG00000 60 AAGACAGGCTTGCGGAGGCTGCAGCACCGAGTAGGGGAGATCCACCTTCTCCGAGAAGCC
ENSG00000 40 L Q K G A E A G Q V S L H S L I E T P A
ENSG00000 120 CTGCAGAAGGGGGCTGAGGCTGGCCAAGTGTCTCTGCACAGCTTGATAGAAACTCCTGCT
ENSG00000 60 N G T G P S E A L A M L L Q E T T G E L
ENSG00000 180 AATGGGACTGGGCCAAGTGAGGCCCTGGCCATGCTACTGCAGGAGACCACTGGAGAGCTA
ENSG00000 80 E A A K A L V L K R I Q I W K R Q Q Q L
ENSG00000 240 GAGGCAGCCAAAGCCCTAGTGCTGAAGAGGATCCAGATTTGGAAACGGCAGCAGCAGCTG
ENSG00000 100 A G N G A P F E E S L A P L Q E R C E S
ENSG00000 300 GCAGGGAATGGCGCACCGTTTGAGGAGAGCCTGGCCCCACTCCAGGAGAGGTGTGAAAGC
ENSG00000 120 L V D I Y S Q L Q Q E V G A A G G E L E
ENSG00000 360 CTGGTGGACATTTATTCCCAGCTACAGCAGGAGGTAGGGGCGGCTGGTGGGGAGCTTGAG
ENSG00000 140 P K T R A S L T G R L D E V L R T L V T
ENSG00000 420 CCCAAGACCCGGGCATCGCTGACTGGCCGGCTGGATGAAGTCCTGAGAACCCTCGTCACC
ENSG00000 160 S C F L V E K Q P P Q V L K T Q T K F Q
ENSG00000 480 AGTTGCTTCCTGGTGGAGAAGCAGCCCCCCCAGGTACTGAAGACTCAGACCAAGTTCCAG
ENSG00000 180 A G V R F L L G L R F L G A P A K P P L
ENSG00000 540 GCTGGAGTTCGATTCCTGTTGGGCTTGAGGTTCCTGGGGGCCCCAGCCAAGCCTCCGCTG
ENSG00000 200 V R A D M V T E K Q A R E L S V P Q G P
ENSG00000 600 GTCAGGGCCGACATGGTGACAGAGAAGCAGGCGCGGGAGCTGAGTGTGCCTCAGGGTCCT
ENSG00000 220 G A G A E S T G E I I N N T V P L E N S
ENSG00000 660 GGGGCTGGAGCAGAAAGCACTGGAGAAATCATCAACAACACTGTGCCCTTGGAGAACAGC
ENSG00000 240 I P G N C C S A L F K N L L L K K I K R
ENSG00000 720 ATTCCTGGGAACTGCTGCTCTGCCCTGTTCAAGAACCTGCTTCTCAAGAAGATCAAGCGG
ENSG00000 260 C E R K G T E S V T E E K C A V L F S A
ENSG00000 780 TGTGAGCGGAAGGGCACTGAGTCTGTCACAGAGGAGAAGTGCGCTGTGCTCTTCTCTGCC
ENSG00000 280 S F T L G P G K L P I Q L Q A L S L P L
ENSG00000 840 AGCTTCACACTTGGCCCCGGCAAACTCCCCATCCAGCTCCAGGCCCTGTCTCTGCCCCTG
ENSG00000 300 V V I V H G N Q D N N A K A T I L W D N
ENSG00000 900 GTGGTCATCGTCCATGGCAACCAAGACAACAATGCCAAAGCCACTATCCTGTGGGACAAT
ENSG00000 320 A F S E M D R V P F V V A E R V P W E K
ENSG00000 960 GCCTTCTCTGAGATGGACCGCGTGCCCTTTGTGGTGGCTGAGCGGGTGCCCTGGGAGAAG
ENSG00000 340 M C E T L N L K F M A E V G T N R G L L
ENSG00000 1020 ATGTGTGAAACTCTGAACCTGAAGTTCATGGCTGAGGTGGGGACCAACCGGGGGCTGCTC
ENSG00000 360 P E H F L F L A Q K I F N D N S L S M E
ENSG00000 1080 CCAGAGCACTTCCTCTTCCTGGCCCAGAAGATCTTCAATGACAACAGCCTCAGTATGGAG
ENSG00000 380 A F Q H R S V S W S Q F N K E I L L G R
ENSG00000 1140 GCCTTCCAGCACCGTTCTGTGTCCTGGTCGCAGTTCAACAAGGAGATCCTGCTGGGCCGT
ENSG00000 400 G F T F W Q W F D G V L D L T K R C L R
ENSG00000 1200 GGCTTCACCTTTTGGCAGTGGTTTGATGGTGTCCTGGACCTCACCAAACGCTGTCTCCGG
ENSG00000 420 S Y W S D R L I I G F I S K Q Y V T S L
ENSG00000 1260 AGCTACTGGTCTGACCGGCTGATCATTGGCTTCATCAGCAAACAGTACGTTACTAGCCTT
ENSG00000 440 L L N E P D G T F L L R F S D S E I G G
ENSG00000 1320 CTTCTCAATGAGCCCGACGGAACCTTTCTCCTCCGCTTCAGCGACTCAGAGATTGGGGGC
ENSG00000 460 I T I A H V I R G Q D G S P Q I E N I Q
ENSG00000 1380 ATCACCATTGCCCATGTCATCCGGGGCCAGGATGGCTCTCCACAGATAGAGAACATCCAG
ENSG00000 480 P F S A K D L S I R S L G D R I R D L A
ENSG00000 1440 CCATTCTCTGCCAAAGACCTGTCCATTCGCTCACTGGGGGACCGAATCCGGGATCTTGCT
ENSG00000 500 Q L K N L Y P K K P K D E A F R S H Y K
ENSG00000 1500 CAGCTCAAAAATCTCTATCCCAAGAAGCCCAAGGATGAGGCTTTCCGGAGCCACTACAAG
ENSG00000 520 P E Q M G K D G R G Y V P A T I K M T V
ENSG00000 1560 CCTGAACAGATGGGTAAGGATGGCAGGGGTTATGTCCCAGCTACCATCAAGATGACCGTG
ENSG00000 540 E R D Q P L P T P E L Q M P T M V P S Y
ENSG00000 1620 GAAAGGGACCAACCACTTCCTACCCCAGAGCTCCAGATGCCTACCATGGTGCCTTCTTAT
ENSG00000 560 D L G M A P D S S M S M Q L G P D M V P
ENSG00000 1680 GACCTTGGAATGGCCCCTGATTCCTCCATGAGCATGCAGCTTGGCCCAGATATGGTGCCC
ENSG00000 580 Q V Y P P H S H S I P P Y Q G L S P E E
ENSG00000 1740 CAGGTGTACCCACCACACTCTCACTCCATCCCCCCGTATCAAGGCCTCTCCCCAGAAGAA
ENSG00000 600 S V N V L S A F Q E P H L Q M P P S L G
ENSG00000 1800 TCAGTCAACGTGTTGTCAGCCTTCCAGGAGCCTCACCTGCAGATGCCCCCCAGCCTGGGC
ENSG00000 620 Q M S L P F D Q P H P Q G L L P C Q P Q
ENSG00000 1860 CAGATGAGCCTGCCCTTTGACCAGCCTCACCCCCAGGGCCTGCTGCCGTGCCAGCCTCAG
ENSG00000 640 E H A V S S P D P L L C S D V T M V E D
ENSG00000 1920 GAGCATGCTGTGTCCAGCCCTGACCCCCTGCTCTGCTCAGATGTGACCATGGTGGAAGAC
ENSG00000 660 S C L S Q P V T A F P Q G T W I G E D I
ENSG00000 1980 AGCTGCCTGAGCCAGCCAGTGACAGCGTTTCCTCAGGGCACTTGGATTGGTGAAGACATA
ENSG00000 680 F P P L L P P T E Q D L T K L L L E G Q
ENSG00000 2040 TTCCCTCCTCTGCTGCCTCCCACTGAACAGGACCTCACTAAGCTTCTCCTGGAGGGGCAA
ENSG00000 700 G E S G G G S L G A Q P L L Q P S H Y G
ENSG00000 2100 GGGGAGTCGGGGGGAGGGTCCTTGGGGGCACAGCCCCTCCTGCAGCCCTCCCACTATGGG
ENSG00000 720 Q S G I S M S H M D L R A N P S W 737
ENSG00000 2160 CAATCTGGGATCTCAATGTCCCACATGGACCTAAGGGCCAACCCCAGTTGG 2211
""",
)
protein_record = protein_alignment.sequences[5]
nucleotide_record = nucleotide_records[protein_record.id]
self.assertEqual(nucleotide_record.id, protein_record.id)
alignments = aligner.align(protein_record, nucleotide_record)
self.assertEqual(len(alignments), 1)
alignment = next(alignments)
codon_alignments.append(alignment)
self.assertTrue(
np.array_equal(alignment.coordinates, np.array([[0, 737], [0, 2211]]))
)
self.assertEqual(
str(alignment),
"""\
ENSG00000 0 M E Q F R H L P M P F H W K Q E E L K F
ENSG00000 0 ATGGAACAGTTCCGCCACTTGCCAATGCCTTTCCACTGGAAGCAGGAAGAACTCAAGTTT
ENSG00000 20 K T G L R R L Q H R V G E I H L L R E A
ENSG00000 60 AAGACAGGCTTGCGGAGGCTGCAGCACCGAGTAGGGGAGATCCACCTTCTCCGAGAAGCC
ENSG00000 40 L Q K G A E A G Q V S L H S L I E T P A
ENSG00000 120 CTGCAGAAGGGGGCTGAGGCTGGCCAAGTGTCTCTGCACAGCTTGATAGAAACTCCTGCT
ENSG00000 60 N G T G P S E A L A M L L Q E T T G E L
ENSG00000 180 AATGGGACTGGGCCAAGTGAGGCCCTGGCCATGCTACTGCAGGAGACCACTGGAGAGCTA
ENSG00000 80 E A A K A L V L K R I Q I W K R Q Q Q L
ENSG00000 240 GAGGCAGCCAAAGCCCTAGTGCTGAAGAGGATCCAGATTTGGAAACGGCAGCAGCAGCTG
ENSG00000 100 A G N G A P F E E S L A P L Q E R C E S
ENSG00000 300 GCAGGGAATGGCGCACCGTTTGAGGAGAGCCTGGCCCCACTCCAGGAGAGGTGTGAAAGC
ENSG00000 120 L V D I Y S Q L Q Q E V G A A G G E L E
ENSG00000 360 CTGGTGGACATTTATTCCCAGCTACAGCAGGAGGTAGGGGCGGCTGGTGGGGAGCTTGAG
ENSG00000 140 P K T R A S L T G R L D E V L R T L V T
ENSG00000 420 CCCAAGACCCGGGCATCGCTGACTGGCCGGCTGGATGAAGTCCTGAGAACCCTCGTCACC
ENSG00000 160 S C F L V E K Q P P Q V L K T Q T K F Q
ENSG00000 480 AGTTGCTTCCTGGTGGAGAAGCAGCCCCCCCAGGTACTGAAGACTCAGACCAAGTTCCAG
ENSG00000 180 A G V R F L L G L R F L G A P A K P P L
ENSG00000 540 GCTGGAGTTCGATTCCTGTTGGGCTTGAGGTTCCTGGGGGCCCCAGCCAAGCCTCCGCTG
ENSG00000 200 V R A D M V T E K Q A R E L S V P Q G P
ENSG00000 600 GTCAGGGCCGACATGGTGACAGAGAAGCAGGCGCGGGAGCTGAGTGTGCCTCAGGGTCCT
ENSG00000 220 G A G A E S T G E I I N N T V P L E N S
ENSG00000 660 GGGGCTGGAGCAGAAAGCACTGGAGAAATCATCAACAACACTGTGCCCTTGGAGAACAGC
ENSG00000 240 I P G N C C S A L F K N L L L K K I K R
ENSG00000 720 ATTCCTGGGAACTGCTGCTCTGCCCTGTTCAAGAACCTGCTTCTCAAGAAGATCAAGCGG
ENSG00000 260 C E R K G T E S V T E E K C A V L F S A
ENSG00000 780 TGTGAGCGGAAGGGCACTGAGTCTGTCACAGAGGAGAAGTGCGCTGTGCTCTTCTCTGCC
ENSG00000 280 S F T L G P G K L P I Q L Q A L S L P L
ENSG00000 840 AGCTTCACACTTGGCCCCGGCAAACTCCCCATCCAGCTCCAGGCCCTGTCTCTGCCCCTG
ENSG00000 300 V V I V H G N Q D N N A K A T I L W D N
ENSG00000 900 GTGGTCATCGTCCATGGCAACCAAGACAACAATGCCAAAGCCACTATCCTGTGGGACAAT
ENSG00000 320 A F S E M D R V P F V V A E R V P W E K
ENSG00000 960 GCCTTCTCTGAGATGGACCGCGTGCCCTTTGTGGTGGCTGAGCGGGTGCCCTGGGAGAAG
ENSG00000 340 M C E T L N L K F M A E V G T N R G L L
ENSG00000 1020 ATGTGTGAAACTCTGAACCTGAAGTTCATGGCTGAGGTGGGGACCAACCGGGGGCTGCTC
ENSG00000 360 P E H F L F L A Q K I F N D N S L S M E
ENSG00000 1080 CCAGAGCACTTCCTCTTCCTGGCCCAGAAGATCTTCAATGACAACAGCCTCAGTATGGAG
ENSG00000 380 A F Q H R S V S W S Q F N K E I L L G R
ENSG00000 1140 GCCTTCCAGCACCGTTCTGTGTCCTGGTCGCAGTTCAACAAGGAGATCCTGCTGGGCCGT
ENSG00000 400 G F T F W Q W F D G V L D L T K R C L R
ENSG00000 1200 GGCTTCACCTTTTGGCAGTGGTTTGATGGTGTCCTGGACCTCACCAAACGCTGTCTCCGG
ENSG00000 420 S Y W S D R L I I G F I S K Q Y V T S L
ENSG00000 1260 AGCTACTGGTCTGACCGGCTGATCATTGGCTTCATCAGCAAACAGTACGTTACTAGCCTT
ENSG00000 440 L L N E P D G T F L L R F S D S E I G G
ENSG00000 1320 CTTCTCAATGAGCCCGACGGAACCTTTCTCCTCCGCTTCAGCGACTCAGAGATTGGGGGC
ENSG00000 460 I T I A H V I R G Q D G S P Q I E N I Q
ENSG00000 1380 ATCACCATTGCCCATGTCATCCGGGGCCAGGATGGCTCTCCACAGATAGAGAACATCCAG
ENSG00000 480 P F S A K D L S I R S L G D R I R D L A
ENSG00000 1440 CCATTCTCTGCCAAAGACCTGTCCATTCGCTCACTGGGGGACCGAATCCGGGATCTTGCT
ENSG00000 500 Q L K N L Y P K K P K D E A F R S H Y K
ENSG00000 1500 CAGCTCAAAAATCTCTATCCCAAGAAGCCCAAGGATGAGGCTTTCCGGAGCCACTACAAG
ENSG00000 520 P E Q M G K D G R G Y V P A T I K M T V
ENSG00000 1560 CCTGAACAGATGGGTAAGGATGGCAGGGGTTATGTCCCAGCTACCATCAAGATGACCGTG
ENSG00000 540 E R D Q P L P T P E L Q M P T M V P S Y
ENSG00000 1620 GAAAGGGACCAACCACTTCCTACCCCAGAGCTCCAGATGCCTACCATGGTGCCTTCTTAT
ENSG00000 560 D L G M A P D S S M S M Q L G P D M V P
ENSG00000 1680 GACCTTGGAATGGCCCCTGATTCCTCCATGAGCATGCAGCTTGGCCCAGATATGGTGCCC
ENSG00000 580 Q V Y P P H S H S I P P Y Q G L S P E E
ENSG00000 1740 CAGGTGTACCCACCACACTCTCACTCCATCCCCCCGTATCAAGGCCTCTCCCCAGAAGAA
ENSG00000 600 S V N V L S A F Q E P H L Q M P P S L G
ENSG00000 1800 TCAGTCAACGTGTTGTCAGCCTTCCAGGAGCCTCACCTGCAGATGCCCCCCAGCCTGGGC
ENSG00000 620 Q M S L P F D Q P H P Q G L L P C Q P Q
ENSG00000 1860 CAGATGAGCCTGCCCTTTGACCAGCCTCACCCCCAGGGCCTGCTGCCGTGCCAGCCTCAG
ENSG00000 640 E H A V S S P D P L L C S D V T M V E D
ENSG00000 1920 GAGCATGCTGTGTCCAGCCCTGACCCCCTGCTCTGCTCAGATGTGACCATGGTGGAAGAC
ENSG00000 660 S C L S Q P V T A F P Q G T W I G E D I
ENSG00000 1980 AGCTGCCTGAGCCAGCCAGTGACAGCGTTTCCTCAGGGCACTTGGATTGGTGAAGACATA
ENSG00000 680 F P P L L P P T E Q D L T K L L L E G Q
ENSG00000 2040 TTCCCTCCTCTGCTGCCTCCCACTGAACAGGACCTCACTAAGCTTCTCCTGGAGGGGCAA
ENSG00000 700 G E S G G G S L G A Q P L L Q P S H Y G
ENSG00000 2100 GGGGAGTCGGGGGGAGGGTCCTTGGGGGCACAGCCCCTCCTGCAGCCCTCCCACTATGGG
ENSG00000 720 Q S G I S M S H M D L R A N P S W 737
ENSG00000 2160 CAATCTGGGATCTCAATGTCCCACATGGACCTAAGGGCCAACCCCAGTTGG 2211
""",
)
protein_record = protein_alignment.sequences[6]
nucleotide_record = nucleotide_records[protein_record.id]
self.assertEqual(nucleotide_record.id, protein_record.id)
alignments = aligner.align(protein_record, nucleotide_record)
self.assertEqual(len(alignments), 1)
alignment = next(alignments)
codon_alignments.append(alignment)
self.assertTrue(
np.array_equal(alignment.coordinates, np.array([[0, 737], [0, 2211]]))
)
self.assertEqual(
str(alignment),
"""\
ENSG00000 0 M E Q F R H L P M P F H W K Q E E L K F
ENSG00000 0 ATGGAACAGTTCCGCCACTTGCCAATGCCTTTCCACTGGAAGCAGGAAGAACTCAAGTTT
ENSG00000 20 K T G L R R L Q H R V G E I H L L R E A
ENSG00000 60 AAGACAGGCTTGCGGAGGCTGCAGCACCGAGTAGGGGAGATCCACCTTCTCCGAGAAGCC
ENSG00000 40 L Q K G A E A G Q V S L H S L I E T P A
ENSG00000 120 CTGCAGAAGGGGGCTGAGGCTGGCCAAGTGTCTCTGCACAGCTTGATAGAAACTCCTGCT
ENSG00000 60 N G T G P S E A L A M L L Q E T T G E L
ENSG00000 180 AATGGGACTGGGCCAAGTGAGGCCCTGGCCATGCTACTGCAGGAGACCACTGGAGAGCTA
ENSG00000 80 E A A K A L V L K R I Q I W K R Q Q Q L
ENSG00000 240 GAGGCAGCCAAAGCCCTAGTGCTGAAGAGGATCCAGATTTGGAAACGGCAGCAGCAGCTG
ENSG00000 100 A G N G A P F E E S L A P L Q E R C E S
ENSG00000 300 GCAGGGAATGGCGCACCGTTTGAGGAGAGCCTGGCCCCACTCCAGGAGAGGTGTGAAAGC
ENSG00000 120 L V D I Y S Q L Q Q E V G A A G G E L E
ENSG00000 360 CTGGTGGACATTTATTCCCAGCTACAGCAGGAGGTAGGGGCGGCTGGTGGGGAGCTTGAG
ENSG00000 140 P K T R A S L T G R L D E V L R T L V T
ENSG00000 420 CCCAAGACCCGGGCATCGCTGACTGGCCGGCTGGATGAAGTCCTGAGAACCCTCGTCACC
ENSG00000 160 S C F L V E K Q P P Q V L K T Q T K F Q
ENSG00000 480 AGTTGCTTCCTGGTGGAGAAGCAGCCCCCCCAGGTACTGAAGACTCAGACCAAGTTCCAG
ENSG00000 180 A G V R F L L G L R F L G A P A K P P L
ENSG00000 540 GCTGGAGTTCGATTCCTGTTGGGCTTGAGGTTCCTGGGGGCCCCAGCCAAGCCTCCGCTG
ENSG00000 200 V R A D M V T E K Q A R E L S V P Q G P
ENSG00000 600 GTCAGGGCCGACATGGTGACAGAGAAGCAGGCGCGGGAGCTGAGTGTGCCTCAGGGTCCT
ENSG00000 220 G A G A E S T G E I I N N T V P L E N S
ENSG00000 660 GGGGCTGGAGCAGAAAGCACTGGAGAAATCATCAACAACACTGTGCCCTTGGAGAACAGC
ENSG00000 240 I P G N C C S A L F K N L L L K K I K R
ENSG00000 720 ATTCCTGGGAACTGCTGCTCTGCCCTGTTCAAGAACCTGCTTCTCAAGAAGATCAAGCGG
ENSG00000 260 C E R K G T E S V T E E K C A V L F S A
ENSG00000 780 TGTGAGCGGAAGGGCACTGAGTCTGTCACAGAGGAGAAGTGCGCTGTGCTCTTCTCTGCC
ENSG00000 280 S F T L G P G K L P I Q L Q A L S L P L
ENSG00000 840 AGCTTCACACTTGGCCCCGGCAAACTCCCCATCCAGCTCCAGGCCCTGTCTCTGCCCCTG
ENSG00000 300 V V I V H G N Q D N N A K A T I L W D N
ENSG00000 900 GTGGTCATCGTCCATGGCAACCAAGACAACAATGCCAAAGCCACTATCCTGTGGGACAAT
ENSG00000 320 A F S E M D R V P F V V A E R V P W E K
ENSG00000 960 GCCTTCTCTGAGATGGACCGCGTGCCCTTTGTGGTGGCTGAGCGGGTGCCCTGGGAGAAG
ENSG00000 340 M C E T L N L K F M A E V G T N R G L L
ENSG00000 1020 ATGTGTGAAACTCTGAACCTGAAGTTCATGGCTGAGGTGGGGACCAACCGGGGGCTGCTC
ENSG00000 360 P E H F L F L A Q K I F N D N S L S M E
ENSG00000 1080 CCAGAGCACTTCCTCTTCCTGGCCCAGAAGATCTTCAATGACAACAGCCTCAGTATGGAG
ENSG00000 380 A F Q H R S V S W S Q F N K E I L L G R
ENSG00000 1140 GCCTTCCAGCACCGTTCTGTGTCCTGGTCGCAGTTCAACAAGGAGATCCTGCTGGGCCGT
ENSG00000 400 G F T F W Q W F D G V L D L T K R C L R
ENSG00000 1200 GGCTTCACCTTTTGGCAGTGGTTTGATGGTGTCCTGGACCTCACCAAACGCTGTCTCCGG
ENSG00000 420 S Y W S D R L I I G F I S K Q Y V T S L
ENSG00000 1260 AGCTACTGGTCTGACCGGCTGATCATTGGCTTCATCAGCAAACAGTACGTTACTAGCCTT
ENSG00000 440 L L N E P D G T F L L R F S D S E I G G
ENSG00000 1320 CTTCTCAATGAGCCCGACGGAACCTTTCTCCTCCGCTTCAGCGACTCAGAGATTGGGGGC
ENSG00000 460 I T I A H V I R G Q D G S P Q I E N I Q
ENSG00000 1380 ATCACCATTGCCCATGTCATCCGGGGCCAGGATGGCTCTCCACAGATAGAGAACATCCAG
ENSG00000 480 P F S A K D L S I R S L G D R I R D L A
ENSG00000 1440 CCATTCTCTGCCAAAGACCTGTCCATTCGCTCACTGGGGGACCGAATCCGGGATCTTGCT
ENSG00000 500 Q L K N L Y P K K P K D E A F R S H Y K
ENSG00000 1500 CAGCTCAAAAATCTCTATCCCAAGAAGCCCAAGGATGAGGCTTTCCGGAGCCACTACAAG
ENSG00000 520 P E Q M G K D G R G Y V P A T I K M T V
ENSG00000 1560 CCTGAACAGATGGGTAAGGATGGCAGGGGTTATGTCCCAGCTACCATCAAGATGACCGTG
ENSG00000 540 E R D Q P L P T P E L Q M P T M V P S Y
ENSG00000 1620 GAAAGGGACCAACCACTTCCTACCCCAGAGCTCCAGATGCCTACCATGGTGCCTTCTTAT
ENSG00000 560 D L G M A P D S S M S M Q L G P D M V P
ENSG00000 1680 GACCTTGGAATGGCCCCTGATTCCTCCATGAGCATGCAGCTTGGCCCAGATATGGTGCCC
ENSG00000 580 Q V Y P P H S H S I P P Y Q G L S P E E
ENSG00000 1740 CAGGTGTACCCACCACACTCTCACTCCATCCCCCCGTATCAAGGCCTCTCCCCAGAAGAA
ENSG00000 600 S V N V L S A F Q E P H L Q M P P S L G
ENSG00000 1800 TCAGTCAACGTGTTGTCAGCCTTCCAGGAGCCTCACCTGCAGATGCCCCCCAGCCTGGGC
ENSG00000 620 Q M S L P F D Q P H P Q G L L P C Q P Q
ENSG00000 1860 CAGATGAGCCTGCCCTTTGACCAGCCTCACCCCCAGGGCCTGCTGCCGTGCCAGCCTCAG
ENSG00000 640 E H A V S S P D P L L C S D V T M V E D
ENSG00000 1920 GAGCATGCTGTGTCCAGCCCTGACCCCCTGCTCTGCTCAGATGTGACCATGGTGGAAGAC
ENSG00000 660 S C L S Q P V T A F P Q G T W I G E D I
ENSG00000 1980 AGCTGCCTGAGCCAGCCAGTGACAGCGTTTCCTCAGGGCACTTGGATTGGTGAAGACATA
ENSG00000 680 F P P L L P P T E Q D L T K L L L E G Q
ENSG00000 2040 TTCCCTCCTCTGCTGCCTCCCACTGAACAGGACCTCACTAAGCTTCTCCTGGAGGGGCAA
ENSG00000 700 G E S G G G S L G A Q P L L Q P S H Y G
ENSG00000 2100 GGGGAGTCGGGGGGAGGGTCCTTGGGGGCACAGCCCCTCCTGCAGCCCTCCCACTATGGG
ENSG00000 720 Q S G I S M S H M D L R A N P S W 737
ENSG00000 2160 CAATCTGGGATCTCAATGTCCCACATGGACCTAAGGGCCAACCCCAGTTGG 2211
""",
)
protein_record = protein_alignment.sequences[7]
nucleotide_record = nucleotide_records[protein_record.id]
self.assertEqual(nucleotide_record.id, protein_record.id)
nucleotide_record = nucleotide_record.upper()
alignments = aligner.align(protein_record, nucleotide_record)
self.assertEqual(len(alignments), 1)
alignment = next(alignments)
codon_alignments.append(alignment)
self.assertTrue(
np.array_equal(alignment.coordinates, np.array([[0, 1021], [0, 3063]]))
)
self.assertEqual(
str(alignment),
"""\
isotig466 0 E V T Q S R R K P V R E G R P W E P S Q
isotig466 0 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
isotig466 20 E L A Q T P E G G C P R Q E S R P E G G
isotig466 60 GAGTTGGCCCAAACCCCTGAGGGAGGCTGTCCTCGGCAGGAGAGCAGACCTGAGGGAGGT
isotig466 40 W C A G P G C P A L P S H P R A G S P E
isotig466 120 TGGTGTGCCGGTCCTGGTTGTCCAGCCCTCCCGTCCCATCCCAGGGCTGGCTCACCAGAA
isotig466 60 K S T G I P G P L G R E Q R V S S C P G
isotig466 180 AAAAGTACAGGCATCCCAGGCCCTCTGGGGCGGGAGCAGAGGGTCTCCTCTTGTCCGGGG
isotig466 80 E D K N K N K K R V C S P H W K S S G A
isotig466 240 GAAGACAAAAACAAAAACAAAAAACGAGTGTGTAGCCCTCACTGGAAGTCTTCTGGTGCT
isotig466 100 L G P F A L G S L A S G H G G R A P P G
isotig466 300 CTGGGGCCGTTTGCACTTGGGAGCCTGGCTTCTGGGCATGGTGGCCGGGCTCCGCCGGGG
isotig466 120 A S A L G K A F L E Q S G W E P T E V P
isotig466 360 GCTTCAGCCCTCGGCAAAGCGTTTCTAGAACAGAGTGGGTGGGAGCCGACTGAAGTCCCA
isotig466 140 E P R T L T H R K A S S G W R N A N P P
isotig466 420 GAACCGCGAACACTGACGCACAGGAAAGCCTCGAGTGGGTGGAGAAATGCAAATCCCCCA
isotig466 160 V A W P Q P L R T L T A D S D F G L E R
isotig466 480 GTGGCATGGCCTCAGCCGCTGCGGACCCTGACGGCCGATTCTGACTTCGGACTTGAGCGG
isotig466 180 D Q H P D P G R A S M S Q W N Q V Q Q L
isotig466 540 GACCAGCACCCGGACCCAGGGCGAGCCAGCATGTCTCAGTGGAATCAAGTCCAACAGTTA
isotig466 200 E I K F L E Q V D Q F Y D D N F P M E I
isotig466 600 GAAATCAAGTTTTTGGAGCAAGTTGATCAGTTCTATGATGACAACTTTCCCATGGAAATC
isotig466 220 R H L L A Q W I E H Q D W E V A S N N E
isotig466 660 CGACATCTGCTGGCCCAGTGGATTGAGCATCAAGACTGGGAGGTGGCCTCTAACAATGAA
isotig466 240 T M A T I L L Q N L L I Q L D E Q L G R
isotig466 720 ACTATGGCAACAATTCTTCTTCAAAACTTATTAATACAATTGGATGAACAGTTAGGTCGT
isotig466 260 V S K E K N L L L I H N L K R I R K V L
isotig466 780 GTTTCCAAAGAGAAAAACCTGCTATTGATCCACAATCTAAAGAGAATTAGAAAAGTACTT
isotig466 280 Q G K F H G N P M H V A V V I S N C L R
isotig466 840 CAGGGGAAGTTTCATGGAAATCCAATGCATGTAGCCGTGGTAATCTCAAATTGTTTAAGG
isotig466 300 E E R R I L A A A N M P I Q G P L E K S
isotig466 900 GAAGAGAGGAGAATACTGGCTGCAGCGAACATGCCTATCCAGGGACCTCTGGAGAAATCC
isotig466 320 L Q S S S V S E R Q R N V E H K V A A I
isotig466 960 TTACAAAGTTCGTCGGTTTCAGAAAGACAGAGAAATGTGGAACACAAAGTGGCTGCCATT
isotig466 340 K N S V Q M T E Q D T K Y L E D L Q D E
isotig466 1020 AAAAACAGTGTGCAGATGACAGAACAAGACACCAAATACTTGGAAGATCTGCAAGATGAA
isotig466 360 F D Y R Y K T I Q T M D Q G D K N S I L
isotig466 1080 TTTGACTACAGGTATAAAACAATTCAGACAATGGACCAGGGTGACAAGAATAGCATCCTA
isotig466 380 M N Q E V L T L Q E M L N S L D F K R K
isotig466 1140 ATGAACCAGGAGGTTTTGACACTCCAAGAAATGCTTAATAGCCTGGACTTCAAGAGAAAG
isotig466 400 E A L T K M T Q I V N E S D L L M S S M
isotig466 1200 GAAGCACTCACTAAGATGACACAGATAGTGAACGAGTCGGACCTGCTGATGAGCAGCATG
isotig466 420 L I E E L Q D W K R R Q Q I A C I G G P
isotig466 1260 CTCATAGAAGAGCTGCAGGACTGGAAGAGGAGGCAGCAGATCGCCTGCATCGGTGGCCCA
isotig466 440 L H N G L D Q L Q N C F T L L A E S L F
isotig466 1320 CTCCACAACGGGCTGGACCAGCTTCAGAACTGCTTTACCCTGTTGGCAGAAAGTCTTTTC
isotig466 460 Q L R R Q L E K L E E Q S S K M T Y E G
isotig466 1380 CAACTCAGACGACAGCTGGAGAAATTAGAGGAGCAGTCTTCCAAGATGACTTACGAAGGA
isotig466 480 D P I P T Q R A H L L E R A T F L I Y N
isotig466 1440 GACCCCATCCCCACGCAGAGAGCACACCTGCTGGAGAGAGCCACCTTCCTGATCTACAAC
isotig466 500 L F K N S F V V E R Q P C M P T H P Q R
isotig466 1500 CTTTTCAAGAACTCATTTGTGGTTGAGCGACAGCCCTGCATGCCAACACACCCTCAGAGG
isotig466 520 P L V L K T L I Q F T A K L R L L I K L
isotig466 1560 CCGCTGGTACTCAAAACCCTCATTCAGTTCACCGCGAAACTGAGACTACTAATAAAATTG
isotig466 540 P E L N Y Q V K V K A S I D K N V S T L
isotig466 1620 CCGGAACTCAACTATCAGGTGAAAGTAAAGGCATCGATCGACAAGAATGTTTCAACGCTA
isotig466 560 S N R R F V L C G T Q V K A M S I E E S
isotig466 1680 AGCAATAGAAGATTTGTGCTTTGTGGAACTCAAGTCAAAGCCATGTCCATCGAGGAATCC
isotig466 580 S N G S L S V E F R H L Q P K E M K S S
isotig466 1740 TCCAATGGGAGCCTCTCAGTAGAATTTAGACATTTGCAACCGAAGGAAATGAAATCCAGT
isotig466 600 A G S K G N E G C H M V T E E L H S I A
isotig466 1800 GCCGGAAGTAAAGGAAATGAGGGCTGCCACATGGTGACGGAAGAGCTGCATTCCATAGCC
isotig466 620 F E T Q I C L Y G L T I D L E T S S L P
isotig466 1860 TTTGAGACCCAGATCTGCCTCTATGGCCTCACCATCGACTTGGAGACAAGCTCATTACCT
isotig466 640 V V M I S N V S Q L P N A W A S I I W Y
isotig466 1920 GTGGTGATGATTTCTAATGTCAGCCAACTGCCTAATGCTTGGGCATCCATCATTTGGTAC
isotig466 660 N V S T N D C Q N L V F F N N P P P V T
isotig466 1980 AATGTGTCAACCAACGATTGCCAGAACTTGGTTTTCTTTAATAATCCTCCGCCTGTCACT
isotig466 680 L S Q L L E V M S W Q F S S Y V G R G L
isotig466 2040 TTGAGTCAACTCCTGGAAGTGATGAGCTGGCAGTTTTCATCCTATGTTGGTCGTGGCCTT
isotig466 700 N S D Q L N M L A E K L T V Q S N Y S D
isotig466 2100 AATTCAGACCAGCTCAACATGCTGGCAGAGAAGCTCACAGTTCAGTCTAACTACAGCGAT
isotig466 720 G H L T W A K F C K E H L P G K P F T F
isotig466 2160 GGTCACCTCACCTGGGCCAAGTTCTGCAAGGAACACTTGCCTGGCAAACCATTTACCTTC
isotig466 740 W T W L E A I L D L I K K H I L P L W I
isotig466 2220 TGGACCTGGCTTGAAGCAATATTGGACCTAATTAAAAAACACATTCTTCCCCTCTGGATT
isotig466 760 D G Y I M G F V S K E K E R F L L K D K
isotig466 2280 GATGGGTACATCATGGGCTTCGTGAGCAAAGAGAAGGAGAGGTTTCTGCTCAAGGATAAA
isotig466 780 M P G T F L L R F S E S H L G G I T F T
isotig466 2340 ATGCCCGGGACATTTTTGTTACGATTCAGTGAGAGCCATCTCGGAGGGATCACCTTCACC
isotig466 800 W V D H S E N G E V R F H S V E P Y N K
isotig466 2400 TGGGTGGACCACTCTGAAAACGGAGAAGTGAGATTCCACTCCGTAGAACCCTACAACAAA
isotig466 820 G R L S A L P F A D I L R D Y K V I M A
isotig466 2460 GGGCGTCTGTCGGCCCTGCCATTTGCTGACATCCTGCGGGACTACAAGGTCATCATGGCT
isotig466 840 E N I P E N P L K Y L Y P D I P K D K A
isotig466 2520 GAGAACATTCCCGAGAACCCTCTCAAGTACCTCTACCCCGACATCCCCAAAGACAAAGCC
isotig466 860 F G K H Y S S Q P C E V S R P T E R G D
isotig466 2580 TTCGGTAAACACTACAGCTCCCAGCCTTGCGAAGTTTCAAGGCCAACAGAACGGGGAGAC
isotig466 880 K G Y V P S V F I P I S T I R S D A M E
isotig466 2640 AAAGGTTATGTTCCTTCAGTTTTTATCCCTATTTCAACAATCCGCAGCGACGCCATGGAG
isotig466 900 P Q S P S D L L P M S P S V Y A V L R E
isotig466 2700 CCGCAGTCTCCTTCAGACCTTCTCCCCATGTCTCCGAGTGTATACGCTGTGCTGAGAGAA
isotig466 920 N L S P T T I E T A M K S P Y S E R Y K
isotig466 2760 AACCTGAGCCCTACCACAATTGAAACAGCAATGAAGTCTCCATATTCTGAGCGGTACAAA
isotig466 940 A T L Q G R E Q M K T E T A L C Q S P Q
isotig466 2820 GCGACTCTTCAAGGAAGAGAGCAGATGAAAACGGAGACTGCTCTTTGCCAAAGTCCACAA
isotig466 960 F I S S A L I L V S R K W H K S E A F L
isotig466 2880 TTCATTTCTTCAGCTTTGATACTGGTTTCTAGAAAATGGCACAAATCCGAAGCTTTCCTC
isotig466 980 S L G D I P Q L G V L L K C K P K L Q I
isotig466 2940 TCACTAGGTGACATTCCCCAACTGGGAGTGCTGCTGAAATGCAAACCAAAGCTTCAGATA
isotig466 1000 N T Q E K T A S R N L C S Q Y N R R L L
isotig466 3000 AACACGCAGGAAAAGACAGCTTCGAGAAACCTATGTTCGCAATATAACAGAAGGCTGCTT
isotig466 1020 C 1021
isotig466 3060 TGC 3063
""",
)
protein_record = protein_alignment.sequences[8]
nucleotide_record = nucleotide_records[protein_record.id]
self.assertEqual(nucleotide_record.id, protein_record.id)
nucleotide_record = nucleotide_record.upper()
alignments = aligner.align(protein_record, nucleotide_record)
self.assertEqual(len(alignments), 1)
alignment = next(alignments)
codon_alignments.append(alignment)
self.assertTrue(
np.array_equal(alignment.coordinates, np.array([[0, 806], [0, 2418]]))
)
self.assertEqual(
str(alignment),
"""\
isotig125 0 A R R G Q A A L G S P A A R T W S Q R S
isotig125 0 GCTAGGAGAGGCCAGGCGGCCCTCGGGAGCCCAGCTGCTCGCACCTGGAGCCAGCGCAGC
isotig125 20 P A S R A S A R E T V T P P D C G R M A
isotig125 60 CCGGCCAGTCGGGCCTCAGCCCGGGAGACAGTTACGCCCCCTGATTGCGGCAGGATGGCC
isotig125 40 Q W N Q L Q Q L D T R Y L E Q L H Q L Y
isotig125 120 CAGTGGAACCAGCTGCAGCAGCTGGACACTCGGTACCTGGAGCAGCTGCACCAGCTGTAC
isotig125 60 S D S F P M E L R Q F L A P W I E S Q D
isotig125 180 AGCGACAGCTTCCCCATGGAGCTGCGGCAGTTCCTGGCACCTTGGATTGAGAGTCAAGAT
isotig125 80 W A Y A A S K E S H A T L V F H N L L G
isotig125 240 TGGGCATATGCAGCCAGCAAAGAGTCACATGCCACACTGGTGTTTCATAATCTCTTGGGT
isotig125 100 E I D Q Q Y S R F L Q E S N V L Y Q H N
isotig125 300 GAGATTGACCAGCAGTACAGCCGATTCCTGCAAGAGTCCAACGTCCTCTATCAGCACAAC
isotig125 120 L R R I G Q F V Q S R Y L E K P M E I A
isotig125 360 CTTCGGAGGATCAAGCAGTTCCTACAGAGCAGGTATCTTGAGAAGCCGATGGAAATCGCC
isotig125 140 R I V A R C L W E E S R L L Q T A A T A
isotig125 420 CGCATCGTGGCCCGATGCCTGTGGGAAGAGTCTCGCCTCCTCCAGACGGCAGCCACTGCA
isotig125 160 A Q Q G G Q A N H P T A A V V T E K Q Q
isotig125 480 GCCCAGCAAGGAGGCCAGGCCAACCACCCAACAGCTGCTGTGGTGACGGAGAAACAGCAG
isotig125 180 M L E Q H L Q D V R K R V Q D L E Q K M
isotig125 540 ATGCTGGAGCAGCATCTTCAGGATGTCCGGAAACGTGTGCAGGATCTAGAACAGAAAATG
isotig125 200 K V V E N L Q D D F D F N Y K T L K S Q
isotig125 600 AAAGTGGTAGAGAATCTCCAGGATGACTTTGATTTCAACTATAAAACCCTCAAGAGTCAA
isotig125 220 G D M Q D L N G N N Q S V T R Q K M Q Q
isotig125 660 GGAGACATGCAGGATCTGAATGGAAACAACCAGTCTGTGACCAGGCAGAAGATGCAGCAG
isotig125 240 L E Q M L T A L D Q M R R S I V S E L A
isotig125 720 CTGGAACAGATGCTCACGGCGCTGGACCAGATGCGGAGAAGCATTGTGAGTGAGCTGGCG
isotig125 260 G L L S A M E Y V Q K T L T D E E L A D
isotig125 780 GGGCTTTTGTCGGCAATGGAGTACGTGCAGAAAACACTCACAGACGAGGAGCTGGCTGAC
isotig125 280 W K R R Q Q I A C I G G P P N I C L D R
isotig125 840 TGGAAGAGGCGGCAGCAGATCGCGTGCATTGGAGGCCCTCCCAACATCTGCCTGGATCGC
isotig125 300 L E N W I T S L A E S Q L Q T R Q Q I K
isotig125 900 CTGGAAAACTGGATAACTTCGTTAGCAGAATCTCAACTTCAGACCCGCCAACAAATTAAG
isotig125 320 K L E E L Q Q K V S Y K G D P I V Q H R
isotig125 960 AAACTGGAGGAGCTACAGCAGAAGGTGTCCTACAAGGGGGACCCCATTGTGCAGCACCGG
isotig125 340 P M L E E R I V E L F R N L M K S A F V
isotig125 1020 CCGATGCTGGAGGAGCGGATCGTGGAGCTGTTCAGAAACTTGATGAAGAGTGCCTTCGTG
isotig125 360 V E R Q P C M P M H P D R P L V I K T G
isotig125 1080 GTGGAGCGACAGCCCTGCATGCCGATGCACCCCGACCGGCCCTTGGTCATCAAGACTGGT
isotig125 380 V Q F T T K V R L L V K F P E L N Y Q L
isotig125 1140 GTCCAGTTCACTACTAAAGTCAGGTTGTTGGTCAAGTTTCCCGAGTTGAATTATCAGCTT
isotig125 400 K I K V C I D K D S G D V A A L R G S R
isotig125 1200 AAAATTAAAGTGTGCATTGACAAAGATTCTGGGGACGTTGCTGCTCTCAGAGGATCTCGG
isotig125 420 K F N I L G T N T K V M N M E E S N N G
isotig125 1260 AAATTTAACATTCTGGGCACAAACACGAAGGTGATGAACATGGAAGAATCCAACAACGGC
isotig125 440 S L S A E F K H L T L R E Q R C G N G G
isotig125 1320 AGCCTGTCTGCGGAGTTCAAGCACTTGACCCTGAGGGAGCAGAGATGTGGGAATGGAGGC
isotig125 460 R A N C D A S L I V T E E L H L I T F E
isotig125 1380 CGTGCCAATTGTGATGCCTCCTTGATTGTGACCGAGGAGCTGCATCTGATCACCTTCGAG
isotig125 480 T E V Y H Q G L K I D L E T H S L P V V
isotig125 1440 ACTGAGGTGTACCACCAAGGCCTCAAGATTGACCTGGAGACCCATTCTTTGCCAGTTGTG
isotig125 500 V I S N I C Q M P N A W A S I L W Y N M
isotig125 1500 GTGATCTCCAACATCTGTCAGATGCCAAATGCCTGGGCATCCATCCTGTGGTATAACATG
isotig125 520 L T N N P K N V N F F T K P P I G T W D
isotig125 1560 CTGACCAACAACCCCAAGAACGTGAACTTCTTCACCAAGCCACCAATCGGAACCTGGGAC
isotig125 540 Q V A E V L S W Q F S S T T K R G L S I
isotig125 1620 CAGGTGGCCGAGGTGCTCAGCTGGCAGTTCTCATCCACCACAAAGCGAGGGCTGAGCATC
isotig125 560 E Q L T T L A E K L L G P G V N Y S G C
isotig125 1680 GAGCAGCTGACTACGCTGGCCGAGAAGCTCCTAGGACCTGGTGTCAACTACTCCGGGTGT
isotig125 580 Q I T W A K F C K E N M A G K G F S F W
isotig125 1740 CAGATCACATGGGCTAAATTTTGCAAAGAAAACATGGCTGGCAAGGGCTTCTCCTTCTGG
isotig125 600 V W L D N I I D L V K K Y I L A L W N E
isotig125 1800 GTGTGGCTAGACAATATCATTGACCTTGTGAAAAAGTATATCTTGGCCCTCTGGAATGAA
isotig125 620 G Y I M G F I S K E R E R A I L S T K P
isotig125 1860 GGGTACATCATGGGCTTCATTAGCAAGGAGCGGGAGCGGGCGATCCTGAGCACGAAACCC
isotig125 640 P G T F L L R F S E S S K E G G V T F T
isotig125 1920 CCGGGCACCTTCCTGCTGAGATTCAGCGAGAGCAGCAAAGAAGGAGGGGTCACTTTCACT
isotig125 660 W V E K D I S G K T Q I Q S V E P Y T K
isotig125 1980 TGGGTGGAAAAGGACATCAGTGGCAAGACCCAGATCCAGTCTGTAGAGCCGTACACCAAG
isotig125 680 Q Q L N N M S F A E I I M G Y K I M D A
isotig125 2040 CAGCAGCTGAACAACATGTCCTTTGCTGAAATCATCATGGGCTACAAGATCATGGATGCC
isotig125 700 T N I L V S P L V Y L Y P D I P K E E A
isotig125 2100 ACCAACATCCTGGTGTCCCCATTGGTCTACCTCTACCCTGACATTCCCAAGGAGGAGGCG
isotig125 720 F G K Y C R P E S Q E H P E A D P G S A
isotig125 2160 TTCGGGAAGTACTGTCGACCAGAGAGCCAGGAGCATCCTGAAGCTGACCCCGGTAGTGCC
isotig125 740 A P Y L K T K F I C V T P T T C S N T I
isotig125 2220 GCCCCTTACCTGAAGACCAAGTTCATCTGTGTGACACCAACGACCTGCAGCAATACCATT
isotig125 760 D L P M S P P H F R F I D A V W K R R C
isotig125 2280 GACCTGCCGATGTCCCCCCCGCACTTTAGATTCATTGATGCAGTTTGGAAACGGAGGTGC
isotig125 780 A L G R R A V V T H V H G S D F G V R Y
isotig125 2340 GCCCTCGGCAGGAGGGCAGTTGTCACTCACGTTCATGGATCTGACTTCGGAGTGCGCTAC
isotig125 800 L P H V R S 806
isotig125 2400 CTCCCCCATGTGAGGAGC 2418
""",
)
protein_record = protein_alignment.sequences[9]
nucleotide_record = nucleotide_records[protein_record.id]
self.assertEqual(nucleotide_record.id, protein_record.id)
nucleotide_record = nucleotide_record.upper()
alignments = aligner.align(protein_record, nucleotide_record)
self.assertEqual(len(alignments), 1)
alignment = next(alignments)
codon_alignments.append(alignment)
self.assertTrue(
np.array_equal(alignment.coordinates, np.array([[0, 796], [0, 2388]]))
)
self.assertEqual(
str(alignment),
"""\
isotig125 0 A R R G Q A A L G S P A A R T W S Q R S
isotig125 0 GCTAGGAGAGGCCAGGCGGCCCTCGGGAGCCCAGCTGCTCGCACCTGGAGCCAGCGCAGC
isotig125 20 P A S R A S A R E T V T P P D C G R M A
isotig125 60 CCGGCCAGTCGGGCCTCAGCCCGGGAGACAGTTACGCCCCCTGATTGCGGCAGGATGGCC
isotig125 40 Q W N Q L Q Q L D T R Y L E Q L H Q L Y
isotig125 120 CAGTGGAACCAGCTGCAGCAGCTGGACACTCGGTACCTGGAGCAGCTGCACCAGCTGTAC
isotig125 60 S D S F P M E L R Q F L A P W I E S Q D
isotig125 180 AGCGACAGCTTCCCCATGGAGCTGCGGCAGTTCCTGGCACCTTGGATTGAGAGTCAAGAT
isotig125 80 W A Y A A S K E S H A T L V F H N L L G
isotig125 240 TGGGCATATGCAGCCAGCAAAGAGTCACATGCCACACTGGTGTTTCATAATCTCTTGGGT
isotig125 100 E I D Q Q Y S R F L Q E S N V L Y Q H N
isotig125 300 GAGATTGACCAGCAGTACAGCCGATTCCTGCAAGAGTCCAACGTCCTCTATCAGCACAAC
isotig125 120 L R R I K Q F L Q S R Y L E K P M E I A
isotig125 360 CTTCGGAGGATCAAGCAGTTCCTACAGAGCAGGTATCTTGAGAAGCCGATGGAAATCGCC
isotig125 140 R I V A R C L W E E S R L L Q T A A T A
isotig125 420 CGCATCGTGGCCCGATGCCTGTGGGAAGAGTCTCGCCTCCTCCAGACGGCAGCCACTGCA
isotig125 160 A Q Q G G Q A N H P T A A V V T E K Q Q
isotig125 480 GCCCAGCAAGGAGGCCAGGCCAACCACCCAACAGCTGCTGTGGTGACGGAGAAACAGCAG
isotig125 180 M L E Q H L Q D V R K R V Q D L E Q K M
isotig125 540 ATGCTGGAGCAGCATCTTCAGGATGTCCGGAAACGTGTGCAGGATCTAGAACAGAAAATG
isotig125 200 K V V E N L Q D D F D F N Y K T L K S Q
isotig125 600 AAAGTGGTAGAGAATCTCCAGGATGACTTTGATTTCAACTATAAAACCCTCAAGAGTCAA
isotig125 220 G D M Q D L N G N N Q S V T R Q K M Q Q
isotig125 660 GGAGACATGCAGGATCTGAATGGAAACAACCAGTCTGTGACCAGGCAGAAGATGCAGCAG
isotig125 240 L E Q M L T A L D Q M R R S I V S E L A
isotig125 720 CTGGAACAGATGCTCACGGCGCTGGACCAGATGCGGAGAAGCATTGTGAGTGAGCTGGCG
isotig125 260 G L L S A M E Y V Q K T L T D E E L A D
isotig125 780 GGGCTTTTGTCGGCAATGGAGTACGTGCAGAAAACACTCACAGACGAGGAGCTGGCTGAC
isotig125 280 W K R R Q Q I A C I G G P P N I C L D R
isotig125 840 TGGAAGAGGCGGCAGCAGATCGCGTGCATTGGAGGCCCTCCCAACATCTGCCTGGATCGC
isotig125 300 L E N W I T S L A E S Q L Q T R Q Q I K
isotig125 900 CTGGAAAACTGGATAACTTCGTTAGCAGAATCTCAACTTCAGACCCGCCAACAAATTAAG
isotig125 320 K L E E L Q Q K V S Y K G D P I V Q H R
isotig125 960 AAACTGGAGGAGCTACAGCAGAAGGTGTCCTACAAGGGGGACCCCATTGTGCAGCACCGG
isotig125 340 P M L E E R I V E L F R N L M K S A F V
isotig125 1020 CCGATGCTGGAGGAGCGGATCGTGGAGCTGTTCAGAAACTTGATGAAGAGTGCCTTCGTG
isotig125 360 V E R Q P C M P M H P D R P L V I K T G
isotig125 1080 GTGGAGCGACAGCCCTGCATGCCGATGCACCCCGACCGGCCCTTGGTCATCAAGACTGGT
isotig125 380 V Q F T T K V R L L V K F P E L N Y Q L
isotig125 1140 GTCCAGTTCACTACTAAAGTCAGGTTGTTGGTCAAGTTTCCCGAGTTGAATTATCAGCTT
isotig125 400 K I K V C I D K D S G D V A A L R G S R
isotig125 1200 AAAATTAAAGTGTGCATTGACAAAGATTCTGGGGACGTTGCTGCTCTCAGAGGATCTCGG
isotig125 420 K F N I L G T N T K V M N M E E S N N G
isotig125 1260 AAATTTAACATTCTGGGCACAAACACGAAGGTGATGAACATGGAAGAATCCAACAACGGC
isotig125 440 S L S A E F K H L T L R E Q R C G N G G
isotig125 1320 AGCCTGTCTGCGGAGTTCAAGCACTTGACCCTGAGGGAGCAGAGATGTGGGAATGGAGGC
isotig125 460 R A N C D A S L I V T E E L H L I T F E
isotig125 1380 CGTGCCAATTGTGATGCCTCCTTGATTGTGACCGAGGAGCTGCATCTGATCACCTTCGAG
isotig125 480 T E V Y H Q G L K I D L E T H S L P V V
isotig125 1440 ACTGAGGTGTACCACCAAGGCCTCAAGATTGACCTGGAGACCCATTCTTTGCCAGTTGTG
isotig125 500 V I S N I C Q M P N A W A S I L W Y N M
isotig125 1500 GTGATCTCCAACATCTGTCAGATGCCAAATGCCTGGGCATCCATCCTGTGGTATAACATG
isotig125 520 L T N N P K N V N F F T K P P I G T W D
isotig125 1560 CTGACCAACAACCCCAAGAACGTGAACTTCTTCACCAAGCCACCAATCGGAACCTGGGAC
isotig125 540 Q V A E V L S W Q F S S T T K R G L S I
isotig125 1620 CAGGTGGCCGAGGTGCTCAGCTGGCAGTTCTCATCCACCACAAAGCGAGGGCTGAGCATC
isotig125 560 E Q L T T L A E K L L G P G V N Y S G C
isotig125 1680 GAGCAGCTGACTACGCTGGCCGAGAAGCTCCTAGGACCTGGTGTCAACTACTCCGGGTGT
isotig125 580 Q I T W A K F C K E N M A G K G F S F W
isotig125 1740 CAGATCACATGGGCTAAATTTTGCAAAGAAAACATGGCTGGCAAGGGCTTCTCCTTCTGG
isotig125 600 V W L D N I I D L V K K Y I L A L W N E
isotig125 1800 GTGTGGCTAGACAATATCATTGACCTTGTGAAAAAGTATATCTTGGCCCTCTGGAATGAA
isotig125 620 G Y I M G F I S K E R E R A I L S T K P
isotig125 1860 GGGTACATCATGGGCTTCATTAGCAAGGAGCGGGAGCGGGCGATCCTGAGCACGAAACCC
isotig125 640 P G T F L L R F S E S S K E G G V T F T
isotig125 1920 CCGGGCACCTTCCTGCTGAGATTCAGCGAGAGCAGCAAAGAAGGAGGGGTCACTTTCACT
isotig125 660 W V E K D I S G K T Q I Q S V E P Y T K
isotig125 1980 TGGGTGGAAAAGGACATCAGTGGCAAGACCCAGATCCAGTCTGTAGAGCCGTACACCAAG
isotig125 680 Q Q L N N M S F A E I I M G Y K I M D A
isotig125 2040 CAGCAGCTGAACAACATGTCCTTTGCTGAAATCATCATGGGCTACAAGATCATGGATGCC
isotig125 700 T N I L V S P L V Y L Y P D I P K E E A
isotig125 2100 ACCAACATCCTGGTGTCCCCATTGGTCTACCTCTACCCTGACATTCCCAAGGAGGAGGCG
isotig125 720 F G K Y C R P E S Q E H P E A D P G S C
isotig125 2160 TTCGGGAAGTACTGTCGACCAGAGAGCCAGGAGCATCCTGAAGCTGACCCCGGTAGTTGT
isotig125 740 F S M V L V S L L G K G G Q C R S L E E
isotig125 2220 TTTTCCATGGTTCTGGTTTCGCTGTTAGGGAAAGGGGGACAGTGCAGGTCCTTGGAGGAG
isotig125 760 R Q G H D R V S G G E S C Y G R A V Y W
isotig125 2280 AGACAAGGACATGACCGGGTGTCTGGTGGTGAGTCCTGCTATGGAAGAGCTGTTTATTGG
isotig125 780 V L Q G D R D S R E D Q N Q A S 796
isotig125 2340 GTACTTCAGGGTGACCGGGATTCAAGAGAAGACCAGAATCAGGCCTCA 2388
""",
)
alignment = protein_alignment.mapall(codon_alignments)
self.assertTrue(
np.array_equal(
alignment.coordinates,
# fmt: off
np.array([[ 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 36, 36, 63, 63,
213, 222, 240, 240, 330, 330, 330, 405,
405, 438, 450, 579, 579, 729, 729, 837,
837, 897, 912, 975, 987, 1020, 1026, 1074,
1077, 1107, 1107, 1116, 1119, 1182, 1188, 1302,
1302, 1392, 1398, 1455, 1458, 1470, 1695, 1695,
1824, 1824, 1887, 1887, 1896, 1902, 1956, 1980,
2022, 2025, 2043, 2046, 2061, 2106, 2187, 2220,
2232, 2253, 2271, 2331, 2334, 2352, 2364, 2373,
2382, 2424, 2463, 2484, 2517, 2541],
[ 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 36, 36, 63, 63,
213, 222, 240, 240, 330, 330, 330, 405,
405, 438, 450, 579, 579, 729, 729, 837,
837, 897, 912, 975, 987, 1020, 1026, 1074,
1077, 1107, 1107, 1116, 1119, 1182, 1188, 1302,
1302, 1392, 1398, 1455, 1458, 1470, 1695, 1695,
1824, 1824, 1887, 1887, 1896, 1902, 1956, 1980,
2022, 2025, 2043, 2046, 2061, 2106, 2187, 2220,
2232, 2253, 2271, 2331, 2334, 2352, 2364, 2373,
2382, 2424, 2463, 2484, 2517, 2541],
[ 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 36, 36, 63, 63,
213, 222, 240, 240, 330, 330, 330, 405,
405, 438, 450, 579, 579, 729, 729, 837,
837, 897, 912, 975, 987, 1020, 1026, 1074,
1077, 1107, 1107, 1116, 1119, 1182, 1188, 1302,
1302, 1392, 1398, 1455, 1458, 1470, 1695, 1695,
1824, 1824, 1887, 1887, 1896, 1902, 1956, 1980,
2022, 2025, 2043, 2046, 2061, 2106, 2187, 2220,
2232, 2253, 2271, 2331, 2334, 2352, 2364, 2373,
2382, 2424, 2463, 2484, 2517, 2541],
[ 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 36, 36, 63, 63,
213, 222, 240, 240, 330, 330, 330, 405,
405, 438, 450, 579, 579, 729, 729, 837,
837, 897, 912, 975, 987, 1020, 1026, 1074,
1077, 1107, 1107, 1116, 1119, 1182, 1188, 1302,
1302, 1392, 1398, 1455, 1458, 1470, 1695, 1695,
1824, 1824, 1887, 1887, 1896, 1902, 1956, 1980,
2022, 2025, 2043, 2046, 2061, 2106, 2187, 2220,
2232, 2253, 2271, 2331, 2334, 2352, 2364, 2373,
2382, 2424, 2463, 2484, 2517, 2541],
[ 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 75,
75, 108, 120, 249, 249, 399, 399, 507,
507, 567, 582, 645, 657, 690, 696, 744,
747, 777, 777, 786, 789, 852, 858, 972,
972, 1062, 1068, 1125, 1128, 1140, 1365, 1365,
1494, 1494, 1557, 1557, 1566, 1572, 1626, 1650,
1692, 1695, 1713, 1716, 1731, 1776, 1857, 1890,
1902, 1923, 1941, 2001, 2004, 2022, 2034, 2043,
2052, 2094, 2133, 2154, 2187, 2211],
[ 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 75,
75, 108, 120, 249, 249, 399, 399, 507,
507, 567, 582, 645, 657, 690, 696, 744,
747, 777, 777, 786, 789, 852, 858, 972,
972, 1062, 1068, 1125, 1128, 1140, 1365, 1365,
1494, 1494, 1557, 1557, 1566, 1572, 1626, 1650,
1692, 1695, 1713, 1716, 1731, 1776, 1857, 1890,
1902, 1923, 1941, 2001, 2004, 2022, 2034, 2043,
2052, 2094, 2133, 2154, 2187, 2211],
[ 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 75,
75, 108, 120, 249, 249, 399, 399, 507,
507, 567, 582, 645, 657, 690, 696, 744,
747, 777, 777, 786, 789, 852, 858, 972,
972, 1062, 1068, 1125, 1128, 1140, 1365, 1365,
1494, 1494, 1557, 1557, 1566, 1572, 1626, 1650,
1692, 1695, 1713, 1716, 1731, 1776, 1857, 1890,
1902, 1923, 1941, 2001, 2004, 2022, 2034, 2043,
2052, 2094, 2133, 2154, 2187, 2211],
[ 0, 12, 21, 357, 378, 417, 444, 474,
516, 549, 564, 570, 606, 615, 642, 645,
795, 795, 813, 828, 918, 918, 999, 1074,
1077, 1110, 1110, 1239, 1251, 1401, 1428, 1536,
1560, 1620, 1620, 1683, 1683, 1716, 1716, 1764,
1764, 1794, 1809, 1818, 1818, 1881, 1881, 1995,
2001, 2091, 2091, 2148, 2148, 2148, 2373, 2373,
2502, 2532, 2595, 2619, 2628, 2628, 2682, 2706,
2706, 2709, 2727, 2727, 2727, 2772, 2772, 2805,
2817, 2817, 2835, 2895, 2898, 2916, 2928, 2937,
2946, 2946, 2985, 3006, 3039, 3063],
[ 0, 0, 9, 9, 30, 30, 57, 57,
99, 99, 114, 114, 150, 159, 186, 189,
339, 339, 357, 372, 462, 465, 546, 621,
624, 657, 669, 798, 810, 960, 987, 1095,
1119, 1179, 1179, 1242, 1254, 1287, 1287, 1335,
1335, 1365, 1380, 1389, 1392, 1455, 1455, 1569,
1575, 1665, 1665, 1722, 1725, 1725, 1950, 1953,
2082, 2112, 2175, 2175, 2184, 2184, 2184, 2208,
2208, 2208, 2226, 2226, 2226, 2271, 2271, 2304,
2304, 2304, 2304, 2304, 2307, 2325, 2337, 2346,
2346, 2346, 2385, 2385, 2418, 2418],
[ 0, 0, 9, 9, 30, 30, 57, 57,
99, 99, 114, 114, 150, 159, 186, 189,
339, 339, 357, 372, 462, 465, 546, 621,
624, 657, 669, 798, 810, 960, 987, 1095,
1119, 1179, 1179, 1242, 1254, 1287, 1287, 1335,
1335, 1365, 1380, 1389, 1392, 1455, 1455, 1569,
1575, 1665, 1665, 1722, 1725, 1725, 1950, 1953,
2082, 2112, 2175, 2175, 2184, 2184, 2184, 2208,
2208, 2208, 2226, 2229, 2229, 2229, 2229, 2262,
2274, 2274, 2274, 2334, 2337, 2337, 2349, 2349,
2349, 2349, 2388, 2388, 2388, 2388]])
# fmt: on
)
)
self.assertEqual(
format(alignment, "clustal"),
"""\
ENSG00000166888:ENST0000030013 --------------------------------------------------
ENSG00000166888:ENST0000054387 --------------------------------------------------
ENSG00000166888:ENST0000055615 --------------------------------------------------
ENSG00000166888:ENST0000045407 --------------------------------------------------
ENSG00000166888:ENST0000053891 --------------------------------------------------
ENSG00000166888:ENST0000053721 --------------------------------------------------
ENSG00000166888:ENST0000053520 --------------------------------------------------
isotig46679 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
isotig12565 ------------GCTAGGAGA-----------------------------
isotig12566 ------------GCTAGGAGA-----------------------------
ENSG00000166888:ENST0000030013 --------------------------------------------------
ENSG00000166888:ENST0000054387 --------------------------------------------------
ENSG00000166888:ENST0000055615 --------------------------------------------------
ENSG00000166888:ENST0000045407 --------------------------------------------------
ENSG00000166888:ENST0000053891 --------------------------------------------------
ENSG00000166888:ENST0000053721 --------------------------------------------------
ENSG00000166888:ENST0000053520 --------------------------------------------------
isotig46679 AAAAAAAAAAGAGTTGGCCCAAACCCCTGAGGGAGGCTGTCCTCGGCAGG
isotig12565 --------------------------------------------------
isotig12566 --------------------------------------------------
ENSG00000166888:ENST0000030013 --------------------------------------------------
ENSG00000166888:ENST0000054387 --------------------------------------------------
ENSG00000166888:ENST0000055615 --------------------------------------------------
ENSG00000166888:ENST0000045407 --------------------------------------------------
ENSG00000166888:ENST0000053891 --------------------------------------------------
ENSG00000166888:ENST0000053721 --------------------------------------------------
ENSG00000166888:ENST0000053520 --------------------------------------------------
isotig46679 AGAGCAGACCTGAGGGAGGTTGGTGTGCCGGTCCTGGTTGTCCAGCCCTC
isotig12565 --------------------------------------------------
isotig12566 --------------------------------------------------
ENSG00000166888:ENST0000030013 --------------------------------------------------
ENSG00000166888:ENST0000054387 --------------------------------------------------
ENSG00000166888:ENST0000055615 --------------------------------------------------
ENSG00000166888:ENST0000045407 --------------------------------------------------
ENSG00000166888:ENST0000053891 --------------------------------------------------
ENSG00000166888:ENST0000053721 --------------------------------------------------
ENSG00000166888:ENST0000053520 --------------------------------------------------
isotig46679 CCGTCCCATCCCAGGGCTGGCTCACCAGAAAAAAGTACAGGCATCCCAGG
isotig12565 --------------------------------------------------
isotig12566 --------------------------------------------------
ENSG00000166888:ENST0000030013 --------------------------------------------------
ENSG00000166888:ENST0000054387 --------------------------------------------------
ENSG00000166888:ENST0000055615 --------------------------------------------------
ENSG00000166888:ENST0000045407 --------------------------------------------------
ENSG00000166888:ENST0000053891 --------------------------------------------------
ENSG00000166888:ENST0000053721 --------------------------------------------------
ENSG00000166888:ENST0000053520 --------------------------------------------------
isotig46679 CCCTCTGGGGCGGGAGCAGAGGGTCTCCTCTTGTCCGGGGGAAGACAAAA
isotig12565 --------------------------------------------------
isotig12566 --------------------------------------------------
ENSG00000166888:ENST0000030013 --------------------------------------------------
ENSG00000166888:ENST0000054387 --------------------------------------------------
ENSG00000166888:ENST0000055615 --------------------------------------------------
ENSG00000166888:ENST0000045407 --------------------------------------------------
ENSG00000166888:ENST0000053891 --------------------------------------------------
ENSG00000166888:ENST0000053721 --------------------------------------------------
ENSG00000166888:ENST0000053520 --------------------------------------------------
isotig46679 ACAAAAACAAAAAACGAGTGTGTAGCCCTCACTGGAAGTCTTCTGGTGCT
isotig12565 --------------------------------------------------
isotig12566 --------------------------------------------------
ENSG00000166888:ENST0000030013 --------------------------------------------------
ENSG00000166888:ENST0000054387 --------------------------------------------------
ENSG00000166888:ENST0000055615 --------------------------------------------------
ENSG00000166888:ENST0000045407 --------------------------------------------------
ENSG00000166888:ENST0000053891 --------------------------------------------------
ENSG00000166888:ENST0000053721 --------------------------------------------------
ENSG00000166888:ENST0000053520 --------------------------------------------------
isotig46679 CTGGGGCCGTTTGCACTTGGGAGCCTGGCTTCTGGGCATGGTGGCCGGGC
isotig12565 --------------------------------------------------
isotig12566 --------------------------------------------------
ENSG00000166888:ENST0000030013 --------------------------------------------------
ENSG00000166888:ENST0000054387 --------------------------------------------------
ENSG00000166888:ENST0000055615 --------------------------------------------------
ENSG00000166888:ENST0000045407 --------------------------------------------------
ENSG00000166888:ENST0000053891 --------------------------------------------------
ENSG00000166888:ENST0000053721 --------------------------------------------------
ENSG00000166888:ENST0000053520 --------------------------------------------------
isotig46679 TCCGCCGGGGGCTTCAGCCCTCGGCAAAGCGTTTCTAGAACAGAGTGGGT
isotig12565 -------GGCCAGGCGGCCCTCGGGAGC----------------------
isotig12566 -------GGCCAGGCGGCCCTCGGGAGC----------------------
ENSG00000166888:ENST0000030013 --------------------------------------------------
ENSG00000166888:ENST0000054387 --------------------------------------------------
ENSG00000166888:ENST0000055615 --------------------------------------------------
ENSG00000166888:ENST0000045407 --------------------------------------------------
ENSG00000166888:ENST0000053891 --------------------------------------------------
ENSG00000166888:ENST0000053721 --------------------------------------------------
ENSG00000166888:ENST0000053520 --------------------------------------------------
isotig46679 GGGAGCCGACTGAAGTCCCAGAACCGCGAACACTGACGCACAGGAAAGCC
isotig12565 -----------------CCAGCTGCTCGCACCTGGAGCCAGCGC------
isotig12566 -----------------CCAGCTGCTCGCACCTGGAGCCAGCGC------
ENSG00000166888:ENST0000030013 --------------------------------------------------
ENSG00000166888:ENST0000054387 --------------------------------------------------
ENSG00000166888:ENST0000055615 --------------------------------------------------
ENSG00000166888:ENST0000045407 --------------------------------------------------
ENSG00000166888:ENST0000053891 --------------------------------------------------
ENSG00000166888:ENST0000053721 --------------------------------------------------
ENSG00000166888:ENST0000053520 --------------------------------------------------
isotig46679 TCGAGTGGGTGGAGAAATGCAAATCCCCCAGTGGCATGGCCTCAGCCGCT
isotig12565 ------------------------AGCCCGGCCAGTCGGGCCTCAGCCCG
isotig12566 ------------------------AGCCCGGCCAGTCGGGCCTCAGCCCG
ENSG00000166888:ENST0000030013 --------------------------------------------------
ENSG00000166888:ENST0000054387 --------------------------------------------------
ENSG00000166888:ENST0000055615 --------------------------------------------------
ENSG00000166888:ENST0000045407 --------------------------------------------------
ENSG00000166888:ENST0000053891 --------------------------------------------------
ENSG00000166888:ENST0000053721 --------------------------------------------------
ENSG00000166888:ENST0000053520 --------------------------------------------------
isotig46679 GCGGACCCTGACGGCCGATTCTGACTTCGGACTTGAGCGGGACCAGCACC
isotig12565 GGAGACAGTTACGCCC---------------------------------C
isotig12566 GGAGACAGTTACGCCC---------------------------------C
ENSG00000166888:ENST0000030013 --------------------ATGTCTCTGTGGGGTCTGGTCTCCAAGATG
ENSG00000166888:ENST0000054387 --------------------ATGTCTCTGTGGGGTCTGGTCTCCAAGATG
ENSG00000166888:ENST0000055615 --------------------ATGTCTCTGTGGGGTCTGGTCTCCAAGATG
ENSG00000166888:ENST0000045407 --------------------ATGTCTCTGTGGGGTCTGGTCTCCAAGATG
ENSG00000166888:ENST0000053891 --------------------------------------------------
ENSG00000166888:ENST0000053721 --------------------------------------------------
ENSG00000166888:ENST0000053520 --------------------------------------------------
isotig46679 CGGACCCAGGGCGAGCCAGCATGTCTCAGTGGAATCAAGTCCAACAGTTA
isotig12565 CTGATTGCGGCAGG------ATGGCCCAGTGGAACCAGCTGCAGCAGCTG
isotig12566 CTGATTGCGGCAGG------ATGGCCCAGTGGAACCAGCTGCAGCAGCTG
ENSG00000166888:ENST0000030013 CCCCCA---------GAAAAAGTGCAGCGGCTCTATGTCGAC---TTTCC
ENSG00000166888:ENST0000054387 CCCCCA---------GAAAAAGTGCAGCGGCTCTATGTCGAC---TTTCC
ENSG00000166888:ENST0000055615 CCCCCA---------GAAAAAGTGCAGCGGCTCTATGTCGAC---TTTCC
ENSG00000166888:ENST0000045407 CCCCCA---------GAAAAAGTGCAGCGGCTCTATGTCGAC---TTTCC
ENSG00000166888:ENST0000053891 --------------------------------------------------
ENSG00000166888:ENST0000053721 --------------------------------------------------
ENSG00000166888:ENST0000053520 --------------------------------------------------
isotig46679 GAAATCAAGTTTTTGGAGCAAGTTGATCAGTTCTATGATGACAACTTTCC
isotig12565 GACACTCGGTACCTGGAGCAGCTGCACCAGCTGTACAGCGACAGCTTCCC
isotig12566 GACACTCGGTACCTGGAGCAGCTGCACCAGCTGTACAGCGACAGCTTCCC
ENSG00000166888:ENST0000030013 CCAACACCTGCGGCATCTTCTGGGTGACTGGCTGGAGAGCCAGCCCTGGG
ENSG00000166888:ENST0000054387 CCAACACCTGCGGCATCTTCTGGGTGACTGGCTGGAGAGCCAGCCCTGGG
ENSG00000166888:ENST0000055615 CCAACACCTGCGGCATCTTCTGGGTGACTGGCTGGAGAGCCAGCCCTGGG
ENSG00000166888:ENST0000045407 CCAACACCTGCGGCATCTTCTGGGTGACTGGCTGGAGAGCCAGCCCTGGG
ENSG00000166888:ENST0000053891 --------------------------------------------------
ENSG00000166888:ENST0000053721 --------------------------------------------------
ENSG00000166888:ENST0000053520 --------------------------------------------------
isotig46679 CATGGAAATCCGACATCTGCTGGCCCAGTGGATTGAGCATCAAGACTGGG
isotig12565 CATGGAGCTGCGGCAGTTCCTGGCACCTTGGATTGAGAGTCAAGATTGGG
isotig12566 CATGGAGCTGCGGCAGTTCCTGGCACCTTGGATTGAGAGTCAAGATTGGG
ENSG00000166888:ENST0000030013 AGTTCCTGGTCGGCTCCGACGCCTTCTGCTGCAACTTGGCTAGTGCCCTA
ENSG00000166888:ENST0000054387 AGTTCCTGGTCGGCTCCGACGCCTTCTGCTGCAACTTGGCTAGTGCCCTA
ENSG00000166888:ENST0000055615 AGTTCCTGGTCGGCTCCGACGCCTTCTGCTGCAACTTGGCTAGTGCCCTA
ENSG00000166888:ENST0000045407 AGTTCCTGGTCGGCTCCGACGCCTTCTGCTGCAACTTGGCTAGTGCCCTA
ENSG00000166888:ENST0000053891 --------------------------------------------------
ENSG00000166888:ENST0000053721 --------------------------------------------------
ENSG00000166888:ENST0000053520 --------------------------------------------------
isotig46679 AGGTGGCCTCTAACAATGAAACTATGGCAACAATTCTTCTTCAAAACTTA
isotig12565 CATATGCAGCCAGCAAAGAGTCACATGCCACACTGGTGTTTCATAATCTC
isotig12566 CATATGCAGCCAGCAAAGAGTCACATGCCACACTGGTGTTTCATAATCTC
ENSG00000166888:ENST0000030013 CTTTCAGACACTGTCCAGCACCTTCAGGCCTCGGTGGGAGAGCAGGGGGA
ENSG00000166888:ENST0000054387 CTTTCAGACACTGTCCAGCACCTTCAGGCCTCGGTGGGAGAGCAGGGGGA
ENSG00000166888:ENST0000055615 CTTTCAGACACTGTCCAGCACCTTCAGGCCTCGGTGGGAGAGCAGGGGGA
ENSG00000166888:ENST0000045407 CTTTCAGACACTGTCCAGCACCTTCAGGCCTCGGTGGGAGAGCAGGGGGA
ENSG00000166888:ENST0000053891 --------------------------------------------------
ENSG00000166888:ENST0000053721 --------------------------------------------------
ENSG00000166888:ENST0000053520 --------------------------------------------------
isotig46679 TTAATACAATTGGATGAACAGTTAGGTCGTGTTTCCAAAGAGAAA-----
isotig12565 TTGGGTGAGATTGACCAGCAGTACAGCCGATTCCTGCAAGAGTCC-----
isotig12566 TTGGGTGAGATTGACCAGCAGTACAGCCGATTCCTGCAAGAGTCC-----
ENSG00000166888:ENST0000030013 GGGGAGCACCATCTTGCAACAC---------------ATCAGCACCCTTG
ENSG00000166888:ENST0000054387 GGGGAGCACCATCTTGCAACAC---------------ATCAGCACCCTTG
ENSG00000166888:ENST0000055615 GGGGAGCACCATCTTGCAACAC---------------ATCAGCACCCTTG
ENSG00000166888:ENST0000045407 GGGGAGCACCATCTTGCAACAC---------------ATCAGCACCCTTG
ENSG00000166888:ENST0000053891 --------------------------------------------------
ENSG00000166888:ENST0000053721 --------------------------------------------------
ENSG00000166888:ENST0000053520 --------------------------------------------------
isotig46679 ----AACCTGCTATTGATCCACAATCTAAAGAGAATTAGAAAAGTACTTC
isotig12565 ----AACGTCCTCTATCAGCACAACCTTCGGAGGATCAAGCAGTTCCTAC
isotig12566 ----AACGTCCTCTATCAGCACAACCTTCGGAGGATCAAGCAGTTCCTAC
ENSG00000166888:ENST0000030013 AGAGCATATATCAGAGGGACCCCCTGAAGCTGGTGGCCACTTTCAGACAA
ENSG00000166888:ENST0000054387 AGAGCATATATCAGAGGGACCCCCTGAAGCTGGTGGCCACTTTCAGACAA
ENSG00000166888:ENST0000055615 AGAGCATATATCAGAGGGACCCCCTGAAGCTGGTGGCCACTTTCAGACAA
ENSG00000166888:ENST0000045407 AGAGCATATATCAGAGGGACCCCCTGAAGCTGGTGGCCACTTTCAGACAA
ENSG00000166888:ENST0000053891 --------------------------------------------------
ENSG00000166888:ENST0000053721 --------------------------------------------------
ENSG00000166888:ENST0000053520 --------------------------------------------------
isotig46679 AGGGGAAGTTTCATGGAAATCCAATGCATGTAGCCGTGGTAATCTCAAAT
isotig12565 AGAGCAGGTATCTTGAGAAGCCGATGGAAATCGCCCGCATCGTGGCCCGA
isotig12566 AGAGCAGGTATCTTGAGAAGCCGATGGAAATCGCCCGCATCGTGGCCCGA
ENSG00000166888:ENST0000030013 ATACTTCAAGGAGAGAAAAAAGCTGTT-----------------------
ENSG00000166888:ENST0000054387 ATACTTCAAGGAGAGAAAAAAGCTGTT-----------------------
ENSG00000166888:ENST0000055615 ATACTTCAAGGAGAGAAAAAAGCTGTT-----------------------
ENSG00000166888:ENST0000045407 ATACTTCAAGGAGAGAAAAAAGCTGTT-----------------------
ENSG00000166888:ENST0000053891 --------------------------------------------------
ENSG00000166888:ENST0000053721 --------------------------------------------------
ENSG00000166888:ENST0000053520 --------------------------------------------------
isotig46679 TGTTTAAGGGAAGAGAGGAGAATACTG---GCTGCAGCGAACATGCCTAT
isotig12565 TGCCTGTGGGAAGAGTCTCGCCTCCTCCAGACGGCAGCCACTGCAGCCCA
isotig12566 TGCCTGTGGGAAGAGTCTCGCCTCCTCCAGACGGCAGCCACTGCAGCCCA
ENSG00000166888:ENST0000030013 --------------------------------------------------
ENSG00000166888:ENST0000054387 --------------------------------------------------
ENSG00000166888:ENST0000055615 --------------------------------------------------
ENSG00000166888:ENST0000045407 --------------------------------------------------
ENSG00000166888:ENST0000053891 --------------------------------------------------
ENSG00000166888:ENST0000053721 --------------------------------------------------
ENSG00000166888:ENST0000053520 --------------------------------------------------
isotig46679 CCAGGGACCTCTGGAGAAATCCTTACAAAGTTCGTCGGTTTCAGAAAGAC
isotig12565 GCAAGGAGGCCAGGCCAACCACCCAACAGCTGCTGTGGTGACGGAGAAAC
isotig12566 GCAAGGAGGCCAGGCCAACCACCCAACAGCTGCTGTGGTGACGGAGAAAC
ENSG00000166888:ENST0000030013 -----------ATGGAACAGTTCCGCCACTTGCCAATGCCTTTCCACTGG
ENSG00000166888:ENST0000054387 -----------ATGGAACAGTTCCGCCACTTGCCAATGCCTTTCCACTGG
ENSG00000166888:ENST0000055615 -----------ATGGAACAGTTCCGCCACTTGCCAATGCCTTTCCACTGG
ENSG00000166888:ENST0000045407 -----------ATGGAACAGTTCCGCCACTTGCCAATGCCTTTCCACTGG
ENSG00000166888:ENST0000053891 -----------ATGGAACAGTTCCGCCACTTGCCAATGCCTTTCCACTGG
ENSG00000166888:ENST0000053721 -----------ATGGAACAGTTCCGCCACTTGCCAATGCCTTTCCACTGG
ENSG00000166888:ENST0000053520 -----------ATGGAACAGTTCCGCCACTTGCCAATGCCTTTCCACTGG
isotig46679 AGAGAAATGTGGAACACAAAGTGGCTGCCATTAAAAACAGTGTGCAGATG
isotig12565 AGCAGATGCTGGAGCAGCATCTTCAGGATGTCCGGAAACGTGTGCAGGAT
isotig12566 AGCAGATGCTGGAGCAGCATCTTCAGGATGTCCGGAAACGTGTGCAGGAT
ENSG00000166888:ENST0000030013 AAGCAGGAAGAACTCAAGTTTAAGACAGGCTTGCGG---AGGCTGCAGCA
ENSG00000166888:ENST0000054387 AAGCAGGAAGAACTCAAGTTTAAGACAGGCTTGCGG---AGGCTGCAGCA
ENSG00000166888:ENST0000055615 AAGCAGGAAGAACTCAAGTTTAAGACAGGCTTGCGG---AGGCTGCAGCA
ENSG00000166888:ENST0000045407 AAGCAGGAAGAACTCAAGTTTAAGACAGGCTTGCGG---AGGCTGCAGCA
ENSG00000166888:ENST0000053891 AAGCAGGAAGAACTCAAGTTTAAGACAGGCTTGCGG---AGGCTGCAGCA
ENSG00000166888:ENST0000053721 AAGCAGGAAGAACTCAAGTTTAAGACAGGCTTGCGG---AGGCTGCAGCA
ENSG00000166888:ENST0000053520 AAGCAGGAAGAACTCAAGTTTAAGACAGGCTTGCGG---AGGCTGCAGCA
isotig46679 ACAGAACAAGACACCAAATACTTGGAAGATCTGCAAGATGAATTTGACTA
isotig12565 CTAGAACAGAAAATGAAAGTGGTAGAGAATCTCCAGGATGACTTTGATTT
isotig12566 CTAGAACAGAAAATGAAAGTGGTAGAGAATCTCCAGGATGACTTTGATTT
ENSG00000166888:ENST0000030013 CCGAGTAGGGGAGATCCACCTTCTCCGAGAAGCCCTGCAGAAGGGGGCTG
ENSG00000166888:ENST0000054387 CCGAGTAGGGGAGATCCACCTTCTCCGAGAAGCCCTGCAGAAGGGGGCTG
ENSG00000166888:ENST0000055615 CCGAGTAGGGGAGATCCACCTTCTCCGAGAAGCCCTGCAGAAGGGGGCTG
ENSG00000166888:ENST0000045407 CCGAGTAGGGGAGATCCACCTTCTCCGAGAAGCCCTGCAGAAGGGGGCTG
ENSG00000166888:ENST0000053891 CCGAGTAGGGGAGATCCACCTTCTCCGAGAAGCCCTGCAGAAGGGGGCTG
ENSG00000166888:ENST0000053721 CCGAGTAGGGGAGATCCACCTTCTCCGAGAAGCCCTGCAGAAGGGGGCTG
ENSG00000166888:ENST0000053520 CCGAGTAGGGGAGATCCACCTTCTCCGAGAAGCCCTGCAGAAGGGGGCTG
isotig46679 CAGGTATAAAACAATTCAGACA------------ATGGACCAGGGTGACA
isotig12565 CAACTATAAAACCCTCAAGAGTCAAGGAGACATGCAGGATCTGAATGGAA
isotig12566 CAACTATAAAACCCTCAAGAGTCAAGGAGACATGCAGGATCTGAATGGAA
ENSG00000166888:ENST0000030013 AGGCTGGCCAAGTGTCTCTGCACAGCTTGATAGAAACTCCTGCTAATGGG
ENSG00000166888:ENST0000054387 AGGCTGGCCAAGTGTCTCTGCACAGCTTGATAGAAACTCCTGCTAATGGG
ENSG00000166888:ENST0000055615 AGGCTGGCCAAGTGTCTCTGCACAGCTTGATAGAAACTCCTGCTAATGGG
ENSG00000166888:ENST0000045407 AGGCTGGCCAAGTGTCTCTGCACAGCTTGATAGAAACTCCTGCTAATGGG
ENSG00000166888:ENST0000053891 AGGCTGGCCAAGTGTCTCTGCACAGCTTGATAGAAACTCCTGCTAATGGG
ENSG00000166888:ENST0000053721 AGGCTGGCCAAGTGTCTCTGCACAGCTTGATAGAAACTCCTGCTAATGGG
ENSG00000166888:ENST0000053520 AGGCTGGCCAAGTGTCTCTGCACAGCTTGATAGAAACTCCTGCTAATGGG
isotig46679 AGAATAGCATCCTAATGAACCAGGAGGTTTTGACACTCCAAGAAATGCTT
isotig12565 ACAACCAGTCTGTGACCAGGCAGAAGATGCAGCAGCTGGAACAGATGCTC
isotig12566 ACAACCAGTCTGTGACCAGGCAGAAGATGCAGCAGCTGGAACAGATGCTC
ENSG00000166888:ENST0000030013 ACTGGGCCAAGTGAGGCCCTGGCCATGCTACTGCAGGAGACCACTGGAGA
ENSG00000166888:ENST0000054387 ACTGGGCCAAGTGAGGCCCTGGCCATGCTACTGCAGGAGACCACTGGAGA
ENSG00000166888:ENST0000055615 ACTGGGCCAAGTGAGGCCCTGGCCATGCTACTGCAGGAGACCACTGGAGA
ENSG00000166888:ENST0000045407 ACTGGGCCAAGTGAGGCCCTGGCCATGCTACTGCAGGAGACCACTGGAGA
ENSG00000166888:ENST0000053891 ACTGGGCCAAGTGAGGCCCTGGCCATGCTACTGCAGGAGACCACTGGAGA
ENSG00000166888:ENST0000053721 ACTGGGCCAAGTGAGGCCCTGGCCATGCTACTGCAGGAGACCACTGGAGA
ENSG00000166888:ENST0000053520 ACTGGGCCAAGTGAGGCCCTGGCCATGCTACTGCAGGAGACCACTGGAGA
isotig46679 AATAGCCTGGACTTCAAGAGAAAGGAAGCACTCACTAAGATGACACAGAT
isotig12565 ACGGCGCTGGACCAGATGCGGAGAAGCATTGTGAGTGAGCTGGCGGGGCT
isotig12566 ACGGCGCTGGACCAGATGCGGAGAAGCATTGTGAGTGAGCTGGCGGGGCT
ENSG00000166888:ENST0000030013 GCTAGAGGCAGCC------------AAAGCCCTAGTGCTGAAGAGGATCC
ENSG00000166888:ENST0000054387 GCTAGAGGCAGCC------------AAAGCCCTAGTGCTGAAGAGGATCC
ENSG00000166888:ENST0000055615 GCTAGAGGCAGCC------------AAAGCCCTAGTGCTGAAGAGGATCC
ENSG00000166888:ENST0000045407 GCTAGAGGCAGCC------------AAAGCCCTAGTGCTGAAGAGGATCC
ENSG00000166888:ENST0000053891 GCTAGAGGCAGCC------------AAAGCCCTAGTGCTGAAGAGGATCC
ENSG00000166888:ENST0000053721 GCTAGAGGCAGCC------------AAAGCCCTAGTGCTGAAGAGGATCC
ENSG00000166888:ENST0000053520 GCTAGAGGCAGCC------------AAAGCCCTAGTGCTGAAGAGGATCC
isotig46679 AGTGAACGAGTCGGACCTGCTGATGAGCAGCATGCTCATAGAAGAGCTGC
isotig12565 TTTGTCGGCAATGGAGTACGTGCAGAAAACACTCACAGACGAGGAGCTGG
isotig12566 TTTGTCGGCAATGGAGTACGTGCAGAAAACACTCACAGACGAGGAGCTGG
ENSG00000166888:ENST0000030013 AGATTTGGAAACGGCAGCAGCAGCTGGCAGGGAATGGCGCACCGTTTGAG
ENSG00000166888:ENST0000054387 AGATTTGGAAACGGCAGCAGCAGCTGGCAGGGAATGGCGCACCGTTTGAG
ENSG00000166888:ENST0000055615 AGATTTGGAAACGGCAGCAGCAGCTGGCAGGGAATGGCGCACCGTTTGAG
ENSG00000166888:ENST0000045407 AGATTTGGAAACGGCAGCAGCAGCTGGCAGGGAATGGCGCACCGTTTGAG
ENSG00000166888:ENST0000053891 AGATTTGGAAACGGCAGCAGCAGCTGGCAGGGAATGGCGCACCGTTTGAG
ENSG00000166888:ENST0000053721 AGATTTGGAAACGGCAGCAGCAGCTGGCAGGGAATGGCGCACCGTTTGAG
ENSG00000166888:ENST0000053520 AGATTTGGAAACGGCAGCAGCAGCTGGCAGGGAATGGCGCACCGTTTGAG
isotig46679 AGGACTGGAAGAGGAGGCAGCAGATCGCCTGCATCGGTGGCCCACTCCAC
isotig12565 CTGACTGGAAGAGGCGGCAGCAGATCGCGTGCATTGGAGGCCCTCCCAAC
isotig12566 CTGACTGGAAGAGGCGGCAGCAGATCGCGTGCATTGGAGGCCCTCCCAAC
ENSG00000166888:ENST0000030013 GAGAGCCTGGCCCCACTCCAGGAGAGGTGTGAAAGCCTGGTGGACATTTA
ENSG00000166888:ENST0000054387 GAGAGCCTGGCCCCACTCCAGGAGAGGTGTGAAAGCCTGGTGGACATTTA
ENSG00000166888:ENST0000055615 GAGAGCCTGGCCCCACTCCAGGAGAGGTGTGAAAGCCTGGTGGACATTTA
ENSG00000166888:ENST0000045407 GAGAGCCTGGCCCCACTCCAGGAGAGGTGTGAAAGCCTGGTGGACATTTA
ENSG00000166888:ENST0000053891 GAGAGCCTGGCCCCACTCCAGGAGAGGTGTGAAAGCCTGGTGGACATTTA
ENSG00000166888:ENST0000053721 GAGAGCCTGGCCCCACTCCAGGAGAGGTGTGAAAGCCTGGTGGACATTTA
ENSG00000166888:ENST0000053520 GAGAGCCTGGCCCCACTCCAGGAGAGGTGTGAAAGCCTGGTGGACATTTA
isotig46679 AACGGGCTGGACCAGCTTCAGAACTGCTTTACCCTGTTGGCAGAAAGTCT
isotig12565 ATCTGCCTGGATCGCCTGGAAAACTGGATAACTTCGTTAGCAGAATCTCA
isotig12566 ATCTGCCTGGATCGCCTGGAAAACTGGATAACTTCGTTAGCAGAATCTCA
ENSG00000166888:ENST0000030013 TTCCCAGCTACAGCAGGAGGTAGGG-------------------------
ENSG00000166888:ENST0000054387 TTCCCAGCTACAGCAGGAGGTAGGG-------------------------
ENSG00000166888:ENST0000055615 TTCCCAGCTACAGCAGGAGGTAGGG-------------------------
ENSG00000166888:ENST0000045407 TTCCCAGCTACAGCAGGAGGTAGGG-------------------------
ENSG00000166888:ENST0000053891 TTCCCAGCTACAGCAGGAGGTAGGG-------------------------
ENSG00000166888:ENST0000053721 TTCCCAGCTACAGCAGGAGGTAGGG-------------------------
ENSG00000166888:ENST0000053520 TTCCCAGCTACAGCAGGAGGTAGGG-------------------------
isotig46679 TTTCCAACTCAGACGACAGCTGGAGAAATTAGAGGAGCAGTCTTCCAAGA
isotig12565 ACTTCAGACCCGCCAACAAATTAAGAAACTGGAGGAGCTACAGCAGAAGG
isotig12566 ACTTCAGACCCGCCAACAAATTAAGAAACTGGAGGAGCTACAGCAGAAGG
ENSG00000166888:ENST0000030013 --GCGGCTGGTGGGGAGCTTGAGCCCAAGACCCGGGCATCGCTGACTGGC
ENSG00000166888:ENST0000054387 --GCGGCTGGTGGGGAGCTTGAGCCCAAGACCCGGGCATCGCTGACTGGC
ENSG00000166888:ENST0000055615 --GCGGCTGGTGGGGAGCTTGAGCCCAAGACCCGGGCATCGCTGACTGGC
ENSG00000166888:ENST0000045407 --GCGGCTGGTGGGGAGCTTGAGCCCAAGACCCGGGCATCGCTGACTGGC
ENSG00000166888:ENST0000053891 --GCGGCTGGTGGGGAGCTTGAGCCCAAGACCCGGGCATCGCTGACTGGC
ENSG00000166888:ENST0000053721 --GCGGCTGGTGGGGAGCTTGAGCCCAAGACCCGGGCATCGCTGACTGGC
ENSG00000166888:ENST0000053520 --GCGGCTGGTGGGGAGCTTGAGCCCAAGACCCGGGCATCGCTGACTGGC
isotig46679 TGACTTACGAAGGAGACCCCATCCCCACGCAGAGAGCACACCTGCTGGAG
isotig12565 TGTCCTACAAGGGGGACCCCATTGTGCAGCACCGGCCGATGCTGGAGGAG
isotig12566 TGTCCTACAAGGGGGACCCCATTGTGCAGCACCGGCCGATGCTGGAGGAG
ENSG00000166888:ENST0000030013 CGGCTGGATGAAGTCCTGAGAACCCTCGTCACCAGTTGCTTCCTGGTGGA
ENSG00000166888:ENST0000054387 CGGCTGGATGAAGTCCTGAGAACCCTCGTCACCAGTTGCTTCCTGGTGGA
ENSG00000166888:ENST0000055615 CGGCTGGATGAAGTCCTGAGAACCCTCGTCACCAGTTGCTTCCTGGTGGA
ENSG00000166888:ENST0000045407 CGGCTGGATGAAGTCCTGAGAACCCTCGTCACCAGTTGCTTCCTGGTGGA
ENSG00000166888:ENST0000053891 CGGCTGGATGAAGTCCTGAGAACCCTCGTCACCAGTTGCTTCCTGGTGGA
ENSG00000166888:ENST0000053721 CGGCTGGATGAAGTCCTGAGAACCCTCGTCACCAGTTGCTTCCTGGTGGA
ENSG00000166888:ENST0000053520 CGGCTGGATGAAGTCCTGAGAACCCTCGTCACCAGTTGCTTCCTGGTGGA
isotig46679 AGAGCCACCTTCCTGATCTACAACCTTTTCAAGAACTCATTTGTGGTTGA
isotig12565 CGGATCGTGGAGCTGTTCAGAAACTTGATGAAGAGTGCCTTCGTGGTGGA
isotig12566 CGGATCGTGGAGCTGTTCAGAAACTTGATGAAGAGTGCCTTCGTGGTGGA
ENSG00000166888:ENST0000030013 GAAGCAGCCC------------------------CCCCAGGTACTGAAGA
ENSG00000166888:ENST0000054387 GAAGCAGCCC------------------------CCCCAGGTACTGAAGA
ENSG00000166888:ENST0000055615 GAAGCAGCCC------------------------CCCCAGGTACTGAAGA
ENSG00000166888:ENST0000045407 GAAGCAGCCC------------------------CCCCAGGTACTGAAGA
ENSG00000166888:ENST0000053891 GAAGCAGCCC------------------------CCCCAGGTACTGAAGA
ENSG00000166888:ENST0000053721 GAAGCAGCCC------------------------CCCCAGGTACTGAAGA
ENSG00000166888:ENST0000053520 GAAGCAGCCC------------------------CCCCAGGTACTGAAGA
isotig46679 GCGACAGCCCTGCATGCCAACACACCCTCAGAGGCCGCTGGTACTCAAAA
isotig12565 GCGACAGCCCTGCATGCCGATGCACCCCGACCGGCCCTTGGTCATCAAGA
isotig12566 GCGACAGCCCTGCATGCCGATGCACCCCGACCGGCCCTTGGTCATCAAGA
ENSG00000166888:ENST0000030013 CTCAGACCAAGTTCCAGGCTGGAGTTCGATTCCTGTTGGGCTTGAGGTTC
ENSG00000166888:ENST0000054387 CTCAGACCAAGTTCCAGGCTGGAGTTCGATTCCTGTTGGGCTTGAGGTTC
ENSG00000166888:ENST0000055615 CTCAGACCAAGTTCCAGGCTGGAGTTCGATTCCTGTTGGGCTTGAGGTTC
ENSG00000166888:ENST0000045407 CTCAGACCAAGTTCCAGGCTGGAGTTCGATTCCTGTTGGGCTTGAGGTTC
ENSG00000166888:ENST0000053891 CTCAGACCAAGTTCCAGGCTGGAGTTCGATTCCTGTTGGGCTTGAGGTTC
ENSG00000166888:ENST0000053721 CTCAGACCAAGTTCCAGGCTGGAGTTCGATTCCTGTTGGGCTTGAGGTTC
ENSG00000166888:ENST0000053520 CTCAGACCAAGTTCCAGGCTGGAGTTCGATTCCTGTTGGGCTTGAGGTTC
isotig46679 CCCTCATTCAGTTCACCGCGAAACTGAGACTACTAATAAAATTG------
isotig12565 CTGGTGTCCAGTTCACTACTAAAGTCAGGTTGTTGGTCAAGTTT------
isotig12566 CTGGTGTCCAGTTCACTACTAAAGTCAGGTTGTTGGTCAAGTTT------
ENSG00000166888:ENST0000030013 CTGGGGGCCCCAGCCAAGCCTCCGCTGGTCAGGGCCGACATGGTGACAGA
ENSG00000166888:ENST0000054387 CTGGGGGCCCCAGCCAAGCCTCCGCTGGTCAGGGCCGACATGGTGACAGA
ENSG00000166888:ENST0000055615 CTGGGGGCCCCAGCCAAGCCTCCGCTGGTCAGGGCCGACATGGTGACAGA
ENSG00000166888:ENST0000045407 CTGGGGGCCCCAGCCAAGCCTCCGCTGGTCAGGGCCGACATGGTGACAGA
ENSG00000166888:ENST0000053891 CTGGGGGCCCCAGCCAAGCCTCCGCTGGTCAGGGCCGACATGGTGACAGA
ENSG00000166888:ENST0000053721 CTGGGGGCCCCAGCCAAGCCTCCGCTGGTCAGGGCCGACATGGTGACAGA
ENSG00000166888:ENST0000053520 CTGGGGGCCCCAGCCAAGCCTCCGCTGGTCAGGGCCGACATGGTGACAGA
isotig46679 ---------CCGGAACTCAACTATCAGGTGAAAGTAAAGGCATCGATCGA
isotig12565 ---------CCCGAGTTGAATTATCAGCTTAAAATTAAAGTGTGCATTGA
isotig12566 ---------CCCGAGTTGAATTATCAGCTTAAAATTAAAGTGTGCATTGA
ENSG00000166888:ENST0000030013 GAAGCAGGCGCGGGAGCTGAGTGTGCCTCAGGGTCCTGGGGCTGGAGCAG
ENSG00000166888:ENST0000054387 GAAGCAGGCGCGGGAGCTGAGTGTGCCTCAGGGTCCTGGGGCTGGAGCAG
ENSG00000166888:ENST0000055615 GAAGCAGGCGCGGGAGCTGAGTGTGCCTCAGGGTCCTGGGGCTGGAGCAG
ENSG00000166888:ENST0000045407 GAAGCAGGCGCGGGAGCTGAGTGTGCCTCAGGGTCCTGGGGCTGGAGCAG
ENSG00000166888:ENST0000053891 GAAGCAGGCGCGGGAGCTGAGTGTGCCTCAGGGTCCTGGGGCTGGAGCAG
ENSG00000166888:ENST0000053721 GAAGCAGGCGCGGGAGCTGAGTGTGCCTCAGGGTCCTGGGGCTGGAGCAG
ENSG00000166888:ENST0000053520 GAAGCAGGCGCGGGAGCTGAGTGTGCCTCAGGGTCCTGGGGCTGGAGCAG
isotig46679 CAAGAATGTTTCAACGCTAAGC------------AATAGAAGATTTGTGC
isotig12565 CAAAGATTCTGGGGACGTTGCTGCTCTCAGAGGATCTCGGAAATTTAACA
isotig12566 CAAAGATTCTGGGGACGTTGCTGCTCTCAGAGGATCTCGGAAATTTAACA
ENSG00000166888:ENST0000030013 AAAGCACTGGAGAAATCATCAACAACACTGTGCCCTTGGAGAACAGCATT
ENSG00000166888:ENST0000054387 AAAGCACTGGAGAAATCATCAACAACACTGTGCCCTTGGAGAACAGCATT
ENSG00000166888:ENST0000055615 AAAGCACTGGAGAAATCATCAACAACACTGTGCCCTTGGAGAACAGCATT
ENSG00000166888:ENST0000045407 AAAGCACTGGAGAAATCATCAACAACACTGTGCCCTTGGAGAACAGCATT
ENSG00000166888:ENST0000053891 AAAGCACTGGAGAAATCATCAACAACACTGTGCCCTTGGAGAACAGCATT
ENSG00000166888:ENST0000053721 AAAGCACTGGAGAAATCATCAACAACACTGTGCCCTTGGAGAACAGCATT
ENSG00000166888:ENST0000053520 AAAGCACTGGAGAAATCATCAACAACACTGTGCCCTTGGAGAACAGCATT
isotig46679 TTTGTGGAACTCAAGTC------AAAGCCATGTCCATCGAGGAATCCTCC
isotig12565 TTCTGGGCACAAACACG------AAGGTGATGAACATGGAAGAATCCAAC
isotig12566 TTCTGGGCACAAACACG------AAGGTGATGAACATGGAAGAATCCAAC
ENSG00000166888:ENST0000030013 CCTGGGAACTGCTGCTCTGCCCTGTTCAAGAACCTGCTTCTCAAGAAGAT
ENSG00000166888:ENST0000054387 CCTGGGAACTGCTGCTCTGCCCTGTTCAAGAACCTGCTTCTCAAGAAGAT
ENSG00000166888:ENST0000055615 CCTGGGAACTGCTGCTCTGCCCTGTTCAAGAACCTGCTTCTCAAGAAGAT
ENSG00000166888:ENST0000045407 CCTGGGAACTGCTGCTCTGCCCTGTTCAAGAACCTGCTTCTCAAGAAGAT
ENSG00000166888:ENST0000053891 CCTGGGAACTGCTGCTCTGCCCTGTTCAAGAACCTGCTTCTCAAGAAGAT
ENSG00000166888:ENST0000053721 CCTGGGAACTGCTGCTCTGCCCTGTTCAAGAACCTGCTTCTCAAGAAGAT
ENSG00000166888:ENST0000053520 CCTGGGAACTGCTGCTCTGCCCTGTTCAAGAACCTGCTTCTCAAGAAGAT
isotig46679 AATGGGAGCCTCTCAGTAGAA---TTTAGACATTTGCAACCGAAGGAAAT
isotig12565 AACGGCAGCCTGTCTGCGGAG---TTCAAGCACTTGACCCTGAGGGAGCA
isotig12566 AACGGCAGCCTGTCTGCGGAG---TTCAAGCACTTGACCCTGAGGGAGCA
ENSG00000166888:ENST0000030013 CAAG---------------CGGTGTGAGCGGAAGGGCACTGAGTCTGTCA
ENSG00000166888:ENST0000054387 CAAG---------------CGGTGTGAGCGGAAGGGCACTGAGTCTGTCA
ENSG00000166888:ENST0000055615 CAAG---------------CGGTGTGAGCGGAAGGGCACTGAGTCTGTCA
ENSG00000166888:ENST0000045407 CAAG---------------CGGTGTGAGCGGAAGGGCACTGAGTCTGTCA
ENSG00000166888:ENST0000053891 CAAG---------------CGGTGTGAGCGGAAGGGCACTGAGTCTGTCA
ENSG00000166888:ENST0000053721 CAAG---------------CGGTGTGAGCGGAAGGGCACTGAGTCTGTCA
ENSG00000166888:ENST0000053520 CAAG---------------CGGTGTGAGCGGAAGGGCACTGAGTCTGTCA
isotig46679 GAAATCCAGTGCCGGAAGTAAAGGAAAT---GAGGGCTGCCACATGGTGA
isotig12565 GAGATGTGGGAATGGAGGCCGTGCCAATTGTGATGCCTCCTTGATTGTGA
isotig12566 GAGATGTGGGAATGGAGGCCGTGCCAATTGTGATGCCTCCTTGATTGTGA
ENSG00000166888:ENST0000030013 CAGAGGAGAAGTGCGCTGTGCTCTTCTCTGCCAGCTTCACACTTGGCCCC
ENSG00000166888:ENST0000054387 CAGAGGAGAAGTGCGCTGTGCTCTTCTCTGCCAGCTTCACACTTGGCCCC
ENSG00000166888:ENST0000055615 CAGAGGAGAAGTGCGCTGTGCTCTTCTCTGCCAGCTTCACACTTGGCCCC
ENSG00000166888:ENST0000045407 CAGAGGAGAAGTGCGCTGTGCTCTTCTCTGCCAGCTTCACACTTGGCCCC
ENSG00000166888:ENST0000053891 CAGAGGAGAAGTGCGCTGTGCTCTTCTCTGCCAGCTTCACACTTGGCCCC
ENSG00000166888:ENST0000053721 CAGAGGAGAAGTGCGCTGTGCTCTTCTCTGCCAGCTTCACACTTGGCCCC
ENSG00000166888:ENST0000053520 CAGAGGAGAAGTGCGCTGTGCTCTTCTCTGCCAGCTTCACACTTGGCCCC
isotig46679 CGGAAGAGCTGCATTCCATAGCCTTTGAGACCCAGATCTGCCTC------
isotig12565 CCGAGGAGCTGCATCTGATCACCTTCGAGACTGAGGTGTACCAC------
isotig12566 CCGAGGAGCTGCATCTGATCACCTTCGAGACTGAGGTGTACCAC------
ENSG00000166888:ENST0000030013 GGCAAACTCCCCATCCAGCTCCAGGCCCTGTCTCTGCCCCTGGTGGTCAT
ENSG00000166888:ENST0000054387 GGCAAACTCCCCATCCAGCTCCAGGCCCTGTCTCTGCCCCTGGTGGTCAT
ENSG00000166888:ENST0000055615 GGCAAACTCCCCATCCAGCTCCAGGCCCTGTCTCTGCCCCTGGTGGTCAT
ENSG00000166888:ENST0000045407 GGCAAACTCCCCATCCAGCTCCAGGCCCTGTCTCTGCCCCTGGTGGTCAT
ENSG00000166888:ENST0000053891 GGCAAACTCCCCATCCAGCTCCAGGCCCTGTCTCTGCCCCTGGTGGTCAT
ENSG00000166888:ENST0000053721 GGCAAACTCCCCATCCAGCTCCAGGCCCTGTCTCTGCCCCTGGTGGTCAT
ENSG00000166888:ENST0000053520 GGCAAACTCCCCATCCAGCTCCAGGCCCTGTCTCTGCCCCTGGTGGTCAT
isotig46679 TATGGCCTCACCATCGACTTGGAGACAAGCTCATTACCTGTGGTGATGAT
isotig12565 CAAGGCCTCAAGATTGACCTGGAGACCCATTCTTTGCCAGTTGTGGTGAT
isotig12566 CAAGGCCTCAAGATTGACCTGGAGACCCATTCTTTGCCAGTTGTGGTGAT
ENSG00000166888:ENST0000030013 CGTCCATGGCAACCAAGACAACAATGCCAAAGCCACTATCCTGTGGGACA
ENSG00000166888:ENST0000054387 CGTCCATGGCAACCAAGACAACAATGCCAAAGCCACTATCCTGTGGGACA
ENSG00000166888:ENST0000055615 CGTCCATGGCAACCAAGACAACAATGCCAAAGCCACTATCCTGTGGGACA
ENSG00000166888:ENST0000045407 CGTCCATGGCAACCAAGACAACAATGCCAAAGCCACTATCCTGTGGGACA
ENSG00000166888:ENST0000053891 CGTCCATGGCAACCAAGACAACAATGCCAAAGCCACTATCCTGTGGGACA
ENSG00000166888:ENST0000053721 CGTCCATGGCAACCAAGACAACAATGCCAAAGCCACTATCCTGTGGGACA
ENSG00000166888:ENST0000053520 CGTCCATGGCAACCAAGACAACAATGCCAAAGCCACTATCCTGTGGGACA
isotig46679 TTCTAATGTCAGCCAACTGCCTAATGCTTGGGCATCCATCATTTGGTACA
isotig12565 CTCCAACATCTGTCAGATGCCAAATGCCTGGGCATCCATCCTGTGGTATA
isotig12566 CTCCAACATCTGTCAGATGCCAAATGCCTGGGCATCCATCCTGTGGTATA
ENSG00000166888:ENST0000030013 ATGCCTTCTCTGAG------ATGGACCGCGTGCCCTTTGTGGTGGCTGAG
ENSG00000166888:ENST0000054387 ATGCCTTCTCTGAG------ATGGACCGCGTGCCCTTTGTGGTGGCTGAG
ENSG00000166888:ENST0000055615 ATGCCTTCTCTGAG------ATGGACCGCGTGCCCTTTGTGGTGGCTGAG
ENSG00000166888:ENST0000045407 ATGCCTTCTCTGAG------ATGGACCGCGTGCCCTTTGTGGTGGCTGAG
ENSG00000166888:ENST0000053891 ATGCCTTCTCTGAG------ATGGACCGCGTGCCCTTTGTGGTGGCTGAG
ENSG00000166888:ENST0000053721 ATGCCTTCTCTGAG------ATGGACCGCGTGCCCTTTGTGGTGGCTGAG
ENSG00000166888:ENST0000053520 ATGCCTTCTCTGAG------ATGGACCGCGTGCCCTTTGTGGTGGCTGAG
isotig46679 ATGTGTCAACCAACGATTGCCAGAACTTGGTTTTCTTTAATAATCCTCCG
isotig12565 ACATGCTGACCAACAACCCCAAGAACGTGAACTTCTTCACCAAGCCACCA
isotig12566 ACATGCTGACCAACAACCCCAAGAACGTGAACTTCTTCACCAAGCCACCA
ENSG00000166888:ENST0000030013 CGGGTGCCCTGGGAGAAGATGTGTGAAACTCTGAACCTGAAGTTCATGGC
ENSG00000166888:ENST0000054387 CGGGTGCCCTGGGAGAAGATGTGTGAAACTCTGAACCTGAAGTTCATGGC
ENSG00000166888:ENST0000055615 CGGGTGCCCTGGGAGAAGATGTGTGAAACTCTGAACCTGAAGTTCATGGC
ENSG00000166888:ENST0000045407 CGGGTGCCCTGGGAGAAGATGTGTGAAACTCTGAACCTGAAGTTCATGGC
ENSG00000166888:ENST0000053891 CGGGTGCCCTGGGAGAAGATGTGTGAAACTCTGAACCTGAAGTTCATGGC
ENSG00000166888:ENST0000053721 CGGGTGCCCTGGGAGAAGATGTGTGAAACTCTGAACCTGAAGTTCATGGC
ENSG00000166888:ENST0000053520 CGGGTGCCCTGGGAGAAGATGTGTGAAACTCTGAACCTGAAGTTCATGGC
isotig46679 CCTGTCACTTTGAGTCAACTCCTGGAAGTGATGAGCTGGCAGTTTTCATC
isotig12565 ATCGGAACCTGGGACCAGGTGGCCGAGGTGCTCAGCTGGCAGTTCTCATC
isotig12566 ATCGGAACCTGGGACCAGGTGGCCGAGGTGCTCAGCTGGCAGTTCTCATC
ENSG00000166888:ENST0000030013 TGAGGTGGGGACCAACCGGGGGCTGCTCCCAGAGCACTTCCTCTTCCTGG
ENSG00000166888:ENST0000054387 TGAGGTGGGGACCAACCGGGGGCTGCTCCCAGAGCACTTCCTCTTCCTGG
ENSG00000166888:ENST0000055615 TGAGGTGGGGACCAACCGGGGGCTGCTCCCAGAGCACTTCCTCTTCCTGG
ENSG00000166888:ENST0000045407 TGAGGTGGGGACCAACCGGGGGCTGCTCCCAGAGCACTTCCTCTTCCTGG
ENSG00000166888:ENST0000053891 TGAGGTGGGGACCAACCGGGGGCTGCTCCCAGAGCACTTCCTCTTCCTGG
ENSG00000166888:ENST0000053721 TGAGGTGGGGACCAACCGGGGGCTGCTCCCAGAGCACTTCCTCTTCCTGG
ENSG00000166888:ENST0000053520 TGAGGTGGGGACCAACCGGGGGCTGCTCCCAGAGCACTTCCTCTTCCTGG
isotig46679 CTATGTTGGT------CGTGGCCTTAATTCAGACCAGCTCAACATGCTGG
isotig12565 CACCACAAAG------CGAGGGCTGAGCATCGAGCAGCTGACTACGCTGG
isotig12566 CACCACAAAG------CGAGGGCTGAGCATCGAGCAGCTGACTACGCTGG
ENSG00000166888:ENST0000030013 CCCAGAAGATCTTCAATGACAACAGCCTCAGTATGGAGGCCTTCCAGCAC
ENSG00000166888:ENST0000054387 CCCAGAAGATCTTCAATGACAACAGCCTCAGTATGGAGGCCTTCCAGCAC
ENSG00000166888:ENST0000055615 CCCAGAAGATCTTCAATGACAACAGCCTCAGTATGGAGGCCTTCCAGCAC
ENSG00000166888:ENST0000045407 CCCAGAAGATCTTCAATGACAACAGCCTCAGTATGGAGGCCTTCCAGCAC
ENSG00000166888:ENST0000053891 CCCAGAAGATCTTCAATGACAACAGCCTCAGTATGGAGGCCTTCCAGCAC
ENSG00000166888:ENST0000053721 CCCAGAAGATCTTCAATGACAACAGCCTCAGTATGGAGGCCTTCCAGCAC
ENSG00000166888:ENST0000053520 CCCAGAAGATCTTCAATGACAACAGCCTCAGTATGGAGGCCTTCCAGCAC
isotig46679 CAGAGAAGCTCACAGTTCAGTCT---------------AACTACAGCGAT
isotig12565 CCGAGAAGCTCCTAGGACCTGGTGTC------------AACTACTCCGGG
isotig12566 CCGAGAAGCTCCTAGGACCTGGTGTC------------AACTACTCCGGG
ENSG00000166888:ENST0000030013 CGTTCTGTGTCCTGGTCGCAGTTCAACAAGGAGATCCTGCTGGGCCGTGG
ENSG00000166888:ENST0000054387 CGTTCTGTGTCCTGGTCGCAGTTCAACAAGGAGATCCTGCTGGGCCGTGG
ENSG00000166888:ENST0000055615 CGTTCTGTGTCCTGGTCGCAGTTCAACAAGGAGATCCTGCTGGGCCGTGG
ENSG00000166888:ENST0000045407 CGTTCTGTGTCCTGGTCGCAGTTCAACAAGGAGATCCTGCTGGGCCGTGG
ENSG00000166888:ENST0000053891 CGTTCTGTGTCCTGGTCGCAGTTCAACAAGGAGATCCTGCTGGGCCGTGG
ENSG00000166888:ENST0000053721 CGTTCTGTGTCCTGGTCGCAGTTCAACAAGGAGATCCTGCTGGGCCGTGG
ENSG00000166888:ENST0000053520 CGTTCTGTGTCCTGGTCGCAGTTCAACAAGGAGATCCTGCTGGGCCGTGG
isotig46679 GGTCACCTCACCTGGGCCAAGTTCTGCAAGGAACACTTGCCTGGCAAACC
isotig12565 TGTCAGATCACATGGGCTAAATTTTGCAAAGAAAACATGGCTGGCAAGGG
isotig12566 TGTCAGATCACATGGGCTAAATTTTGCAAAGAAAACATGGCTGGCAAGGG
ENSG00000166888:ENST0000030013 CTTCACCTTTTGGCAGTGGTTTGATGGTGTCCTGGACCTCACCAAACGCT
ENSG00000166888:ENST0000054387 CTTCACCTTTTGGCAGTGGTTTGATGGTGTCCTGGACCTCACCAAACGCT
ENSG00000166888:ENST0000055615 CTTCACCTTTTGGCAGTGGTTTGATGGTGTCCTGGACCTCACCAAACGCT
ENSG00000166888:ENST0000045407 CTTCACCTTTTGGCAGTGGTTTGATGGTGTCCTGGACCTCACCAAACGCT
ENSG00000166888:ENST0000053891 CTTCACCTTTTGGCAGTGGTTTGATGGTGTCCTGGACCTCACCAAACGCT
ENSG00000166888:ENST0000053721 CTTCACCTTTTGGCAGTGGTTTGATGGTGTCCTGGACCTCACCAAACGCT
ENSG00000166888:ENST0000053520 CTTCACCTTTTGGCAGTGGTTTGATGGTGTCCTGGACCTCACCAAACGCT
isotig46679 ATTTACCTTCTGGACCTGGCTTGAAGCAATATTGGACCTAATTAAAAAAC
isotig12565 CTTCTCCTTCTGGGTGTGGCTAGACAATATCATTGACCTTGTGAAAAAGT
isotig12566 CTTCTCCTTCTGGGTGTGGCTAGACAATATCATTGACCTTGTGAAAAAGT
ENSG00000166888:ENST0000030013 GTCTCCGGAGCTACTGGTCTGACCGGCTGATCATTGGCTTCATCAGCAAA
ENSG00000166888:ENST0000054387 GTCTCCGGAGCTACTGGTCTGACCGGCTGATCATTGGCTTCATCAGCAAA
ENSG00000166888:ENST0000055615 GTCTCCGGAGCTACTGGTCTGACCGGCTGATCATTGGCTTCATCAGCAAA
ENSG00000166888:ENST0000045407 GTCTCCGGAGCTACTGGTCTGACCGGCTGATCATTGGCTTCATCAGCAAA
ENSG00000166888:ENST0000053891 GTCTCCGGAGCTACTGGTCTGACCGGCTGATCATTGGCTTCATCAGCAAA
ENSG00000166888:ENST0000053721 GTCTCCGGAGCTACTGGTCTGACCGGCTGATCATTGGCTTCATCAGCAAA
ENSG00000166888:ENST0000053520 GTCTCCGGAGCTACTGGTCTGACCGGCTGATCATTGGCTTCATCAGCAAA
isotig46679 ACATTCTTCCCCTCTGGATTGATGGGTACATCATGGGCTTCGTGAGCAAA
isotig12565 ATATCTTGGCCCTCTGGAATGAAGGGTACATCATGGGCTTCATTAGCAAG
isotig12566 ATATCTTGGCCCTCTGGAATGAAGGGTACATCATGGGCTTCATTAGCAAG
ENSG00000166888:ENST0000030013 CAGTACGTTACTAGCCTTCTTCTCAATGAGCCCGACGGAACCTTTCTCCT
ENSG00000166888:ENST0000054387 CAGTACGTTACTAGCCTTCTTCTCAATGAGCCCGACGGAACCTTTCTCCT
ENSG00000166888:ENST0000055615 CAGTACGTTACTAGCCTTCTTCTCAATGAGCCCGACGGAACCTTTCTCCT
ENSG00000166888:ENST0000045407 CAGTACGTTACTAGCCTTCTTCTCAATGAGCCCGACGGAACCTTTCTCCT
ENSG00000166888:ENST0000053891 CAGTACGTTACTAGCCTTCTTCTCAATGAGCCCGACGGAACCTTTCTCCT
ENSG00000166888:ENST0000053721 CAGTACGTTACTAGCCTTCTTCTCAATGAGCCCGACGGAACCTTTCTCCT
ENSG00000166888:ENST0000053520 CAGTACGTTACTAGCCTTCTTCTCAATGAGCCCGACGGAACCTTTCTCCT
isotig46679 GAGAAGGAGAGGTTTCTGCTCAAGGATAAAATGCCCGGGACATTTTTGTT
isotig12565 GAGCGGGAGCGGGCGATCCTGAGCACGAAACCCCCGGGCACCTTCCTGCT
isotig12566 GAGCGGGAGCGGGCGATCCTGAGCACGAAACCCCCGGGCACCTTCCTGCT
ENSG00000166888:ENST0000030013 CCGCTTCAGCGAC---TCAGAGATTGGGGGCATCACCATTGCCCATGTCA
ENSG00000166888:ENST0000054387 CCGCTTCAGCGAC---TCAGAGATTGGGGGCATCACCATTGCCCATGTCA
ENSG00000166888:ENST0000055615 CCGCTTCAGCGAC---TCAGAGATTGGGGGCATCACCATTGCCCATGTCA
ENSG00000166888:ENST0000045407 CCGCTTCAGCGAC---TCAGAGATTGGGGGCATCACCATTGCCCATGTCA
ENSG00000166888:ENST0000053891 CCGCTTCAGCGAC---TCAGAGATTGGGGGCATCACCATTGCCCATGTCA
ENSG00000166888:ENST0000053721 CCGCTTCAGCGAC---TCAGAGATTGGGGGCATCACCATTGCCCATGTCA
ENSG00000166888:ENST0000053520 CCGCTTCAGCGAC---TCAGAGATTGGGGGCATCACCATTGCCCATGTCA
isotig46679 ACGATTCAGTGAG---AGCCATCTCGGAGGGATCACCTTCACCTGGGTGG
isotig12565 GAGATTCAGCGAGAGCAGCAAAGAAGGAGGGGTCACTTTCACTTGGGTGG
isotig12566 GAGATTCAGCGAGAGCAGCAAAGAAGGAGGGGTCACTTTCACTTGGGTGG
ENSG00000166888:ENST0000030013 TCCGGGGCCAGGATGGCTCTCCACAGATAGAGAACATCCAGCCATTCTCT
ENSG00000166888:ENST0000054387 TCCGGGGCCAGGATGGCTCTCCACAGATAGAGAACATCCAGCCATTCTCT
ENSG00000166888:ENST0000055615 TCCGGGGCCAGGATGGCTCTCCACAGATAGAGAACATCCAGCCATTCTCT
ENSG00000166888:ENST0000045407 TCCGGGGCCAGGATGGCTCTCCACAGATAGAGAACATCCAGCCATTCTCT
ENSG00000166888:ENST0000053891 TCCGGGGCCAGGATGGCTCTCCACAGATAGAGAACATCCAGCCATTCTCT
ENSG00000166888:ENST0000053721 TCCGGGGCCAGGATGGCTCTCCACAGATAGAGAACATCCAGCCATTCTCT
ENSG00000166888:ENST0000053520 TCCGGGGCCAGGATGGCTCTCCACAGATAGAGAACATCCAGCCATTCTCT
isotig46679 ACCACTCTGAAAACGGAGAAGTGAGATTCCACTCCGTAGAACCCTACAAC
isotig12565 AAAAGGACATCAGTGGCAAGACCCAGATCCAGTCTGTAGAGCCGTACACC
isotig12566 AAAAGGACATCAGTGGCAAGACCCAGATCCAGTCTGTAGAGCCGTACACC
ENSG00000166888:ENST0000030013 GCCAAAGACCTGTCCATTCGCTCACTGGGGGACCGAATCCGGGAT-----
ENSG00000166888:ENST0000054387 GCCAAAGACCTGTCCATTCGCTCACTGGGGGACCGAATCCGGGAT-----
ENSG00000166888:ENST0000055615 GCCAAAGACCTGTCCATTCGCTCACTGGGGGACCGAATCCGGGAT-----
ENSG00000166888:ENST0000045407 GCCAAAGACCTGTCCATTCGCTCACTGGGGGACCGAATCCGGGAT-----
ENSG00000166888:ENST0000053891 GCCAAAGACCTGTCCATTCGCTCACTGGGGGACCGAATCCGGGAT-----
ENSG00000166888:ENST0000053721 GCCAAAGACCTGTCCATTCGCTCACTGGGGGACCGAATCCGGGAT-----
ENSG00000166888:ENST0000053520 GCCAAAGACCTGTCCATTCGCTCACTGGGGGACCGAATCCGGGAT-----
isotig46679 AAAGGGCGTCTGTCGGCCCTGCCATTTGCTGACATCCTGCGGGACTACAA
isotig12565 AAGCAGCAGCTGAACAACATGTCCTTTGCTGAAATCATCATGGGCTACAA
isotig12566 AAGCAGCAGCTGAACAACATGTCCTTTGCTGAAATCATCATGGGCTACAA
ENSG00000166888:ENST0000030013 -------------------------CTTGCTCAGCTCAAAAATCTCTATC
ENSG00000166888:ENST0000054387 -------------------------CTTGCTCAGCTCAAAAATCTCTATC
ENSG00000166888:ENST0000055615 -------------------------CTTGCTCAGCTCAAAAATCTCTATC
ENSG00000166888:ENST0000045407 -------------------------CTTGCTCAGCTCAAAAATCTCTATC
ENSG00000166888:ENST0000053891 -------------------------CTTGCTCAGCTCAAAAATCTCTATC
ENSG00000166888:ENST0000053721 -------------------------CTTGCTCAGCTCAAAAATCTCTATC
ENSG00000166888:ENST0000053520 -------------------------CTTGCTCAGCTCAAAAATCTCTATC
isotig46679 GGTCATCATGGCTGAGAACATTCCCGAGAACCCTCTCAAGTACCTCTACC
isotig12565 GATCATGGATGCCACCAACATCCTGGTGTCCCCATTGGTCTACCTCTACC
isotig12566 GATCATGGATGCCACCAACATCCTGGTGTCCCCATTGGTCTACCTCTACC
ENSG00000166888:ENST0000030013 CCAAGAAGCCCAAGGATGAGGCTTTCCGGAGCCACTAC------------
ENSG00000166888:ENST0000054387 CCAAGAAGCCCAAGGATGAGGCTTTCCGGAGCCACTAC------------
ENSG00000166888:ENST0000055615 CCAAGAAGCCCAAGGATGAGGCTTTCCGGAGCCACTAC------------
ENSG00000166888:ENST0000045407 CCAAGAAGCCCAAGGATGAGGCTTTCCGGAGCCACTAC------------
ENSG00000166888:ENST0000053891 CCAAGAAGCCCAAGGATGAGGCTTTCCGGAGCCACTAC------------
ENSG00000166888:ENST0000053721 CCAAGAAGCCCAAGGATGAGGCTTTCCGGAGCCACTAC------------
ENSG00000166888:ENST0000053520 CCAAGAAGCCCAAGGATGAGGCTTTCCGGAGCCACTAC------------
isotig46679 CCGACATCCCCAAAGACAAAGCCTTCGGTAAACACTACAGCTCCCAGCCT
isotig12565 CTGACATTCCCAAGGAGGAGGCGTTCGGGAAGTACTGT------------
isotig12566 CTGACATTCCCAAGGAGGAGGCGTTCGGGAAGTACTGT------------
ENSG00000166888:ENST0000030013 ------------AAGCCTGAACAGATGGGTAAGGATGGCAGGGGTTATGT
ENSG00000166888:ENST0000054387 ------------AAGCCTGAACAGATGGGTAAGGATGGCAGGGGTTATGT
ENSG00000166888:ENST0000055615 ------------AAGCCTGAACAGATGGGTAAGGATGGCAGGGGTTATGT
ENSG00000166888:ENST0000045407 ------------AAGCCTGAACAGATGGGTAAGGATGGCAGGGGTTATGT
ENSG00000166888:ENST0000053891 ------------AAGCCTGAACAGATGGGTAAGGATGGCAGGGGTTATGT
ENSG00000166888:ENST0000053721 ------------AAGCCTGAACAGATGGGTAAGGATGGCAGGGGTTATGT
ENSG00000166888:ENST0000053520 ------------AAGCCTGAACAGATGGGTAAGGATGGCAGGGGTTATGT
isotig46679 TGCGAAGTTTCAAGGCCAACA------GAACGGGGAGACAAAGGTTATGT
isotig12565 ------------CGACCAGAG-----------------------------
isotig12566 ------------CGACCAGAG-----------------------------
ENSG00000166888:ENST0000030013 CCCAGCTACCATCAAGATGACCGTGGAAAGGGACCAACCACTTCCTACCC
ENSG00000166888:ENST0000054387 CCCAGCTACCATCAAGATGACCGTGGAAAGGGACCAACCACTTCCTACCC
ENSG00000166888:ENST0000055615 CCCAGCTACCATCAAGATGACCGTGGAAAGGGACCAACCACTTCCTACCC
ENSG00000166888:ENST0000045407 CCCAGCTACCATCAAGATGACCGTGGAAAGGGACCAACCACTTCCTACCC
ENSG00000166888:ENST0000053891 CCCAGCTACCATCAAGATGACCGTGGAAAGGGACCAACCACTTCCTACCC
ENSG00000166888:ENST0000053721 CCCAGCTACCATCAAGATGACCGTGGAAAGGGACCAACCACTTCCTACCC
ENSG00000166888:ENST0000053520 CCCAGCTACCATCAAGATGACCGTGGAAAGGGACCAACCACTTCCTACCC
isotig46679 TCCTTCAGTTTTTATCCCTATTTCAACAATCCGCAGCGACGCCATGGAGC
isotig12565 -------------------------------AGCCAGGAGCATCCTGAAG
isotig12566 -------------------------------AGCCAGGAGCATCCTGAAG
ENSG00000166888:ENST0000030013 CAGAGCTCCAGATGCCTACCATGGTGCCTTCTTATGACCTTGGAATGGCC
ENSG00000166888:ENST0000054387 CAGAGCTCCAGATGCCTACCATGGTGCCTTCTTATGACCTTGGAATGGCC
ENSG00000166888:ENST0000055615 CAGAGCTCCAGATGCCTACCATGGTGCCTTCTTATGACCTTGGAATGGCC
ENSG00000166888:ENST0000045407 CAGAGCTCCAGATGCCTACCATGGTGCCTTCTTATGACCTTGGAATGGCC
ENSG00000166888:ENST0000053891 CAGAGCTCCAGATGCCTACCATGGTGCCTTCTTATGACCTTGGAATGGCC
ENSG00000166888:ENST0000053721 CAGAGCTCCAGATGCCTACCATGGTGCCTTCTTATGACCTTGGAATGGCC
ENSG00000166888:ENST0000053520 CAGAGCTCCAGATGCCTACCATGGTGCCTTCTTATGACCTTGGAATGGCC
isotig46679 CGCAG------------------------------------------TCT
isotig12565 CTGAC---------------------------------------------
isotig12566 CTGAC---------------------------------------------
ENSG00000166888:ENST0000030013 CCTGATTCCTCCATGAGCATGCAGCTTGGCCCAGATATGGTGCCCCAGGT
ENSG00000166888:ENST0000054387 CCTGATTCCTCCATGAGCATGCAGCTTGGCCCAGATATGGTGCCCCAGGT
ENSG00000166888:ENST0000055615 CCTGATTCCTCCATGAGCATGCAGCTTGGCCCAGATATGGTGCCCCAGGT
ENSG00000166888:ENST0000045407 CCTGATTCCTCCATGAGCATGCAGCTTGGCCCAGATATGGTGCCCCAGGT
ENSG00000166888:ENST0000053891 CCTGATTCCTCCATGAGCATGCAGCTTGGCCCAGATATGGTGCCCCAGGT
ENSG00000166888:ENST0000053721 CCTGATTCCTCCATGAGCATGCAGCTTGGCCCAGATATGGTGCCCCAGGT
ENSG00000166888:ENST0000053520 CCTGATTCCTCCATGAGCATGCAGCTTGGCCCAGATATGGTGCCCCAGGT
isotig46679 CCTTCAGACCTTCTCCCC------------------ATGTCTCCGAGTGT
isotig12565 CCCGGTAGTGCCGCCCCT------------------TACCTGAAGACCAA
isotig12566 CCCGGTAGTTGTTTTTCCATG-----------------------------
ENSG00000166888:ENST0000030013 GTACCCACCACACTCTCACTCCATCCCCCCGTATCAAGGCCTCTCCCCAG
ENSG00000166888:ENST0000054387 GTACCCACCACACTCTCACTCCATCCCCCCGTATCAAGGCCTCTCCCCAG
ENSG00000166888:ENST0000055615 GTACCCACCACACTCTCACTCCATCCCCCCGTATCAAGGCCTCTCCCCAG
ENSG00000166888:ENST0000045407 GTACCCACCACACTCTCACTCCATCCCCCCGTATCAAGGCCTCTCCCCAG
ENSG00000166888:ENST0000053891 GTACCCACCACACTCTCACTCCATCCCCCCGTATCAAGGCCTCTCCCCAG
ENSG00000166888:ENST0000053721 GTACCCACCACACTCTCACTCCATCCCCCCGTATCAAGGCCTCTCCCCAG
ENSG00000166888:ENST0000053520 GTACCCACCACACTCTCACTCCATCCCCCCGTATCAAGGCCTCTCCCCAG
isotig46679 ATACGCTGTGCTGAGAGAAAACCTGAGCCCT-------------------
isotig12565 GTTCATCTGTGTGACACCAACGACCTGCAGC-------------------
isotig12566 --------------------------------------------------
ENSG00000166888:ENST0000030013 AAGAATCAGTCAACGTGTTGTCAGCCTTCCAGGAGCCTCACCTGCAGATG
ENSG00000166888:ENST0000054387 AAGAATCAGTCAACGTGTTGTCAGCCTTCCAGGAGCCTCACCTGCAGATG
ENSG00000166888:ENST0000055615 AAGAATCAGTCAACGTGTTGTCAGCCTTCCAGGAGCCTCACCTGCAGATG
ENSG00000166888:ENST0000045407 AAGAATCAGTCAACGTGTTGTCAGCCTTCCAGGAGCCTCACCTGCAGATG
ENSG00000166888:ENST0000053891 AAGAATCAGTCAACGTGTTGTCAGCCTTCCAGGAGCCTCACCTGCAGATG
ENSG00000166888:ENST0000053721 AAGAATCAGTCAACGTGTTGTCAGCCTTCCAGGAGCCTCACCTGCAGATG
ENSG00000166888:ENST0000053520 AAGAATCAGTCAACGTGTTGTCAGCCTTCCAGGAGCCTCACCTGCAGATG
isotig46679 --------------------------------------------------
isotig12565 --------------------------------------------------
isotig12566 --------------------------------------------------
ENSG00000166888:ENST0000030013 CCCCCCAGCCTGGGCCAGATGAGCCTGCCCTTTGACCAGCCTCACCCCCA
ENSG00000166888:ENST0000054387 CCCCCCAGCCTGGGCCAGATGAGCCTGCCCTTTGACCAGCCTCACCCCCA
ENSG00000166888:ENST0000055615 CCCCCCAGCCTGGGCCAGATGAGCCTGCCCTTTGACCAGCCTCACCCCCA
ENSG00000166888:ENST0000045407 CCCCCCAGCCTGGGCCAGATGAGCCTGCCCTTTGACCAGCCTCACCCCCA
ENSG00000166888:ENST0000053891 CCCCCCAGCCTGGGCCAGATGAGCCTGCCCTTTGACCAGCCTCACCCCCA
ENSG00000166888:ENST0000053721 CCCCCCAGCCTGGGCCAGATGAGCCTGCCCTTTGACCAGCCTCACCCCCA
ENSG00000166888:ENST0000053520 CCCCCCAGCCTGGGCCAGATGAGCCTGCCCTTTGACCAGCCTCACCCCCA
isotig46679 ------------ACCACAATTGAAACAGCAATGAAGTCTCCATATTCTGA
isotig12565 ------------AATACCATTGACCTGCCGATGTCCCCCCCGCAC-----
isotig12566 ------------GTTCTGGTTTCGCTGTTAGGGAAAGGGGGACAGTGCAG
ENSG00000166888:ENST0000030013 GGGCCTGCTGCCGTGCCAGCCTCAGGAGCATGCTGTGTCCAGCCCTGACC
ENSG00000166888:ENST0000054387 GGGCCTGCTGCCGTGCCAGCCTCAGGAGCATGCTGTGTCCAGCCCTGACC
ENSG00000166888:ENST0000055615 GGGCCTGCTGCCGTGCCAGCCTCAGGAGCATGCTGTGTCCAGCCCTGACC
ENSG00000166888:ENST0000045407 GGGCCTGCTGCCGTGCCAGCCTCAGGAGCATGCTGTGTCCAGCCCTGACC
ENSG00000166888:ENST0000053891 GGGCCTGCTGCCGTGCCAGCCTCAGGAGCATGCTGTGTCCAGCCCTGACC
ENSG00000166888:ENST0000053721 GGGCCTGCTGCCGTGCCAGCCTCAGGAGCATGCTGTGTCCAGCCCTGACC
ENSG00000166888:ENST0000053520 GGGCCTGCTGCCGTGCCAGCCTCAGGAGCATGCTGTGTCCAGCCCTGACC
isotig46679 GCGGTAC---------------------AAAGCGACTCTTCAAGGAAGAG
isotig12565 --------------------------------------------------
isotig12566 GTCCTTG---------------------------------------GAGG
ENSG00000166888:ENST0000030013 CCCTGCTCTGCTCAGATGTGACCATGGTGGAAGACAGCTGCCTGAGCCAG
ENSG00000166888:ENST0000054387 CCCTGCTCTGCTCAGATGTGACCATGGTGGAAGACAGCTGCCTGAGCCAG
ENSG00000166888:ENST0000055615 CCCTGCTCTGCTCAGATGTGACCATGGTGGAAGACAGCTGCCTGAGCCAG
ENSG00000166888:ENST0000045407 CCCTGCTCTGCTCAGATGTGACCATGGTGGAAGACAGCTGCCTGAGCCAG
ENSG00000166888:ENST0000053891 CCCTGCTCTGCTCAGATGTGACCATGGTGGAAGACAGCTGCCTGAGCCAG
ENSG00000166888:ENST0000053721 CCCTGCTCTGCTCAGATGTGACCATGGTGGAAGACAGCTGCCTGAGCCAG
ENSG00000166888:ENST0000053520 CCCTGCTCTGCTCAGATGTGACCATGGTGGAAGACAGCTGCCTGAGCCAG
isotig46679 AGCAGATGAAAACGGAGACTGCTCTTTGCCAAAGTCCACAATTCATTTCT
isotig12565 --------------------------------------------------
isotig12566 AGAGACAAGGACATGACCGGGTGTCTGGTGGTGAGTCCTGCTATGGAAGA
ENSG00000166888:ENST0000030013 CCAGTGACAGCGTTTCCTCAGGGCACTTGGATTGGTGAAGACATATTCCC
ENSG00000166888:ENST0000054387 CCAGTGACAGCGTTTCCTCAGGGCACTTGGATTGGTGAAGACATATTCCC
ENSG00000166888:ENST0000055615 CCAGTGACAGCGTTTCCTCAGGGCACTTGGATTGGTGAAGACATATTCCC
ENSG00000166888:ENST0000045407 CCAGTGACAGCGTTTCCTCAGGGCACTTGGATTGGTGAAGACATATTCCC
ENSG00000166888:ENST0000053891 CCAGTGACAGCGTTTCCTCAGGGCACTTGGATTGGTGAAGACATATTCCC
ENSG00000166888:ENST0000053721 CCAGTGACAGCGTTTCCTCAGGGCACTTGGATTGGTGAAGACATATTCCC
ENSG00000166888:ENST0000053520 CCAGTGACAGCGTTTCCTCAGGGCACTTGGATTGGTGAAGACATATTCCC
isotig46679 TCAGCTTTGATACTGGTTTCTAGAAAATGGCACAAATCCGAAGCTTTCCT
isotig12565 ------TTTAGATTCATTGATGCAGTTTGGAAACGGAGGTGCGCCCTC--
isotig12566 GCTGTTTAT------------------TGGGTACTTCAG-----------
ENSG00000166888:ENST0000030013 TCCTCTGCTGCCTCCCACTGAACAGGACCTCACTAAGCTTCTCCTGGAGG
ENSG00000166888:ENST0000054387 TCCTCTGCTGCCTCCCACTGAACAGGACCTCACTAAGCTTCTCCTGGAGG
ENSG00000166888:ENST0000055615 TCCTCTGCTGCCTCCCACTGAACAGGACCTCACTAAGCTTCTCCTGGAGG
ENSG00000166888:ENST0000045407 TCCTCTGCTGCCTCCCACTGAACAGGACCTCACTAAGCTTCTCCTGGAGG
ENSG00000166888:ENST0000053891 TCCTCTGCTGCCTCCCACTGAACAGGACCTCACTAAGCTTCTCCTGGAGG
ENSG00000166888:ENST0000053721 TCCTCTGCTGCCTCCCACTGAACAGGACCTCACTAAGCTTCTCCTGGAGG
ENSG00000166888:ENST0000053520 TCCTCTGCTGCCTCCCACTGAACAGGACCTCACTAAGCTTCTCCTGGAGG
isotig46679 CTCACTA------------------------------------------G
isotig12565 -------------------------------------------------G
isotig12566 -------------------------------------------------G
ENSG00000166888:ENST0000030013 GGCAAGGGGAGTCGGGGGGAGGGTCCTTGGGGGCACAGCCCCTCCTGCAG
ENSG00000166888:ENST0000054387 GGCAAGGGGAGTCGGGGGGAGGGTCCTTGGGGGCACAGCCCCTCCTGCAG
ENSG00000166888:ENST0000055615 GGCAAGGGGAGTCGGGGGGAGGGTCCTTGGGGGCACAGCCCCTCCTGCAG
ENSG00000166888:ENST0000045407 GGCAAGGGGAGTCGGGGGGAGGGTCCTTGGGGGCACAGCCCCTCCTGCAG
ENSG00000166888:ENST0000053891 GGCAAGGGGAGTCGGGGGGAGGGTCCTTGGGGGCACAGCCCCTCCTGCAG
ENSG00000166888:ENST0000053721 GGCAAGGGGAGTCGGGGGGAGGGTCCTTGGGGGCACAGCCCCTCCTGCAG
ENSG00000166888:ENST0000053520 GGCAAGGGGAGTCGGGGGGAGGGTCCTTGGGGGCACAGCCCCTCCTGCAG
isotig46679 GTGACATTCCCCAACTGGGAGTGCTGCTGAAATGCAAACCAAAGCTTCAG
isotig12565 GCAGGAGGGCAGTTGTCACTCACGTTCATGGATCTGAC------------
isotig12566 GTGACCGGGATTCAAGAGAAGACCAGAATCAGGCCTCA------------
ENSG00000166888:ENST0000030013 CCCTCCCACTATGGGCAATCTGGGATCTCAATGTCCCACATGGACCTAAG
ENSG00000166888:ENST0000054387 CCCTCCCACTATGGGCAATCTGGGATCTCAATGTCCCACATGGACCTAAG
ENSG00000166888:ENST0000055615 CCCTCCCACTATGGGCAATCTGGGATCTCAATGTCCCACATGGACCTAAG
ENSG00000166888:ENST0000045407 CCCTCCCACTATGGGCAATCTGGGATCTCAATGTCCCACATGGACCTAAG
ENSG00000166888:ENST0000053891 CCCTCCCACTATGGGCAATCTGGGATCTCAATGTCCCACATGGACCTAAG
ENSG00000166888:ENST0000053721 CCCTCCCACTATGGGCAATCTGGGATCTCAATGTCCCACATGGACCTAAG
ENSG00000166888:ENST0000053520 CCCTCCCACTATGGGCAATCTGGGATCTCAATGTCCCACATGGACCTAAG
isotig46679 ATAAACACGCAGGAAAAGACAGCTTCGAGAAACCTATGTTCGCAATATAA
isotig12565 ---------TTCGGAGTGCGCTACCTCCCCCATGTGAGGAGC--------
isotig12566 --------------------------------------------------
ENSG00000166888:ENST0000030013 GGCCAACCCCAGTTGG
ENSG00000166888:ENST0000054387 GGCCAACCCCAGTTGG
ENSG00000166888:ENST0000055615 GGCCAACCCCAGTTGG
ENSG00000166888:ENST0000045407 GGCCAACCCCAGTTGG
ENSG00000166888:ENST0000053891 GGCCAACCCCAGTTGG
ENSG00000166888:ENST0000053721 GGCCAACCCCAGTTGG
ENSG00000166888:ENST0000053520 GGCCAACCCCAGTTGG
isotig46679 CAGAAGGCTGCTTTGC
isotig12565 ----------------
isotig12566 ----------------
""",
)
def test5(self):
aligner = CodonAligner()
# aligner.frameshift_score = -10.0
nucleotide_records = SeqIO.parse("codonalign/nucl5.fa", "fasta")
protein_alignment = Align.read("codonalign/pro5.aln", "clustal")
self.assertEqual(len(protein_alignment.sequences), 3)
codon_alignments = []
nucleotide_record = next(nucleotide_records)
protein_record = protein_alignment.sequences[0]
self.assertEqual(nucleotide_record.id, protein_record.id)
alignments = aligner.align(protein_record, nucleotide_record)
self.assertEqual(len(alignments), 1)
alignment = next(alignments)
codon_alignments.append(alignment)
self.assertTrue(
np.array_equal(alignment.coordinates, np.array([[0, 183], [0, 549]]))
)
self.assertEqual(
str(alignment),
"""\
isotig697 0 R G D Q R S N F Q L S P S T M Q I S T G
isotig697 0 TGAGGCGATCAACGCAGCAACTTCCAGCTGTCTCCCTCCACCATGCAGATCTCCACAGGG
isotig697 20 L L C L L L V A T G F T S Q V L A H P G
isotig697 60 CTTCTGTGCcTGCTGCTTGTGGCCACTGGCTTCACTTCCCAGGTGCTGGCTCACCCAGGC
isotig697 40 S I P S T Y C F V M T S K K I P K S L L
isotig697 120 TCTATCCCATCTACCTaCTGCTTTGTTATGACCAGTAAGAaGATCCCCAAATCACTACTG
isotig697 60 K S Y K R I S N S R C T L K A I L F K T
isotig697 180 AaGAGCTACAAAaGAATCTCCAACAGCAGATGCACCcTGAAAGCCATACTCTTCAAGACC
isotig697 80 K S G K E I C A D P K K K W V Q D A T K
isotig697 240 AAGTCGGGCAAAGAGATCTGTGCTGACCCCAAGAAGAAGTGGGTCcAGGATGCCACAAAG
isotig697 100 H L D Q I L Q T P K P T I P S F E T H P
isotig697 300 CACCTGGACCAAATCCTTCAAACTCCAAAACCGACAATCCCCTCTTTTGAGACTCACCCA
isotig697 120 E T K K C F I H S P F L R R A P R S T Q
isotig697 360 GAGACTAAGAAATGCTTCATTCATTCTCCATTCCTAAGACGTGCTCCAAGGTCAACTCAG
isotig697 140 H H S P R T W L H L V M D R T E S H Y V
isotig697 420 CACCATTCCCCAAGGACTTGGCTTCATTTAGTTATGGATAGAACTGAAAGTCATTATGTT
isotig697 160 Q N K P D L K R L C N F L N M Q N L K R
isotig697 480 CAGAATAAGCCAGACTTGAAGAGGTTGTGTAATTTCTTGAATATGCAAAATCTTAAAAGG
isotig697 180 G A C 183
isotig697 540 GGGGCATGC 549
""",
)
nucleotide_record = next(nucleotide_records)
protein_record = protein_alignment.sequences[1]
self.assertEqual(nucleotide_record.id, protein_record.id)
alignments = aligner.align(protein_record, nucleotide_record)
self.assertEqual(len(alignments), 1)
alignment = next(alignments)
codon_alignments.append(alignment)
self.assertTrue(
np.array_equal(alignment.coordinates, np.array([[0, 65], [0, 195]]))
)
self.assertEqual(
str(alignment),
"""\
ENSG00000 0 M K V S A A L L C L L L I A A T F I P Q
ENSG00000 0 ATGAAAGTCTCTGCCGCCCTTCTGTGCCTGCTGCTCATAGCAGCCACCTTCATTCCCCAA
ENSG00000 20 G L A Q P D A I N A P V T C C Y N F T N
ENSG00000 60 GGGCTCGCTCAGCCAGATGCAATCAATGCCCCAGTCACCTGCTGTTATAACTTCACCAAT
ENSG00000 40 R K I S V Q R L A S Y R R I T S S K C P
ENSG00000 120 AGGAAGATCTCAGTGCAGAGGCTCGCGAGCTATAGAAGAATCACCAGCAGCAAGTGTCCC
ENSG00000 60 K E A V M 65
ENSG00000 180 AAAGAAGCTGTGATG 195
""",
)
nucleotide_record = next(nucleotide_records)
protein_record = protein_alignment.sequences[2]
self.assertEqual(nucleotide_record.id, protein_record.id)
alignments = aligner.align(protein_record, nucleotide_record)
self.assertEqual(len(alignments), 1)
alignment = next(alignments)
codon_alignments.append(alignment)
self.assertTrue(
np.array_equal(alignment.coordinates, np.array([[0, 99], [9, 306]]))
)
self.assertEqual(
str(alignment),
"""\
ENSG00000 0 M K V S A A L L C L L L I A A T F I P Q
ENSG00000 9 ATGAAAGTCTCTGCCGCCCTTCTGTGCCTGCTGCTCATAGCAGCCACCTTCATTCCCCAA
ENSG00000 20 G L A Q P D A I N A P V T C C Y N F T N
ENSG00000 69 GGGCTCGCTCAGCCAGATGCAATCAATGCCCCAGTCACCTGCTGTTATAACTTCACCAAT
ENSG00000 40 R K I S V Q R L A S Y R R I T S S K C P
ENSG00000 129 AGGAAGATCTCAGTGCAGAGGCTCGCGAGCTATAGAAGAATCACCAGCAGCAAGTGTCCC
ENSG00000 60 K E A V I F K T I V A K E I C A D P K Q
ENSG00000 189 AAAGAAGCTGTGATCTTCAAGACCATTGTGGCCAAGGAGATCTGTGCTGACCCCAAGCAG
ENSG00000 80 K W V Q D S M D H L D K Q T Q T P K T
ENSG00000 249 AAGTGGGTTCAGGATTCCATGGACCACCTGGACAAGCAAACCCAAACTCCGAAGACT
ENSG00000 99
ENSG00000 306
""",
)
alignment = protein_alignment.mapall(codon_alignments)
self.assertTrue(
np.array_equal(
alignment.coordinates,
# fmt: off
np.array([[0, 42, 126, 126, 231, 333, 549],
[0, 0, 84, 90, 195, 195, 195],
[9, 9, 93, 99, 204, 306, 306]])
# fmt: on
)
)
self.assertEqual(
format(alignment, "clustal"),
"""\
isotig69710 TGAGGCGATCAACGCAGCAACTTCCAGCTGTCTCCCTCCACCATGCAGAT
ENSG00000108691:ENST0000058090 ------------------------------------------ATGAAAGT
ENSG00000108691:ENST0000022583 ------------------------------------------ATGAAAGT
isotig69710 CTCCACAGGGCTTCTGTGCcTGCTGCTTGTGGCCACTGGCTTCACTTCCC
ENSG00000108691:ENST0000058090 CTCTGCCGCCCTTCTGTGCCTGCTGCTCATAGCAGCCACCTTCATTCCCC
ENSG00000108691:ENST0000022583 CTCTGCCGCCCTTCTGTGCCTGCTGCTCATAGCAGCCACCTTCATTCCCC
isotig69710 AGGTGCTGGCTCACCCAGGCTCTATC------CCATCTACCTaCTGCTTT
ENSG00000108691:ENST0000058090 AAGGGCTCGCTCAGCCAGATGCAATCAATGCCCCAGTCACCTGCTGTTAT
ENSG00000108691:ENST0000022583 AAGGGCTCGCTCAGCCAGATGCAATCAATGCCCCAGTCACCTGCTGTTAT
isotig69710 GTTATGACCAGTAAGAaGATCCCCAAATCACTACTGAaGAGCTACAAAaG
ENSG00000108691:ENST0000058090 AACTTCACCAATAGGAAGATCTCAGTGCAGAGGCTCGCGAGCTATAGAAG
ENSG00000108691:ENST0000022583 AACTTCACCAATAGGAAGATCTCAGTGCAGAGGCTCGCGAGCTATAGAAG
isotig69710 AATCTCCAACAGCAGATGCACCcTGAAAGCCATACTCTTCAAGACCAAGT
ENSG00000108691:ENST0000058090 AATCACCAGCAGCAAGTGTCCCAAAGAAGCTGTGATG-------------
ENSG00000108691:ENST0000022583 AATCACCAGCAGCAAGTGTCCCAAAGAAGCTGTGATCTTCAAGACCATTG
isotig69710 CGGGCAAAGAGATCTGTGCTGACCCCAAGAAGAAGTGGGTCcAGGATGCC
ENSG00000108691:ENST0000058090 --------------------------------------------------
ENSG00000108691:ENST0000022583 TGGCCAAGGAGATCTGTGCTGACCCCAAGCAGAAGTGGGTTCAGGATTCC
isotig69710 ACAAAGCACCTGGACCAAATCCTTCAAACTCCAAAACCGACAATCCCCTC
ENSG00000108691:ENST0000058090 --------------------------------------------------
ENSG00000108691:ENST0000022583 ATGGACCACCTGGACAAGCAAACCCAAACTCCGAAGACT-----------
isotig69710 TTTTGAGACTCACCCAGAGACTAAGAAATGCTTCATTCATTCTCCATTCC
ENSG00000108691:ENST0000058090 --------------------------------------------------
ENSG00000108691:ENST0000022583 --------------------------------------------------
isotig69710 TAAGACGTGCTCCAAGGTCAACTCAGCACCATTCCCCAAGGACTTGGCTT
ENSG00000108691:ENST0000058090 --------------------------------------------------
ENSG00000108691:ENST0000022583 --------------------------------------------------
isotig69710 CATTTAGTTATGGATAGAACTGAAAGTCATTATGTTCAGAATAAGCCAGA
ENSG00000108691:ENST0000058090 --------------------------------------------------
ENSG00000108691:ENST0000022583 --------------------------------------------------
isotig69710 CTTGAAGAGGTTGTGTAATTTCTTGAATATGCAAAATCTTAAAAGGGGGG
ENSG00000108691:ENST0000058090 --------------------------------------------------
ENSG00000108691:ENST0000022583 --------------------------------------------------
isotig69710 CATGC
ENSG00000108691:ENST0000058090 -----
ENSG00000108691:ENST0000022583 -----
""",
)
class Test_build(unittest.TestCase):
def test_build1(self):
aligner = CodonAligner()
codon_alignments = []
seq1 = SeqRecord(
Seq(
"TCAGGGACTGCGAGAACCAAGCTACTGCTGCTGCTGGCTGCGCTCTGCGCCGCAGGTGGGGCGCTGGAG"
),
id="pro1",
)
seq2 = SeqRecord(
Seq("TCAGGGACTTCGAGAACCAAGCGCTCCTGCTGCTGGCTGCGCTCGGCGCCGCAGGTGGAGCACTGGAG"),
id="pro2",
)
pro1 = SeqRecord(Seq("SGTARTKLLLLLAALCAAGGALE"), id="pro1")
pro2 = SeqRecord(Seq("SGTSRTKRLLLLAALGAAGGALE"), id="pro2")
alignments = aligner.align(pro1, seq1)
self.assertEqual(len(alignments), 1)
alignment = next(alignments)
codon_alignments.append(alignment)
self.assertTrue(
np.array_equal(alignment.coordinates, np.array([[0, 23], [0, 69]]))
)
self.assertEqual(
str(alignment),
"""\
pro1 0 S G T A R T K L L L L L A A L C A A G G
pro1 0 TCAGGGACTGCGAGAACCAAGCTACTGCTGCTGCTGGCTGCGCTCTGCGCCGCAGGTGGG
pro1 20 A L E 23
pro1 60 GCGCTGGAG 69
""",
)
alignments = aligner.align(pro2, seq2)
self.assertEqual(len(alignments), 1)
alignment = next(alignments)
codon_alignments.append(alignment)
self.assertTrue(
np.array_equal(
alignment.coordinates, np.array([[0, 8, 8, 23], [0, 24, 23, 68]])
)
)
self.assertEqual(
str(alignment),
"""\
pro2 0 S G T S R T K R 8
pro2 0 TCAGGGACTTCGAGAACCAAGCGC 24
pro2 8 L L L L A A L G A A G G A L E 23
pro2 23 CTCCTGCTGCTGGCTGCGCTCGGCGCCGCAGGTGGAGCACTGGAG 68
""",
)
alignment = Alignment([pro1, pro2])
alignment = alignment.mapall(codon_alignments)
self.assertTrue(
np.array_equal(
alignment.coordinates,
# fmt: off
np.array([[0, 24, 24, 69],
[0, 24, 23, 68]])
# fmt: on
)
)
self.assertEqual(
str(alignment),
"""\
pro1 0 TCAGGGACTGCGAGAACCAAGCTA 24
0 |||||||||.||||||||||||..
pro2 0 TCAGGGACTTCGAGAACCAAGCGC 24
pro1 24 CTGCTGCTGCTGGCTGCGCTCTGCGCCGCAGGTGGGGCGCTGGAG 69
24 ||.||||||||||||||||||.|||||||||||||.||.|||||| 69
pro2 23 CTCCTGCTGCTGGCTGCGCTCGGCGCCGCAGGTGGAGCACTGGAG 68
""",
)
def test_build2(self):
aligner = CodonAligner()
codon_alignments = []
seq1 = SeqRecord(
Seq(
"ATGAAAAAGCACGAGTTACTTTGCCAAGGGACAAGTAACAAGCTCACCCAGTTGGGCACTTTTGAAGACCACTTTCTGAGCCTACAGAGGATGTTCAACAACTGTGAGGTGGTCCTTGGGAATTTGGAAATTACCTACATGCAGAGTAGTTACAACCTTTCTTTTCTCAAGACCATCCAGGAGGTTGCCGGCTATGTACTCATTGCCCTC"
),
id="pro1",
)
seq2 = SeqRecord(
Seq(
"ATGAAAAAGCACGAGTTCTTTGCCAAGGGACAAGTAACAAGCTCACCCAGTTGGGCACTTTTGAAGACCACTTTCTGAGCCTACAGAGGATGTTCAACAATGTGAGGTGGTCCTTGGGAATTTGGAAATTACCTACATGCAGAGTAGTTACAACCTTTCTTTTCTCAAGACCATCCAGGAGGTTGCCGGCTATGTACTCATTGCCCTC"
),
id="pro2",
)
seq3 = SeqRecord(
Seq(
"ATGAAAAAGCACGAGTTACTTTGCCAAGGGACAAGTAACAAGCTCACCCTTGGGCACTTTTGAAGACCACTTTCTGAGCCTACAGAGGATGTTCAACAACTGTGAGGTGGTCCTTGGGAATTTGGAAATTACCTACATGCAGAGTAGTTACAACCTTTCTTTTCTCAAGACCATCCAGGAGGTTGCCGGCTATGTACTCATTGCCCTC"
),
id="pro3",
)
pro1 = SeqRecord(
Seq(
"MKKHELLCQGTSNKLTQLGTFEDHFLSLQRMFNNCEVVLGNLEITYMQSSYNLSFLKTIQEVAGYVLIAL"
),
id="pro1",
)
pro2 = SeqRecord(
Seq(
"MKKHEFLCQGTSNKLTQLGTFEDHFLSLQRMFNNCEVVLGNLEITYMQSSYNLSFLKTIQEVAGYVLIAL"
),
id="pro2",
)
pro3 = SeqRecord(
Seq(
"MKKHELLCQGTSNKLTLLGTFEDHFLSLQRMFNNCEVVLGNLEITYMQSSYNLSFLKTIQEVAGYVLIAL"
),
id="pro3",
)
alignments = aligner.align(pro1, seq1)
self.assertEqual(len(alignments), 1)
alignment = next(alignments)
codon_alignments.append(alignment)
self.assertTrue(
np.array_equal(alignment.coordinates, np.array([[0, 70], [0, 210]]))
)
self.assertEqual(
str(alignment),
"""\
pro1 0 M K K H E L L C Q G T S N K L T Q L G T
pro1 0 ATGAAAAAGCACGAGTTACTTTGCCAAGGGACAAGTAACAAGCTCACCCAGTTGGGCACT
pro1 20 F E D H F L S L Q R M F N N C E V V L G
pro1 60 TTTGAAGACCACTTTCTGAGCCTACAGAGGATGTTCAACAACTGTGAGGTGGTCCTTGGG
pro1 40 N L E I T Y M Q S S Y N L S F L K T I Q
pro1 120 AATTTGGAAATTACCTACATGCAGAGTAGTTACAACCTTTCTTTTCTCAAGACCATCCAG
pro1 60 E V A G Y V L I A L 70
pro1 180 GAGGTTGCCGGCTATGTACTCATTGCCCTC 210
""",
)
alignments = aligner.align(pro2, seq2)
self.assertEqual(len(alignments), 1)
alignment = next(alignments)
codon_alignments.append(alignment)
self.assertTrue(
np.array_equal(
alignment.coordinates,
np.array([[0, 6, 6, 34, 34, 70], [0, 18, 17, 101, 100, 208]]),
)
)
self.assertEqual(
str(alignment),
"""\
pro2 0 M K K H E F 6
pro2 0 ATGAAAAAGCACGAGTTC 18
pro2 6 L C Q G T S N K L T Q L G T F E D H F L
pro2 17 CTTTGCCAAGGGACAAGTAACAAGCTCACCCAGTTGGGCACTTTTGAAGACCACTTTCTG
pro2 26 S L Q R M F N N 34
pro2 77 AGCCTACAGAGGATGTTCAACAAT 101
pro2 34 C E V V L G N L E I T Y M Q S S Y N L S
pro2 100 TGTGAGGTGGTCCTTGGGAATTTGGAAATTACCTACATGCAGAGTAGTTACAACCTTTCT
pro2 54 F L K T I Q E V A G Y V L I A L 70
pro2 160 TTTCTCAAGACCATCCAGGAGGTTGCCGGCTATGTACTCATTGCCCTC 208
""",
)
alignments = aligner.align(pro3, seq3)
self.assertEqual(len(alignments), 1)
alignment = next(alignments)
codon_alignments.append(alignment)
self.assertTrue(
np.array_equal(
alignment.coordinates, np.array([[0, 17, 17, 70], [0, 51, 49, 208]])
)
)
self.assertEqual(
str(alignment),
"""\
pro3 0 M K K H E L L C Q G T S N K L T L 17
pro3 0 ATGAAAAAGCACGAGTTACTTTGCCAAGGGACAAGTAACAAGCTCACCCTT 51
pro3 17 L G T F E D H F L S L Q R M F N N C E V
pro3 49 TTGGGCACTTTTGAAGACCACTTTCTGAGCCTACAGAGGATGTTCAACAACTGTGAGGTG
pro3 37 V L G N L E I T Y M Q S S Y N L S F L K
pro3 109 GTCCTTGGGAATTTGGAAATTACCTACATGCAGAGTAGTTACAACCTTTCTTTTCTCAAG
pro3 57 T I Q E V A G Y V L I A L 70
pro3 169 ACCATCCAGGAGGTTGCCGGCTATGTACTCATTGCCCTC 208
""",
)
alignment = Alignment([pro1, pro2, pro3])
alignment = alignment.mapall(codon_alignments)
self.assertEqual(
str(alignment),
"""\
pro1 0 ATGAAAAAGCACGAGTTA 18
pro2 0 ATGAAAAAGCACGAGTTC 18
pro3 0 ATGAAAAAGCACGAGTTA 18
pro1 18 CTTTGCCAAGGGACAAGTAACAAGCTCACCCAG 51
pro2 17 CTTTGCCAAGGGACAAGTAACAAGCTCACCCAG 50
pro3 18 CTTTGCCAAGGGACAAGTAACAAGCTCACCCTT 51
pro1 51 TTGGGCACTTTTGAAGACCACTTTCTGAGCCTACAGAGGATGTTCAACAAC 102
pro2 50 TTGGGCACTTTTGAAGACCACTTTCTGAGCCTACAGAGGATGTTCAACAAT 101
pro3 49 TTGGGCACTTTTGAAGACCACTTTCTGAGCCTACAGAGGATGTTCAACAAC 100
pro1 102 TGTGAGGTGGTCCTTGGGAATTTGGAAATTACCTACATGCAGAGTAGTTACAACCTTTCT
pro2 100 TGTGAGGTGGTCCTTGGGAATTTGGAAATTACCTACATGCAGAGTAGTTACAACCTTTCT
pro3 100 TGTGAGGTGGTCCTTGGGAATTTGGAAATTACCTACATGCAGAGTAGTTACAACCTTTCT
pro1 162 TTTCTCAAGACCATCCAGGAGGTTGCCGGCTATGTACTCATTGCCCTC 210
pro2 160 TTTCTCAAGACCATCCAGGAGGTTGCCGGCTATGTACTCATTGCCCTC 208
pro3 160 TTTCTCAAGACCATCCAGGAGGTTGCCGGCTATGTACTCATTGCCCTC 208
""",
)
self.assertTrue(
np.array_equal(
alignment.coordinates,
# fmt: off
np.array([[0, 18, 18, 51, 51, 102, 102, 210],
[0, 18, 17, 50, 50, 101, 100, 208],
[0, 18, 18, 51, 49, 100, 100, 208]])
# fmt: on
)
)
def test_build3(self):
# use Yeast mitochondrial codon table
codon_table = CodonTable.unambiguous_dna_by_id[3]
aligner = CodonAligner(codon_table=codon_table)
codon_alignments = []
seq1 = SeqRecord(
Seq(
"ATGGCAAGGGACCACCCAGTTGGGCACTGATATGATCGGGTGTATTTGCAGAGTAGTAACCTTTCTTTTCTCAAGACCATCCAG"
),
id="pro1",
)
seq2 = SeqRecord(
Seq(
"ATGGCAAGGCACCATCCAGTTGAGCACTGATATGATCGGGTGTATTTGCAGAGTAGTAACGTGTCTCTGCTCAAGACCATCCAG"
),
id="pro2",
)
seq3 = SeqRecord(
Seq(
"ATGGCAGGGGACCACCCAGTTGGGCACTGATATGATCGTGTGTATCTGCAGAGTAGTAACCACTCTTTTCTCATGACCATCCAG"
),
id="pro3",
)
pro1 = SeqRecord(Seq("MARDHPVGHWYDRVYLQSSNTSFTKTIQ"), id="pro1")
pro2 = SeqRecord(Seq("MARHHPVEHWYDRVYLQSSNVSTTKTIQ"), id="pro2")
pro3 = SeqRecord(Seq("MAGDHPVGHWYDRVYTQSSNHSFTMTIQ"), id="pro3")
alignments = aligner.align(pro1, seq1)
self.assertEqual(len(alignments), 1)
alignment = next(alignments)
codon_alignments.append(alignment)
self.assertTrue(
np.array_equal(alignment.coordinates, np.array([[0, 28], [0, 84]]))
)
self.assertEqual(
str(alignment),
"""\
pro1 0 M A R D H P V G H W Y D R V Y L Q S S N
pro1 0 ATGGCAAGGGACCACCCAGTTGGGCACTGATATGATCGGGTGTATTTGCAGAGTAGTAAC
pro1 20 T S F T K T I Q 28
pro1 60 CTTTCTTTTCTCAAGACCATCCAG 84
""",
)
alignments = aligner.align(pro2, seq2)
self.assertEqual(len(alignments), 1)
alignment = next(alignments)
codon_alignments.append(alignment)
self.assertTrue(
np.array_equal(alignment.coordinates, np.array([[0, 28], [0, 84]]))
)
self.assertEqual(
str(alignment),
"""\
pro2 0 M A R H H P V E H W Y D R V Y L Q S S N
pro2 0 ATGGCAAGGCACCATCCAGTTGAGCACTGATATGATCGGGTGTATTTGCAGAGTAGTAAC
pro2 20 V S T T K T I Q 28
pro2 60 GTGTCTCTGCTCAAGACCATCCAG 84
""",
)
alignments = aligner.align(pro3, seq3)
self.assertEqual(len(alignments), 1)
alignment = next(alignments)
codon_alignments.append(alignment)
self.assertTrue(
np.array_equal(alignment.coordinates, np.array([[0, 28], [0, 84]]))
)
self.assertEqual(
str(alignment),
"""\
pro3 0 M A G D H P V G H W Y D R V Y T Q S S N
pro3 0 ATGGCAGGGGACCACCCAGTTGGGCACTGATATGATCGTGTGTATCTGCAGAGTAGTAAC
pro3 20 H S F T M T I Q 28
pro3 60 CACTCTTTTCTCATGACCATCCAG 84
""",
)
alignment = Alignment([pro1, pro2, pro3])
alignment = alignment.mapall(codon_alignments)
self.assertTrue(
np.array_equal(
alignment.coordinates,
# fmt: off
np.array([[0, 84],
[0, 84],
[0, 84]])
# fmt: on
)
)
self.assertEqual(
str(alignment),
"""\
pro1 0 ATGGCAAGGGACCACCCAGTTGGGCACTGATATGATCGGGTGTATTTGCAGAGTAGTAAC
pro2 0 ATGGCAAGGCACCATCCAGTTGAGCACTGATATGATCGGGTGTATTTGCAGAGTAGTAAC
pro3 0 ATGGCAGGGGACCACCCAGTTGGGCACTGATATGATCGTGTGTATCTGCAGAGTAGTAAC
pro1 60 CTTTCTTTTCTCAAGACCATCCAG 84
pro2 60 GTGTCTCTGCTCAAGACCATCCAG 84
pro3 60 CACTCTTTTCTCATGACCATCCAG 84
""",
)
class Test_dn_ds(unittest.TestCase):
def test_dn_ds(self):
aligner = CodonAligner()
nucleotide_records = SeqIO.index("codonalign/egfr_nucl.fa", "fasta")
protein_alignment = Align.read("codonalign/egfr_pro.aln", "clustal")
self.assertEqual(len(protein_alignment.sequences), 6)
codon_alignments = []
protein_record = protein_alignment.sequences[0]
self.assertEqual(protein_record.id, "gi|17136534|ref|NP_476758.1|")
nucleotide_record = nucleotide_records["gi|24657088|ref|NM_057410.3|"]
alignments = aligner.align(protein_record, nucleotide_record)
self.assertEqual(len(alignments), 1)
alignment = next(alignments)
codon_alignments.append(alignment)
self.assertTrue(
np.array_equal(alignment.coordinates, np.array([[0, 1377], [84, 4215]]))
)
self.assertEqual(
str(alignment),
"""\
gi|171365 0 M M I I S M W M S I S R G L W D S S S I
gi|246570 84 ATGATGATTATCAGCATGTGGATGAGCATATCGCGAGGATTGTGGGACAGCAGCTCCATC
gi|171365 20 W S V L L I L A C M A S I T T S S S V S
gi|246570 144 TGGTCGGTGCTGCTGATCCTCGCCTGCATGGCATCCATCACCACAAGCTCATCGGTCAGC
gi|171365 40 N A G Y V D N G N M K V C I G T K S R L
gi|246570 204 AATGCCGGCTATGTGGATAATGGCAATATGAAAGTCTGCATCGGCACTAAATCTCGGCTC
gi|171365 60 S V P S N K E H H Y R N L R D R Y T N C
gi|246570 264 TCCGTGCCCTCCAACAAGGAACATCATTACCGGAACCTCAGAGATCGGTACACGAACTGT
gi|171365 80 T Y V D G N L E L T W L P N E N L D L S
gi|246570 324 ACGTATGTGGATGGCAACCTGGAGCTGACCTGGCTGCCCAACGAGAATTTGGACCTCAGC
gi|171365 100 F L D N I R E V T G Y I L I S H V D V K
gi|246570 384 TTCCTGGACAACATACGGGAGGTCACCGGCTATATTCTGATCAGTCATGTGGACGTTAAG
gi|171365 120 K V V F P K L Q I I R G R T L F S L S V
gi|246570 444 AAAGTGGTATTTCCCAAACTACAAATCATTCGCGGACGCACGCTGTTCAGCTTATCCGTG
gi|171365 140 E E E K Y A L F V T Y S K M Y T L E I P
gi|246570 504 GAGGAGGAGAAGTATGCCTTGTTCGTCACTTATTCCAAAATGTACACGCTGGAGATTCCC
gi|171365 160 D L R D V L N G Q V G F H N N Y N L C H
gi|246570 564 GATCTACGCGATGTCTTAAATGGCCAAGTGGGCTTCCACAACAACTACAATCTCTGCCAC
gi|171365 180 M R T I Q W S E I V S N G T D A Y Y N Y
gi|246570 624 ATGCGAACGATCCAGTGGTCGGAGATTGTATCCAACGGCACGGATGCATACTACAACTAC
gi|171365 200 D F T A P E R E C P K C H E S C T H G C
gi|246570 684 GACTTTACTGCTCCGGAGCGCGAGTGTCCCAAGTGCCACGAGAGCTGCACGCACGGATGT
gi|171365 220 W G E G P K N C Q K F S K L T C S P Q C
gi|246570 744 TGGGGCGAGGGTCCCAAGAATTGCCAGAAGTTCAGCAAGCTCACCTGCTCGCCACAGTGT
gi|171365 240 A G G R C Y G P K P R E C C H L F C A G
gi|246570 804 GCCGGAGGTCGTTGCTATGGACCAAAGCCGCGGGAGTGTTGTCACCTCTTCTGCGCCGGA
gi|171365 260 G C T G P T Q K D C I A C K N F F D E G
gi|246570 864 GGATGCACTGGTCCCACGCAAAAGGATTGCATCGCCTGCAAGAACTTCTTCGACGAGGGC
gi|171365 280 V C K E E C P P M R K Y N P T T Y V L E
gi|246570 924 GTATGCAAGGAGGAATGCCCGCCCATGCGCAAGTACAATCCCACCACCTATGTTCTTGAA
gi|171365 300 T N P E G K Y A Y G A T C V K E C P G H
gi|246570 984 ACGAATCCTGAGGGAAAGTATGCCTATGGTGCCACCTGCGTCAAGGAGTGTCCCGGTCAT
gi|171365 320 L L R D N G A C V R S C P Q D K M D K G
gi|246570 1044 CTGTTGCGTGATAATGGCGCCTGCGTGCGCAGCTGTCCCCAGGACAAGATGGACAAGGGG
gi|171365 340 G E C V P C N G P C P K T C P G V T V L
gi|246570 1104 GGCGAGTGTGTGCCCTGCAATGGACCGTGCCCCAAAACCTGCCCGGGCGTTACTGTCCTG
gi|171365 360 H A G N I D S F R N C T V I D G N I R I
gi|246570 1164 CATGCCGGCAACATTGACTCGTTCCGGAATTGTACGGTGATCGATGGCAACATTCGCATT
gi|171365 380 L D Q T F S G F Q D V Y A N Y T M G P R
gi|246570 1224 TTGGATCAGACCTTCTCGGGCTTCCAGGATGTCTATGCCAACTACACGATGGGACCACGA
gi|171365 400 Y I P L D P E R L E V F S T V K E I T G
gi|246570 1284 TACATACCGCTGGATCCCGAGCGACTGGAGGTGTTCTCCACGGTGAAGGAGATCACCGGG
gi|171365 420 Y L N I E G T H P Q F R N L S Y F R N L
gi|246570 1344 TATCTGAATATCGAGGGAACCCACCCGCAGTTCCGGAATCTGTCGTACTTCCGCAATCTG
gi|171365 440 E T I H G R Q L M E S M F A A L A I V K
gi|246570 1404 GAAACAATTCATGGCCGCCAGCTGATGGAGAGCATGTTTGCCGCTTTGGCGATCGTTAAG
gi|171365 460 S S L Y S L E M R N L K Q I S S G S V V
gi|246570 1464 TCATCCCTGTACAGCCTGGAGATGCGCAATCTGAAGCAGATTAGTTCCGGCAGTGTGGTC
gi|171365 480 I Q H N R D L C Y V S N I R W P A I Q K
gi|246570 1524 ATCCAGCATAATAGAGACCTCTGCTACGTAAGCAATATCCGTTGGCCGGCCATTCAGAAG
gi|171365 500 E P E Q K V W V N E N L R A D L C E K N
gi|246570 1584 GAGCCCGAACAGAAGGTGTGGGTCAACGAGAATCTCAGGGCGGATCTATGCGAGAAAAAT
gi|171365 520 G T I C S D Q C N E D G C W G A G T D Q
gi|246570 1644 GGAACCATTTGCTCGGATCAGTGCAACGAGGACGGCTGCTGGGGAGCTGGCACGGATCAG
gi|171365 540 C L T C K N F N F N G T C I A D C G Y I
gi|246570 1704 TGCCTTACCTGCAAGAACTTCAATTTCAATGGCACCTGCATCGCCGACTGTGGTTATATA
gi|171365 560 S N A Y K F D N R T C K I C H P E C R T
gi|246570 1764 TCCAATGCCTACAAGTTTGACAATAGAACGTGCAAGATATGCCATCCAGAGTGCCGGACT
gi|171365 580 C N G A G A D H C Q E C V H V R D G Q H
gi|246570 1824 TGCAATGGAGCTGGAGCAGATCACTGCCAGGAGTGCGTCCATGTGAGGGACGGTCAGCAC
gi|171365 600 C V S E C P K N K Y N D R G V C R E C H
gi|246570 1884 TGTGTGTCCGAGTGCCCGAAGAACAAGTACAACGATCGTGGTGTCTGCCGAGAGTGCCAC
gi|171365 620 A T C D G C T G P K D T I G I G A C T T
gi|246570 1944 GCCACCTGCGATGGATGCACTGGGCCCAAGGACACCATCGGCATTGGAGCGTGTACAACG
gi|171365 640 C N L A I I N N D A T V K R C L L K D D
gi|246570 2004 TGCAATTTGGCCATTATCAACAATGACGCCACAGTAAAACGCTGCCTGCTGAAGGACGAC
gi|171365 660 K C P D G Y F W E Y V H P Q E Q G S L K
gi|246570 2064 AAGTGCCCCGATGGGTACTTCTGGGAGTATGTGCATCCACAAGAGCAGGGATCGCTAAAG
gi|171365 680 P L A G R A V C R K C H P L C E L C T N
gi|246570 2124 CCATTGGCCGGCAGAGCAGTTTGCCGAAAGTGCCATCCCCTTTGCGAGCTGTGCACCAAC
gi|171365 700 Y G Y H E Q V C S K C T H Y K R R E Q C
gi|246570 2184 TACGGATACCATGAACAGGTGTGCTCCAAGTGCACCCACTACAAGCGACGAGAGCAGTGC
gi|171365 720 E T E C P A D H Y T D E E Q R E C F Q C
gi|246570 2244 GAGACCGAGTGTCCGGCCGATCACTACACGGATGAGGAGCAGCGCGAGTGCTTCCAGTGC
gi|171365 740 H P E C N G C T G P G A D D C K S C R N
gi|246570 2304 CACCCAGAATGCAACGGTTGCACTGGTCCGGGTGCCGACGATTGCAAGTCTTGTCGCAAC
gi|171365 760 F K L F D A N E T G P Y V N S T M F N C
gi|246570 2364 TTCAAGTTGTTCGACGCGAATGAGACGGGTCCCTATGTGAACTCCACGATGTTCAATTGC
gi|171365 780 T S K C P L E M R H V N Y Q Y T A I G P
gi|246570 2424 ACCTCGAAGTGTCCCTTGGAGATGCGACATGTGAACTATCAGTACACGGCCATTGGACCC
gi|171365 800 Y C A A S P P R S S K I T A N L D V N M
gi|246570 2484 TACTGTGCAGCTAGTCCGCCGAGGAGCAGCAAGATAACTGCCAATCTGGATGTGAACATG
gi|171365 820 I F I I T G A V L V P T I C I L C V V T
gi|246570 2544 ATCTTCATTATCACTGGTGCTGTTCTGGTGCCGACGATCTGCATCCTCTGCGTGGTCACA
gi|171365 840 Y I C R Q K Q K A K K E T V K M T M A L
gi|246570 2604 TACATTTGTCGGCAAAAGCAAAAGGCCAAGAAAGAAACAGTGAAGATGACCATGGCTCTG
gi|171365 860 S G C E D S E P L R P S N I G A N L C K
gi|246570 2664 TCCGGCTGTGAGGATTCCGAGCCGCTGCGTCCCTCGAACATTGGAGCCAATCTATGCAAG
gi|171365 880 L R I V K D A E L R K G G V L G M G A F
gi|246570 2724 TTGCGCATTGTCAAGGACGCCGAGTTGCGCAAGGGCGGAGTCCTCGGAATGGGAGCCTTT
gi|171365 900 G R V Y K G V W V P E G E N V K I P V A
gi|246570 2784 GGACGAGTGTACAAGGGCGTTTGGGTGCCGGAGGGTGAGAACGTCAAGATTCCAGTGGCC
gi|171365 920 I K E L L K S T G A E S S E E F L R E A
gi|246570 2844 ATTAAGGAGCTGCTCAAGTCCACAGGCGCCGAGTCAAGCGAAGAGTTCCTCCGCGAAGCC
gi|171365 940 Y I M A S V E H V N L L K L L A V C M S
gi|246570 2904 TACATCATGGCCTCTGTGGAGCACGTTAATCTGCTGAAGCTCCTGGCCGTCTGCATGTCC
gi|171365 960 S Q M M L I T Q L M P L G C L L D Y V R
gi|246570 2964 TCACAAATGATGCTAATCACGCAACTGATGCCGCTTGGCTGCCTGTTGGACTATGTGCGA
gi|171365 980 N N R D K I G S K A L L N W S T Q I A K
gi|246570 3024 AATAACCGGGACAAGATCGGCTCTAAGGCTCTGCTCAACTGGAGCACGCAAATCGCCAAG
gi|171365 1000 G M S Y L E E K R L V H R D L A A R N V
gi|246570 3084 GGCATGTCGTATCTGGAGGAGAAGCGACTGGTCCACAGAGACTTGGCTGCCCGCAATGTC
gi|171365 1020 L V Q T P S L V K I T D F G L A K L L S
gi|246570 3144 CTGGTGCAGACTCCCTCGCTGGTGAAGATCACCGACTTTGGGCTGGCCAAGTTGCTGAGC
gi|171365 1040 S D S N E Y K A A G G K M P I K W L A L
gi|246570 3204 AGCGATTCCAATGAGTACAAGGCTGCTGGCGGCAAGATGCCCATCAAGTGGTTGGCACTG
gi|171365 1060 E C I R N R V F T S K S D V W A F G V T
gi|246570 3264 GAGTGCATTCGCAATCGTGTATTCACCAGCAAGTCCGATGTCTGGGCCTTTGGTGTGACA
gi|171365 1080 I W E L L T F G Q R P H E N I P A K D I
gi|246570 3324 ATTTGGGAACTGCTGACCTTTGGCCAGCGTCCACACGAGAACATCCCCGCTAAGGATATT
gi|171365 1100 P D L I E V G L K L E Q P E I C S L D I
gi|246570 3384 CCCGATCTTATTGAAGTCGGTCTGAAGCTGGAGCAGCCGGAGATTTGTTCGCTGGACATT
gi|171365 1120 Y C T L L S C W H L D A A M R P T F K Q
gi|246570 3444 TACTGCACACTTCTCTCGTGCTGGCACTTGGATGCCGCCATGCGTCCAACCTTCAAGCAG
gi|171365 1140 L T T V F A E F A R D P G R Y L A I P G
gi|246570 3504 CTGACTACGGTCTTTGCTGAGTTCGCCAGAGATCCGGGTCGCTATCTGGCCATTCCCGGG
gi|171365 1160 D K F T R L P A Y T S Q D E K D L I R K
gi|246570 3564 GATAAGTTCACCCGGCTGCCGGCCTACACGAGTCAGGATGAGAAGGATCTCATCCGAAAA
gi|171365 1180 L A P T T D G S E A I A E P D D Y L Q P
gi|246570 3624 TTGGCTCCCACCACCGATGGGTCCGAAGCCATTGCGGAACCCGATGACTACCTGCAACCC
gi|171365 1200 K A A P G P S H R T D C T D E I P K L N
gi|246570 3684 AAGGCAGCACCTGGTCCTAGTCACAGAACCGACTGCACGGATGAGATACCCAAGCTGAAC
gi|171365 1220 R Y C K D P S N K N S S T G D D E T D S
gi|246570 3744 CGCTACTGCAAGGATCCTAGCAACAAGAATTCGAGTACCGGAGACGATGAGACGGATTCG
gi|171365 1240 S A R E V G V G N L R L D L P V D E D D
gi|246570 3804 AGTGCCCGGGAAGTGGGCGTGGGTAATCTGCGCCTCGATCTACCAGTCGATGAGGATGAT
gi|171365 1260 Y L M P T C Q P G P N N N N N I N N P N
gi|246570 3864 TACCTGATGCCCACATGCCAACCGGGGCCCAACAACAACAACAACATAAATAATCCCAAT
gi|171365 1280 Q N N M A A V G V A A G Y M D L I G V P
gi|246570 3924 CAAAACAATATGGCAGCTGTGGGCGTGGCTGCCGGCTACATGGATCTCATCGGAGTGCCC
gi|171365 1300 V S V D N P E Y L L N A Q T L G V G E S
gi|246570 3984 GTTAGTGTGGACAATCCGGAGTATCTGCTAAACGCGCAGACACTGGGTGTTGGGGAGTCG
gi|171365 1320 P I P T Q T I G I P V M G V P G T M E V
gi|246570 4044 CCGATACCCACCCAGACCATCGGGATACCGGTGATGGGAGTCCCGGGCACCATGGAGGTC
gi|171365 1340 K V P M P G S E P T S S D H E Y Y N D T
gi|246570 4104 AAGGTGCCAATGCCAGGCAGTGAGCCAACGAGCTCCGATCACGAGTACTACAATGATACC
gi|171365 1360 Q R E L Q P L H R N R N T E T R V 1377
gi|246570 4164 CAACGGGAGTTGCAGCCACTGCATCGAAACCGCAACACGGAGACGAGGGTG 4215
""",
)
protein_record = protein_alignment.sequences[1]
self.assertEqual(protein_record.id, "gi|17136536|ref|NP_476759.1|")
nucleotide_record = nucleotide_records["gi|24657104|ref|NM_057411.3|"]
alignments = aligner.align(protein_record, nucleotide_record)
self.assertEqual(len(alignments), 1)
alignment = next(alignments)
codon_alignments.append(alignment)
self.assertTrue(
np.array_equal(alignment.coordinates, np.array([[0, 1426], [22, 4300]]))
)
self.assertEqual(
str(alignment),
"""\
gi|171365 0 M L L R R R N G P C P F P L L L L L L A
gi|246571 22 ATGCTGCTGCGACGGCGCAACGGCCCCTGCCCCTTCCCCCTGCTGCTCCTGCTCCTGGCC
gi|171365 20 H C I C I W P A S A A R D R Y A R Q N N
gi|246571 82 CACTGCATTTGCATTTGGCCCGCGTCGGCGGCCCGCGATCGCTACGCCCGCCAGAACAAT
gi|171365 40 R Q R H Q D I D R D R D R D R F L Y R S
gi|246571 142 CGCCAGCGCCATCAGGATATAGATCGCGATCGGGATCGAGATCGATTCCTATACCGCAGC
gi|171365 60 S S A Q N R Q R G G A N F A L G L G A N
gi|246571 202 AGTTCGGCCCAAAATCGACAGAGGGGCGGGGCCAACTTCGCCCTGGGACTGGGAGCCAAC
gi|171365 80 G V T I P T S L E D K N K N E F V K G K
gi|246571 262 GGAGTCACCATTCCCACCAGTCTGGAGGATAAGAACAAGAACGAGTTCGTCAAGGGGAAA
gi|171365 100 I C I G T K S R L S V P S N K E H H Y R
gi|246571 322 ATCTGCATCGGCACTAAATCTCGGCTCTCCGTGCCCTCCAACAAGGAACATCATTACCGG
gi|171365 120 N L R D R Y T N C T Y V D G N L E L T W
gi|246571 382 AACCTCAGAGATCGGTACACGAACTGTACGTATGTGGATGGCAACCTGGAGCTGACCTGG
gi|171365 140 L P N E N L D L S F L D N I R E V T G Y
gi|246571 442 CTGCCCAACGAGAATTTGGACCTCAGCTTCCTGGACAACATACGGGAGGTCACCGGCTAT
gi|171365 160 I L I S H V D V K K V V F P K L Q I I R
gi|246571 502 ATTCTGATCAGTCATGTGGACGTTAAGAAAGTGGTATTTCCCAAACTACAAATCATTCGC
gi|171365 180 G R T L F S L S V E E E K Y A L F V T Y
gi|246571 562 GGACGCACGCTGTTCAGCTTATCCGTGGAGGAGGAGAAGTATGCCTTGTTCGTCACTTAT
gi|171365 200 S K M Y T L E I P D L R D V L N G Q V G
gi|246571 622 TCCAAAATGTACACGCTGGAGATTCCCGATCTACGCGATGTCTTAAATGGCCAAGTGGGC
gi|171365 220 F H N N Y N L C H M R T I Q W S E I V S
gi|246571 682 TTCCACAACAACTACAATCTCTGCCACATGCGAACGATCCAGTGGTCGGAGATTGTATCC
gi|171365 240 N G T D A Y Y N Y D F T A P E R E C P K
gi|246571 742 AACGGCACGGATGCATACTACAACTACGACTTTACTGCTCCGGAGCGCGAGTGTCCCAAG
gi|171365 260 C H E S C T H G C W G E G P K N C Q K F
gi|246571 802 TGCCACGAGAGCTGCACGCACGGATGTTGGGGCGAGGGTCCCAAGAATTGCCAGAAGTTC
gi|171365 280 S K L T C S P Q C A G G R C Y G P K P R
gi|246571 862 AGCAAGCTCACCTGCTCGCCACAGTGTGCCGGAGGTCGTTGCTATGGACCAAAGCCGCGG
gi|171365 300 E C C H L F C A G G C T G P T Q K D C I
gi|246571 922 GAGTGTTGTCACCTCTTCTGCGCCGGAGGATGCACTGGTCCCACGCAAAAGGATTGCATC
gi|171365 320 A C K N F F D E G V C K E E C P P M R K
gi|246571 982 GCCTGCAAGAACTTCTTCGACGAGGGCGTATGCAAGGAGGAATGCCCGCCCATGCGCAAG
gi|171365 340 Y N P T T Y V L E T N P E G K Y A Y G A
gi|246571 1042 TACAATCCCACCACCTATGTTCTTGAAACGAATCCTGAGGGAAAGTATGCCTATGGTGCC
gi|171365 360 T C V K E C P G H L L R D N G A C V R S
gi|246571 1102 ACCTGCGTCAAGGAGTGTCCCGGTCATCTGTTGCGTGATAATGGCGCCTGCGTGCGCAGC
gi|171365 380 C P Q D K M D K G G E C V P C N G P C P
gi|246571 1162 TGTCCCCAGGACAAGATGGACAAGGGGGGCGAGTGTGTGCCCTGCAATGGACCGTGCCCC
gi|171365 400 K T C P G V T V L H A G N I D S F R N C
gi|246571 1222 AAAACCTGCCCGGGCGTTACTGTCCTGCATGCCGGCAACATTGACTCGTTCCGGAATTGT
gi|171365 420 T V I D G N I R I L D Q T F S G F Q D V
gi|246571 1282 ACGGTGATCGATGGCAACATTCGCATTTTGGATCAGACCTTCTCGGGCTTCCAGGATGTC
gi|171365 440 Y A N Y T M G P R Y I P L D P E R L E V
gi|246571 1342 TATGCCAACTACACGATGGGACCACGATACATACCGCTGGATCCCGAGCGACTGGAGGTG
gi|171365 460 F S T V K E I T G Y L N I E G T H P Q F
gi|246571 1402 TTCTCCACGGTGAAGGAGATCACCGGGTATCTGAATATCGAGGGAACCCACCCGCAGTTC
gi|171365 480 R N L S Y F R N L E T I H G R Q L M E S
gi|246571 1462 CGGAATCTGTCGTACTTCCGCAATCTGGAAACAATTCATGGCCGCCAGCTGATGGAGAGC
gi|171365 500 M F A A L A I V K S S L Y S L E M R N L
gi|246571 1522 ATGTTTGCCGCTTTGGCGATCGTTAAGTCATCCCTGTACAGCCTGGAGATGCGCAATCTG
gi|171365 520 K Q I S S G S V V I Q H N R D L C Y V S
gi|246571 1582 AAGCAGATTAGTTCCGGCAGTGTGGTCATCCAGCATAATAGAGACCTCTGCTACGTAAGC
gi|171365 540 N I R W P A I Q K E P E Q K V W V N E N
gi|246571 1642 AATATCCGTTGGCCGGCCATTCAGAAGGAGCCCGAACAGAAGGTGTGGGTCAACGAGAAT
gi|171365 560 L R A D L C E K N G T I C S D Q C N E D
gi|246571 1702 CTCAGGGCGGATCTATGCGAGAAAAATGGAACCATTTGCTCGGATCAGTGCAACGAGGAC
gi|171365 580 G C W G A G T D Q C L T C K N F N F N G
gi|246571 1762 GGCTGCTGGGGAGCTGGCACGGATCAGTGCCTTACCTGCAAGAACTTCAATTTCAATGGC
gi|171365 600 T C I A D C G Y I S N A Y K F D N R T C
gi|246571 1822 ACCTGCATCGCCGACTGTGGTTATATATCCAATGCCTACAAGTTTGACAATAGAACGTGC
gi|171365 620 K I C H P E C R T C N G A G A D H C Q E
gi|246571 1882 AAGATATGCCATCCAGAGTGCCGGACTTGCAATGGAGCTGGAGCAGATCACTGCCAGGAG
gi|171365 640 C V H V R D G Q H C V S E C P K N K Y N
gi|246571 1942 TGCGTCCATGTGAGGGACGGTCAGCACTGTGTGTCCGAGTGCCCGAAGAACAAGTACAAC
gi|171365 660 D R G V C R E C H A T C D G C T G P K D
gi|246571 2002 GATCGTGGTGTCTGCCGAGAGTGCCACGCCACCTGCGATGGATGCACTGGGCCCAAGGAC
gi|171365 680 T I G I G A C T T C N L A I I N N D A T
gi|246571 2062 ACCATCGGCATTGGAGCGTGTACAACGTGCAATTTGGCCATTATCAACAATGACGCCACA
gi|171365 700 V K R C L L K D D K C P D G Y F W E Y V
gi|246571 2122 GTAAAACGCTGCCTGCTGAAGGACGACAAGTGCCCCGATGGGTACTTCTGGGAGTATGTG
gi|171365 720 H P Q E Q G S L K P L A G R A V C R K C
gi|246571 2182 CATCCACAAGAGCAGGGATCGCTAAAGCCATTGGCCGGCAGAGCAGTTTGCCGAAAGTGC
gi|171365 740 H P L C E L C T N Y G Y H E Q V C S K C
gi|246571 2242 CATCCCCTTTGCGAGCTGTGCACCAACTACGGATACCATGAACAGGTGTGCTCCAAGTGC
gi|171365 760 T H Y K R R E Q C E T E C P A D H Y T D
gi|246571 2302 ACCCACTACAAGCGACGAGAGCAGTGCGAGACCGAGTGTCCGGCCGATCACTACACGGAT
gi|171365 780 E E Q R E C F Q C H P E C N G C T G P G
gi|246571 2362 GAGGAGCAGCGCGAGTGCTTCCAGTGCCACCCAGAATGCAACGGTTGCACTGGTCCGGGT
gi|171365 800 A D D C K S C R N F K L F D A N E T G P
gi|246571 2422 GCCGACGATTGCAAGTCTTGTCGCAACTTCAAGTTGTTCGACGCGAATGAGACGGGTCCC
gi|171365 820 Y V N S T M F N C T S K C P L E M R H V
gi|246571 2482 TATGTGAACTCCACGATGTTCAATTGCACCTCGAAGTGTCCCTTGGAGATGCGACATGTG
gi|171365 840 N Y Q Y T A I G P Y C A A S P P R S S K
gi|246571 2542 AACTATCAGTACACGGCCATTGGACCCTACTGTGCAGCTAGTCCGCCGAGGAGCAGCAAG
gi|171365 860 I T A N L D V N M I F I I T G A V L V P
gi|246571 2602 ATAACTGCCAATCTGGATGTGAACATGATCTTCATTATCACTGGTGCTGTTCTGGTGCCG
gi|171365 880 T I C I L C V V T Y I C R Q K Q K A K K
gi|246571 2662 ACGATCTGCATCCTCTGCGTGGTCACATACATTTGTCGGCAAAAGCAAAAGGCCAAGAAA
gi|171365 900 E T V K M T M A L S G C E D S E P L R P
gi|246571 2722 GAAACAGTGAAGATGACCATGGCTCTGTCCGGCTGTGAGGATTCCGAGCCGCTGCGTCCC
gi|171365 920 S N I G A N L C K L R I V K D A E L R K
gi|246571 2782 TCGAACATTGGAGCCAATCTATGCAAGTTGCGCATTGTCAAGGACGCCGAGTTGCGCAAG
gi|171365 940 G G V L G M G A F G R V Y K G V W V P E
gi|246571 2842 GGCGGAGTCCTCGGAATGGGAGCCTTTGGACGAGTGTACAAGGGCGTTTGGGTGCCGGAG
gi|171365 960 G E N V K I P V A I K E L L K S T G A E
gi|246571 2902 GGTGAGAACGTCAAGATTCCAGTGGCCATTAAGGAGCTGCTCAAGTCCACAGGCGCCGAG
gi|171365 980 S S E E F L R E A Y I M A S V E H V N L
gi|246571 2962 TCAAGCGAAGAGTTCCTCCGCGAAGCCTACATCATGGCCTCTGTGGAGCACGTTAATCTG
gi|171365 1000 L K L L A V C M S S Q M M L I T Q L M P
gi|246571 3022 CTGAAGCTCCTGGCCGTCTGCATGTCCTCACAAATGATGCTAATCACGCAACTGATGCCG
gi|171365 1020 L G C L L D Y V R N N R D K I G S K A L
gi|246571 3082 CTTGGCTGCCTGTTGGACTATGTGCGAAATAACCGGGACAAGATCGGCTCTAAGGCTCTG
gi|171365 1040 L N W S T Q I A K G M S Y L E E K R L V
gi|246571 3142 CTCAACTGGAGCACGCAAATCGCCAAGGGCATGTCGTATCTGGAGGAGAAGCGACTGGTC
gi|171365 1060 H R D L A A R N V L V Q T P S L V K I T
gi|246571 3202 CACAGAGACTTGGCTGCCCGCAATGTCCTGGTGCAGACTCCCTCGCTGGTGAAGATCACC
gi|171365 1080 D F G L A K L L S S D S N E Y K A A G G
gi|246571 3262 GACTTTGGGCTGGCCAAGTTGCTGAGCAGCGATTCCAATGAGTACAAGGCTGCTGGCGGC
gi|171365 1100 K M P I K W L A L E C I R N R V F T S K
gi|246571 3322 AAGATGCCCATCAAGTGGTTGGCACTGGAGTGCATTCGCAATCGTGTATTCACCAGCAAG
gi|171365 1120 S D V W A F G V T I W E L L T F G Q R P
gi|246571 3382 TCCGATGTCTGGGCCTTTGGTGTGACAATTTGGGAACTGCTGACCTTTGGCCAGCGTCCA
gi|171365 1140 H E N I P A K D I P D L I E V G L K L E
gi|246571 3442 CACGAGAACATCCCCGCTAAGGATATTCCCGATCTTATTGAAGTCGGTCTGAAGCTGGAG
gi|171365 1160 Q P E I C S L D I Y C T L L S C W H L D
gi|246571 3502 CAGCCGGAGATTTGTTCGCTGGACATTTACTGCACACTTCTCTCGTGCTGGCACTTGGAT
gi|171365 1180 A A M R P T F K Q L T T V F A E F A R D
gi|246571 3562 GCCGCCATGCGTCCAACCTTCAAGCAGCTGACTACGGTCTTTGCTGAGTTCGCCAGAGAT
gi|171365 1200 P G R Y L A I P G D K F T R L P A Y T S
gi|246571 3622 CCGGGTCGCTATCTGGCCATTCCCGGGGATAAGTTCACCCGGCTGCCGGCCTACACGAGT
gi|171365 1220 Q D E K D L I R K L A P T T D G S E A I
gi|246571 3682 CAGGATGAGAAGGATCTCATCCGAAAATTGGCTCCCACCACCGATGGGTCCGAAGCCATT
gi|171365 1240 A E P D D Y L Q P K A A P G P S H R T D
gi|246571 3742 GCGGAACCCGATGACTACCTGCAACCCAAGGCAGCACCTGGTCCTAGTCACAGAACCGAC
gi|171365 1260 C T D E I P K L N R Y C K D P S N K N S
gi|246571 3802 TGCACGGATGAGATACCCAAGCTGAACCGCTACTGCAAGGATCCTAGCAACAAGAATTCG
gi|171365 1280 S T G D D E T D S S A R E V G V G N L R
gi|246571 3862 AGTACCGGAGACGATGAGACGGATTCGAGTGCCCGGGAAGTGGGCGTGGGTAATCTGCGC
gi|171365 1300 L D L P V D E D D Y L M P T C Q P G P N
gi|246571 3922 CTCGATCTACCAGTCGATGAGGATGATTACCTGATGCCCACATGCCAACCGGGGCCCAAC
gi|171365 1320 N N N N I N N P N Q N N M A A V G V A A
gi|246571 3982 AACAACAACAACATAAATAATCCCAATCAAAACAATATGGCAGCTGTGGGCGTGGCTGCC
gi|171365 1340 G Y M D L I G V P V S V D N P E Y L L N
gi|246571 4042 GGCTACATGGATCTCATCGGAGTGCCCGTTAGTGTGGACAATCCGGAGTATCTGCTAAAC
gi|171365 1360 A Q T L G V G E S P I P T Q T I G I P V
gi|246571 4102 GCGCAGACACTGGGTGTTGGGGAGTCGCCGATACCCACCCAGACCATCGGGATACCGGTG
gi|171365 1380 M G V P G T M E V K V P M P G S E P T S
gi|246571 4162 ATGGGAGTCCCGGGCACCATGGAGGTCAAGGTGCCAATGCCAGGCAGTGAGCCAACGAGC
gi|171365 1400 S D H E Y Y N D T Q R E L Q P L H R N R
gi|246571 4222 TCCGATCACGAGTACTACAATGATACCCAACGGGAGTTGCAGCCACTGCATCGAAACCGC
gi|171365 1420 N T E T R V 1426
gi|246571 4282 AACACGGAGACGAGGGTG 4300
""",
)
protein_record = protein_alignment.sequences[2]
self.assertEqual(protein_record.id, "gi|302179501|gb|ADK98534.1|")
nucleotide_record = nucleotide_records["gi|302179500|gb|HM749883.1|"]
alignments = aligner.align(protein_record, nucleotide_record)
self.assertEqual(len(alignments), 1)
alignment = next(alignments)
codon_alignments.append(alignment)
self.assertTrue(
np.array_equal(alignment.coordinates, np.array([[0, 1185], [0, 3555]]))
)
self.assertEqual(
str(alignment),
"""\
gi|302179 0 M K K H E L L C Q G T S N K L T Q L G T
gi|302179 0 ATGAAAAAGCACGAGTTACTTTGCCAAGGGACAAGTAACAAGCTCACCCAGTTGGGCACT
gi|302179 20 F E D H F L S L Q R M F N N C E V V L G
gi|302179 60 TTTGAAGACCACTTTCTGAGCCTACAGAGGATGTTCAACAACTGTGAGGTGGTCCTTGGG
gi|302179 40 N L E I T Y M Q S S Y N L S F L K T I Q
gi|302179 120 AATTTGGAAATTACCTACATGCAGAGTAGTTACAACCTTTCTTTTCTCAAGACCATCCAG
gi|302179 60 E V A G Y V L I A L N T V E K I P L E N
gi|302179 180 GAGGTTGCCGGCTATGTACTCATTGCCCTCAACACAGTGGAGAAGATTCCGCTGGAAAAC
gi|302179 80 L Q I I R G N V L Y E N T H A L A V L S
gi|302179 240 CTGCAGATCATCCGAGGAAATGTGCTTTATGAAAACACCCATGCCTTAGCCGTCTTATCC
gi|302179 100 N Y G A N K T G L R E L P L R N L Q E I
gi|302179 300 AACTATGGAGCAAACAAAACCGGACTGAGGGAGCTGCCCTTGAGAAACTTACAGGAAATT
gi|302179 120 L Q G A V R F S N N P V L C N V E T I Q
gi|302179 360 CTGCAAGGTGCCGTGAGATTCAGCAACAACCCTGTCCTCTGCAACGTGGAGACCATCCAG
gi|302179 140 W R D I V N P D F L S N M T G D F Q N Q
gi|302179 420 TGGCGGGACATCGTCAACCCTGATTTTCTAAGCAACATGACAGGGGACTTTCAGAACCAG
gi|302179 160 Q G N C P K C D P A C L N R S C W G A G
gi|302179 480 CAGGGCAACTGCCCAAAGTGTGATCCAGCCTGTCTCAACAGAAGCTGCTGGGGTGCCGGG
gi|302179 180 E E N C Q K L T K I I C A Q Q C S G R C
gi|302179 540 GAGGAGAACTGTCAGAAATTGACCAAAATCATCTGTGCCCAGCAGTGTTCCGGGCGCTGC
gi|302179 200 R G R S P S D C C H N Q C A A G C T G P
gi|302179 600 CGTGGCAGGTCCCCCAGTGACTGCTGCCACAACCAGTGTGCCGCTGGCTGCACAGGGCCA
gi|302179 220 R E S D C L V C R R F R D E A T C K D T
gi|302179 660 CGGGAGAGCGACTGCCTGGTCTGCCGCAGGTTCCGTGATGAAGCCACCTGCAAGGACACG
gi|302179 240 C P P L M L Y D P T T Y E M K V N P L G
gi|302179 720 TGTCCGCCACTCATGCTCTATGACCCTACCACCTACGAAATGAAGGTCAACCCGCTGGGG
gi|302179 260 K Y S F G A T C V K K C P R N Y V V T D
gi|302179 780 AAGTACAGCTTTGGCGCCACCTGTGTCAAGAAGTGTCCCCGTAACTACGTGGTGACAGAC
gi|302179 280 H G S C V R A C S S D S Q E V E E D G V
gi|302179 840 CACGGCTCCTGCGTCCGCGCCTGCAGTTCTGACAGCCAGGAGGTAGAGGAAGACGGTGTC
gi|302179 300 R K C K K C D G P C G K V C N G I G I G
gi|302179 900 CGCAAGTGTAAAAAGTGTGACGGGCCTTGTGGCAAAGTTTGTAACGGAATAGGAATCGGT
gi|302179 320 E F K D T L S I N A T N I K H F R N C T
gi|302179 960 GAGTTTAAAGACACACTTTCCATAAATGCTACAAACATTAAACACTTCAGAAACTGCACA
gi|302179 340 S I S G D L H I L P V A F R G D S F T R
gi|302179 1020 TCCATCAGTGGAGATCTTCATATCCTGCCAGTAGCATTTAGGGGTGACTCCTTCACACGT
gi|302179 360 T A P L D P K E L D I L R T V K E I T G
gi|302179 1080 ACTGCACCTCTGGACCCGAAAGAACTGGACATTCTAAGAACTGTAAAAGAAATAACAGGG
gi|302179 380 F L L I Q A W P E N R T D L H A F E N L
gi|302179 1140 TTTTTGCTGATTCAGGCCTGGCCCGAAAACAGGACTGACCTCCATGCTTTTGAGAACCTG
gi|302179 400 E I I R G R T K Q H G Q F S L A V V G L
gi|302179 1200 GAAATCATACGTGGCAGAACGAAGCAGCATGGCCAGTTTTCTCTTGCGGTTGTCGGCCTG
gi|302179 420 D I T S L G L R S L K E I S D G D V I I
gi|302179 1260 GATATAACATCTTTGGGATTACGCTCCCTCAAGGAGATAAGTGATGGTGATGTGATAATT
gi|302179 440 S G N R N L C Y A D T I R W K K L F G T
gi|302179 1320 TCAGGAAATCGAAACTTGTGCTATGCAGATACAATACGCTGGAAAAAACTTTTTGGGACC
gi|302179 460 S T Q K T K I L N N R S E K Q C K A A G
gi|302179 1380 TCAACTCAGAAAACCAAAATTTTAAACAACAGGAGTGAAAAACAGTGCAAGGCCGCAGGC
gi|302179 480 H I C H P L C S S E G C W G P G P K Y C
gi|302179 1440 CACATCTGTCACCCGCTGTGCTCATCAGAGGGCTGCTGGGGACCGGGACCCAAATACTGC
gi|302179 500 M S C Q N F S R G K E C V G K C N I L E
gi|302179 1500 ATGTCCTGCCAGAACTTCAGTCGTGGCAAGGAGTGTGTGGGAAAGTGCAACATTCTAGAG
gi|302179 520 G E P R E F V E N S E C V Q C H P E C L
gi|302179 1560 GGAGAGCCCAGAGAATTCGTGGAGAACTCCGAGTGTGTGCAGTGCCATCCAGAATGCCTG
gi|302179 540 P Q A M N V T C T G R G P G N C V K C A
gi|302179 1620 CCCCAGGCCATGAACGTGACCTGCACTGGACGCGGACCAGGCAACTGTGTAAAGTGCGCC
gi|302179 560 H Y I D G P H C V K T C P A G V A G E N
gi|302179 1680 CACTACATTGATGGCCCTCACTGCGTCAAGACCTGCCCTGCTGGAGTCGCGGGAGAGAAT
gi|302179 580 G T L I W K F A D A N H V C L L C H P N
gi|302179 1740 GGCACCCTGATCTGGAAGTTTGCAGATGCCAACCACGTGTGTCTCCTGTGCCACCCCAAC
gi|302179 600 C T Y G C E G P G L E G C P Q K G P K I
gi|302179 1800 TGCACCTATGGCTGTGAAGGGCCAGGTCTCGAAGGCTGTCCACAAAAAGGGCCCAAGATC
gi|302179 620 P S I A T G I V G G L L L V V V L A L S
gi|302179 1860 CCGTCCATTGCCACGGGCATCGTGGGCGGCCTGCTGCTGGTGGTGGTGCTGGCCCTGAGC
gi|302179 640 V G L F M R R R H I V R K R T L R R L L
gi|302179 1920 GTCGGCCTCTTCATGCGCAGGCGCCACATCGTGCGCAAGCGCACACTGCGCCGGCTGCTG
gi|302179 660 Q E R E L V E P L T P S G E A P N Q A L
gi|302179 1980 CAGGAGCGTGAGCTCGTGGAGCCTCTGACGCCCAGCGGAGAAGCTCCCAACCAAGCTCTC
gi|302179 680 L R I L K E T E F K K V K V L G S G A F
gi|302179 2040 TTGAGGATCCTAAAGGAAACAGAATTCAAGAAGGTCAAGGTGCTGGGCTCGGGAGCATTT
gi|302179 700 G T V Y K G L W I P E G E K V K I P V A
gi|302179 2100 GGCACCGTGTACAAGGGACTCTGGATCCCAGAAGGCGAGAAGGTTAAAATTCCTGTAGCT
gi|302179 720 I K E L R E A T S P K A N K E I L D E A
gi|302179 2160 ATCAAGGAATTAAGAGAAGCCACATCTCCAAAAGCCAACAAGGAAATTCTTGATGAGGCC
gi|302179 740 Y V M A S V D N P H V C R L L G I C L T
gi|302179 2220 TACGTGATGGCCAGTGTGGACAACCCCCATGTGTGCCGCCTCCTGGGCATCTGCCTGACC
gi|302179 760 S T V Q L I T Q L M P F G C L L D Y V R
gi|302179 2280 TCCACCGTGCAGCTCATCACACAGCTCATGCCCTTCGGCTGCCTGCTGGACTACGTCCGC
gi|302179 780 E H K D N V G S Q Y L L N W C V Q I A K
gi|302179 2340 GAGCACAAGGACAATGTCGGCTCCCAGTACCTGCTCAACTGGTGTGTGCAGATCGCAAAG
gi|302179 800 G M N Y L E D R R L V H R D L A A R N V
gi|302179 2400 GGCATGAATTACCTGGAAGACCGGCGCTTGGTGCATAGGGACCTGGCAGCCAGGAACGTG
gi|302179 820 L V K T P Q H V K I T D F G L A K L L G
gi|302179 2460 CTGGTGAAGACGCCGCAGCACGTGAAGATCACAGACTTCGGGCTGGCCAAGCTGCTGGGT
gi|302179 840 A E E K E Y H A E G G K V P I K W M A L
gi|302179 2520 GCCGAGGAGAAGGAGTATCATGCAGAAGGAGGCAAGGTCCCTATCAAATGGATGGCTTTG
gi|302179 860 E S I L H R I Y T H Q S D V W S Y G V T
gi|302179 2580 GAATCAATTTTACACCGAATTTATACCCATCAGAGTGATGTCTGGAGCTATGGAGTCACT
gi|302179 880 V W E L M T F G S K P Y D G I P A S E I
gi|302179 2640 GTTTGGGAGTTGATGACCTTTGGATCCAAGCCTTACGATGGAATCCCTGCGAGTGAGATC
gi|302179 900 S T V L E K G E R L P Q P P I C T I D V
gi|302179 2700 TCGACTGTCCTGGAGAAAGGAGAGCGCCTCCCACAGCCACCCATCTGCACCATCGACGTC
gi|302179 920 Y M I M V K C W M I D A D S R P K F R E
gi|302179 2760 TACATGATCATGGTCAAGTGCTGGATGATAGATGCAGACAGTCGCCCAAAGTTCCGTGAG
gi|302179 940 L I L E F S K M A R D P Q R Y L V I Q G
gi|302179 2820 TTGATCCTTGAATTCTCCAAGATGGCCCGAGACCCCCAGCGCTACCTTGTCATCCAGGGG
gi|302179 960 D E R M H L P S P T D S N F Y R A L M D
gi|302179 2880 GACGAGAGAATGCATTTGCCAAGCCCTACGGACTCCAACTTCTACCGCGCCCTGATGGAT
gi|302179 980 E E D M E D V V D A D E Y L V P Q Q G F
gi|302179 2940 GAGGAGGACATGGAGGATGTTGTGGATGCCGATGAGTACCTCGTCCCCCAGCAGGGCTTC
gi|302179 1000 F H S P T T S R T P L L S S L S T S S N
gi|302179 3000 TTCCACAGCCCCACCACCTCCCGGACACCCCTCCTCAGCTCGCTGAGCACCTCCAGCAAC
gi|302179 1020 T P T V T C V D R N G S Y P L K E D S F
gi|302179 3060 ACTCCCACTGTGACTTGCGTTGATAGAAATGGGAGCTACCCTCTCAAGGAAGACAGCTTC
gi|302179 1040 L Q R Y S S D P T G A L I E D S M D D A
gi|302179 3120 CTGCAGCGCTACAGCTCAGACCCCACTGGTGCCCTCATCGAGGACAGCATGGACGACGCT
gi|302179 1060 F L P V P E Y V N Q S V P K R P A G S V
gi|302179 3180 TTCCTCCCAGTACCCGAATATGTAAACCAATCTGTTCCCAAAAGACCCGCAGGCTCTGTC
gi|302179 1080 Q N P V Y H N Q P L Y P A P G R D P Q Y
gi|302179 3240 CAGAACCCTGTCTATCACAATCAGCCTCTATATCCAGCTCCTGGCAGAGACCCTCAGTAC
gi|302179 1100 Q N S L S N A V D N P E Y L N T T H P A
gi|302179 3300 CAAAATTCACTCAGCAACGCCGTGGACAACCCTGAGTATCTCAACACCACCCATCCTGCC
gi|302179 1120 C I N G V L D G P A L W A Q K G S H Q F
gi|302179 3360 TGTATCAATGGTGTGCTCGACGGCCCTGCCCTCTGGGCTCAGAAGGGCAGTCACCAATTT
gi|302179 1140 S L D N P D Y Q Q A F F P K E A K S N G
gi|302179 3420 AGCCTAGACAACCCTGACTACCAGCAGGCCTTCTTTCCCAAGGAAGCCAAGTCGAATGGC
gi|302179 1160 I F K G P A A E N A E Y L R A A P A G S
gi|302179 3480 ATCTTTAAGGGGCCTGCAGCTGAAAATGCAGAATACCTGCGGGCAGCACCAGCAGGCAGT
gi|302179 1180 D F T G A 1185
gi|302179 3540 GACTTTACTGGGGCC 3555
""",
)
protein_record = protein_alignment.sequences[3]
self.assertEqual(protein_record.id, "gi|47522840|ref|NP_999172.1|")
nucleotide_record = nucleotide_records["gi|47522839|ref|NM_214007.1|"]
alignments = aligner.align(protein_record, nucleotide_record)
self.assertEqual(len(alignments), 1)
alignment = next(alignments)
codon_alignments.append(alignment)
self.assertTrue(
np.array_equal(alignment.coordinates, np.array([[0, 1209], [126, 3753]]))
)
self.assertEqual(
str(alignment),
"""\
gi|475228 0 M R R S W A G G A A L L A L L A A H F Q
gi|475228 126 ATGCGACGCTCCTGGGCGGGCGGCGCCGCGCTCCTGGCGCTGCTGGCCGCGCACTTCCAG
gi|475228 20 A S P A L E E K K V C Q G T S N K L T Q
gi|475228 186 GCGAGTCCGGCGCTGGAGGAGAAGAAAGTTTGCCAAGGTACAAGTAACAAGCTCACCCAG
gi|475228 40 L G T F E D H F L S L Q R M F N N C E V
gi|475228 246 CTGGGCACTTTCGAAGACCACTTTCTGAGCCTCCAGAGGATGTTCAATAACTGCGAGGTG
gi|475228 60 V L G N L E I T Y M Q N S Y N L S F L K
gi|475228 306 GTCCTTGGGAACTTGGAGATCACCTACATGCAGAACAGCTACAACCTGTCTTTCCTAAAG
gi|475228 80 T I Q E V A G Y V L I A L N T V E K I P
gi|475228 366 ACCATTCAGGAGGTCGCCGGCTACGTGCTCATCGCCCTCAACACCGTGGAGAAGATCCCT
gi|475228 100 L E N L Q I I R G N V L Y E N T H A L A
gi|475228 426 TTGGAAAACCTGCAGATCATCCGAGGAAATGTACTGTATGAAAACACCCATGCCTTAGCC
gi|475228 120 V L S N Y G A N K T G L R E L P M R N L
gi|475228 486 GTCTTATCCAACTACGGGGCCAATAAAACCGGCCTGAGGGAGCTGCCCATGAGGAACTTA
gi|475228 140 Q E I L Q G A V R F S N N P A L C H A E
gi|475228 546 CAAGAGATCCTGCAAGGCGCCGTGCGCTTCAGCAACAACCCTGCCCTCTGTCACGCGGAG
gi|475228 160 S I Q W R D I V N S D F L S N M S M D F
gi|475228 606 TCCATCCAGTGGAGGGACATTGTCAACAGCGACTTTCTAAGCAACATGTCCATGGACTTT
gi|475228 180 Q S Q L G S C P K C D P G C L N G S C W
gi|475228 666 CAGAGCCAGCTGGGCAGCTGCCCGAAGTGTGATCCAGGCTGTCTCAATGGGAGCTGCTGG
gi|475228 200 G A G K E N C Q K L T K V I C A Q Q C S
gi|475228 726 GGTGCTGGGAAGGAGAACTGCCAGAAATTGACCAAAGTCATCTGTGCCCAGCAGTGCTCC
gi|475228 220 G R C R G R S P S D C C H N Q C A A G C
gi|475228 786 GGGCGCTGCCGCGGCCGGTCGCCCAGTGACTGCTGCCACAACCAGTGCGCCGCTGGCTGC
gi|475228 240 T G P R E S D C L V C R R F R D E A T C
gi|475228 846 ACGGGGCCGCGGGAGAGCGACTGCCTGGTTTGCCGCAGATTCCGTGACGAGGCCACCTGC
gi|475228 260 K D T C P P L M L Y N P T T Y Q M D V N
gi|475228 906 AAGGACACATGCCCGCCGCTCATGCTCTACAACCCCACCACCTACCAGATGGACGTCAAC
gi|475228 280 P L G K Y S F G A T C V K K C P R N Y V
gi|475228 966 CCGCTGGGGAAGTACAGCTTTGGCGCCACCTGTGTCAAGAAGTGCCCTCGTAACTACGTG
gi|475228 300 V T D H G S C V R A C S S D S Y E V E E
gi|475228 1026 GTGACAGACCATGGCTCCTGTGTCCGTGCCTGCAGCTCCGACAGCTACGAGGTGGAGGAG
gi|475228 320 D G V R K C K K C D G P C G K V C N G I
gi|475228 1086 GACGGCGTCCGCAAGTGTAAAAAGTGTGACGGGCCCTGCGGCAAAGTTTGTAACGGGATA
gi|475228 340 G I G E F K D T L S I N A T N I K H F R
gi|475228 1146 GGGATTGGCGAGTTTAAAGACACACTTTCCATAAATGCTACGAATATCAAGCACTTCAGG
gi|475228 360 N C T S I S G D L H I L P V A F R G D S
gi|475228 1206 AACTGCACCTCGATCAGCGGAGATCTTCATATCCTGCCGGTAGCATTTAGGGGTGACTCC
gi|475228 380 F T R T P P L D P K E L D I L K T V K E
gi|475228 1266 TTCACACGCACGCCGCCTCTGGACCCCAAGGAACTGGACATCCTGAAAACCGTGAAGGAA
gi|475228 400 I T G F L L I Q A W P E N R T G L H A F
gi|475228 1326 ATAACAGGGTTTTTACTGATTCAGGCCTGGCCTGAAAACAGGACTGGCCTCCATGCTTTT
gi|475228 420 E N L E I I R G R T K Q H G Q F S L A V
gi|475228 1386 GAGAACCTGGAAATCATACGTGGCAGGACGAAGCAACATGGTCAGTTTTCCCTCGCGGTT
gi|475228 440 V G L D I A S L G L R S L K E I S D G D
gi|475228 1446 GTTGGCCTGGACATAGCGTCCTTGGGGATGCGCTCCCTCAAGGAGATCAGCGACGGAGAC
gi|475228 460 V I V S G N R N L C Y A N T I S W K K L
gi|475228 1506 GTGATCGTCTCAGGAAACCGAAACCTGTGCTATGCAAATACAATCAGCTGGAAAAAACTA
gi|475228 480 F G T A S Q K T K I I N N R S E K E C K
gi|475228 1566 TTTGGGACCGCAAGTCAGAAAACCAAAATTATAAACAACAGGAGCGAAAAAGAGTGCAAA
gi|475228 500 A M G H I C N P L C S S E G C W G P E P
gi|475228 1626 GCCATGGGCCACATCTGTAACCCGCTGTGCTCATCAGAGGGCTGCTGGGGCCCTGAACCC
gi|475228 520 R D C M S C R N F S R G K E C V E K C N
gi|475228 1686 AGAGACTGCATGTCCTGTCGAAACTTTAGCCGCGGCAAGGAATGTGTGGAGAAGTGCAAC
gi|475228 540 V L E G E P R E F V E N A E C V Q C H P
gi|475228 1746 GTTCTGGAGGGGGAGCCGAGAGAGTTCGTGGAGAATGCCGAGTGTGTGCAGTGCCACCCG
gi|475228 560 E C L P Q A K N V T C M G R G P D S C V
gi|475228 1806 GAGTGCCTGCCCCAGGCCAAGAACGTGACCTGCATGGGACGCGGACCGGACAGCTGTGTC
gi|475228 580 R C A H Y I D G P H C V K T C P A G I A
gi|475228 1866 CGGTGTGCTCACTACATCGACGGCCCTCACTGTGTCAAGACCTGCCCCGCGGGAATCGCA
gi|475228 600 G E N S T L I W K F A D A N H V C H L C
gi|475228 1926 GGAGAAAACAGCACCCTCATCTGGAAGTTTGCGGATGCCAACCACGTGTGTCACCTGTGC
gi|475228 620 H P N C T Y G C V G P G L E G C A V D R
gi|475228 1986 CACCCCAACTGCACCTACGGCTGTGTCGGACCAGGTCTCGAGGGCTGTGCGGTGGACAGG
gi|475228 640 P K I P S I A T G I V G G L L L A V V L
gi|475228 2046 CCCAAGATCCCGTCCATCGCCACCGGGATAGTGGGGGGCCTGCTTCTGGCCGTGGTGCTG
gi|475228 660 A L G V G L F L R R R H I V R K R T L R
gi|475228 2106 GCCCTGGGGGTCGGCCTCTTTCTGCGCAGGCGCCACATCGTCCGCAAGCGCACGCTGCGC
gi|475228 680 R L L Q E R E L V E P L T P S G E A P N
gi|475228 2166 CGGCTGCTGCAGGAGCGGGAGCTGGTTGAGCCTCTCACACCCAGTGGAGAAGCTCCCAAC
gi|475228 700 Q A L L R I L K E T E F K K V K V L G S
gi|475228 2226 CAAGCTCTCTTGAGGATCCTGAAGGAGACGGAATTCAAAAAGGTCAAGGTGCTGGGCTCC
gi|475228 720 G A F G T V Y K G L W I P E G E K V K I
gi|475228 2286 GGCGCGTTCGGCACGGTGTACAAGGGCCTCTGGATCCCAGAAGGTGAGAAGGTGAAAATT
gi|475228 740 P V A I K E L R E A T S P K A N K E I L
gi|475228 2346 CCTGTGGCTATCAAGGAATTAAGAGAAGCCACTTCTCCAAAAGCCAACAAGGAAATTCTT
gi|475228 760 D E A Y V M A S V D N P H V C R L L G I
gi|475228 2406 GACGAAGCCTACGTGATGGCCAGTGTGGACAATCCTCATGTGTGCCGCCTCCTGGGCATC
gi|475228 780 C L T S T V Q L I T Q L M P F G C L L D
gi|475228 2466 TGCCTGACCTCCACGGTGCAGCTCATCACGCAGCTCATGCCCTTCGGCTGCCTCCTGGAC
gi|475228 800 Y V R E H K D N I G S Q H L L N W C V Q
gi|475228 2526 TACGTCCGCGAGCACAAGGACAACATCGGCTCCCAGCACCTGCTCAACTGGTGTGTGCAG
gi|475228 820 I A K G M N Y L E D R R L V H R D L A A
gi|475228 2586 ATCGCAAAGGGCATGAACTATCTGGAAGACCGGCGCTTGGTGCACCGAGACCTGGCGGCC
gi|475228 840 R N V L V K T P Q H V K I T D F G L A K
gi|475228 2646 AGGAATGTGCTGGTGAAGACACCGCAGCATGTCAAGATCACTGACTTTGGGCTGGCCAAG
gi|475228 860 L L G A E E K E Y H A E G G K V P I K W
gi|475228 2706 CTGCTGGGCGCCGAGGAGAAAGAGTACCACGCGGAAGGAGGCAAAGTGCCCATCAAGTGG
gi|475228 880 L A L E S I L H R V Y T H Q S D V W S Y
gi|475228 2766 CTGGCTCTAGAGTCAATCCTGCACCGTGTATACACCCACCAGAGTGACGTCTGGAGCTAC
gi|475228 900 G V T V W E L M T F G S K P Y D G I P A
gi|475228 2826 GGAGTCACCGTTTGGGAGCTGATGACCTTTGGGTCCAAGCCTTATGACGGGATCCCCGCG
gi|475228 920 S E I S T V L E K G E R L P Q P P I C T
gi|475228 2886 AGTGAGATCTCGACCGTCCTGGAGAAGGGAGAGCGCCTCCCGCAGCCCCCCATCTGCACC
gi|475228 940 I D V Y M I M V K C W M I D A D S R P K
gi|475228 2946 ATTGATGTCTACATGATCATGGTCAAGTGCTGGATGATAGATGCTGATAGTCGCCCAAAG
gi|475228 960 F R E L I I E F S K M A R D P Q R Y L V
gi|475228 3006 TTCCGTGAGCTGATCATCGAATTCTCCAAAATGGCCCGAGACCCCCAGCGCTACCTTGTC
gi|475228 980 I Q G D E R M H L P S P T D S N F Y R A
gi|475228 3066 ATCCAGGGAGACGAGCGAATGCACTTGCCAAGCCCTACGGACTCCAACTTCTACCGCGCC
gi|475228 1000 L M D E E D M E D V V D A D E Y L V P Q
gi|475228 3126 CTGATGGACGAGGAGGACATGGAGGATGTGGTGGACGCCGACGAGTACCTCGTCCCCCAG
gi|475228 1020 Q G F F H S P A T S R T P L L S S L S A
gi|475228 3186 CAGGGCTTCTTCCACAGCCCCGCCACCTCCCGGACGCCGCTGCTCAGCTCTCTGAGCGCC
gi|475228 1040 T S S T P A V A C V D R N G Q S Y P L K
gi|475228 3246 ACCAGCAGCACCCCCGCTGTGGCTTGCGTTGACAGAAACGGGCAGAGTTATCCCCTCAAG
gi|475228 1060 E D S F L Q R Y S S D P T G A L T E D S
gi|475228 3306 GAAGACAGCTTCCTGCAGCGGTACAGCTCCGACCCCACTGGCGCCCTGACCGAGGACAGC
gi|475228 1080 L D D T F L P A P E Y V N Q S V P K R P
gi|475228 3366 CTAGACGACACTTTTCTCCCAGCACCCGAATATGTAAACCAGTCTGTTCCCAAGAGGCCC
gi|475228 1100 A G S V Q N P V Y H N Q P L S A A P G R
gi|475228 3426 GCGGGCTCCGTCCAGAACCCTGTCTACCACAATCAGCCTCTCAGTGCAGCTCCTGGCCGG
gi|475228 1120 D P H Y Q N S H S N A V G N P E Y L N T
gi|475228 3486 GACCCCCACTACCAGAACTCCCACAGCAATGCCGTGGGCAACCCTGAGTATCTCAACACC
gi|475228 1140 P R P A C I N G G L D G P A F W A Q T G
gi|475228 3546 CCCCGCCCCGCCTGCATCAACGGAGGACTGGACGGCCCTGCCTTCTGGGCACAGACAGGC
gi|475228 1160 S H Q I N L D N P D Y Q Q A F F P K E A
gi|475228 3606 AGCCACCAGATTAATCTGGACAACCCAGACTACCAGCAGGCCTTCTTCCCCAAGGAAGCC
gi|475228 1180 K S N G I C K G P A A E N A E Y L R A A
gi|475228 3666 AAGTCAAACGGCATCTGTAAGGGTCCCGCCGCCGAAAACGCAGAGTACCTAAGGGCGGCA
gi|475228 1200 P A S S D L T G A 1209
gi|475228 3726 CCAGCCAGCAGTGACCTTACTGGGGCA 3753
""",
)
protein_record = protein_alignment.sequences[4]
self.assertEqual(protein_record.id, "gi|29725609|ref|NP_005219.2|")
nucleotide_record = nucleotide_records["gi|41327737|ref|NM_005228.3|"]
alignments = aligner.align(protein_record, nucleotide_record)
self.assertEqual(len(alignments), 1)
alignment = next(alignments)
codon_alignments.append(alignment)
self.assertTrue(
np.array_equal(alignment.coordinates, np.array([[0, 1210], [246, 3876]]))
)
self.assertEqual(
str(alignment),
"""\
gi|297256 0 M R P S G T A G A A L L A L L A A L C P
gi|413277 246 ATGCGACCCTCCGGGACGGCCGGGGCAGCGCTCCTGGCGCTGCTGGCTGCGCTCTGCCCG
gi|297256 20 A S R A L E E K K V C Q G T S N K L T Q
gi|413277 306 GCGAGTCGGGCTCTGGAGGAAAAGAAAGTTTGCCAAGGCACGAGTAACAAGCTCACGCAG
gi|297256 40 L G T F E D H F L S L Q R M F N N C E V
gi|413277 366 TTGGGCACTTTTGAAGATCATTTTCTCAGCCTCCAGAGGATGTTCAATAACTGTGAGGTG
gi|297256 60 V L G N L E I T Y V Q R N Y D L S F L K
gi|413277 426 GTCCTTGGGAATTTGGAAATTACCTATGTGCAGAGGAATTATGATCTTTCCTTCTTAAAG
gi|297256 80 T I Q E V A G Y V L I A L N T V E R I P
gi|413277 486 ACCATCCAGGAGGTGGCTGGTTATGTCCTCATTGCCCTCAACACAGTGGAGCGAATTCCT
gi|297256 100 L E N L Q I I R G N M Y Y E N S Y A L A
gi|413277 546 TTGGAAAACCTGCAGATCATCAGAGGAAATATGTACTACGAAAATTCCTATGCCTTAGCA
gi|297256 120 V L S N Y D A N K T G L K E L P M R N L
gi|413277 606 GTCTTATCTAACTATGATGCAAATAAAACCGGACTGAAGGAGCTGCCCATGAGAAATTTA
gi|297256 140 Q E I L H G A V R F S N N P A L C N V E
gi|413277 666 CAGGAAATCCTGCATGGCGCCGTGCGGTTCAGCAACAACCCTGCCCTGTGCAACGTGGAG
gi|297256 160 S I Q W R D I V S S D F L S N M S M D F
gi|413277 726 AGCATCCAGTGGCGGGACATAGTCAGCAGTGACTTTCTCAGCAACATGTCGATGGACTTC
gi|297256 180 Q N H L G S C Q K C D P S C P N G S C W
gi|413277 786 CAGAACCACCTGGGCAGCTGCCAAAAGTGTGATCCAAGCTGTCCCAATGGGAGCTGCTGG
gi|297256 200 G A G E E N C Q K L T K I I C A Q Q C S
gi|413277 846 GGTGCAGGAGAGGAGAACTGCCAGAAACTGACCAAAATCATCTGTGCCCAGCAGTGCTCC
gi|297256 220 G R C R G K S P S D C C H N Q C A A G C
gi|413277 906 GGGCGCTGCCGTGGCAAGTCCCCCAGTGACTGCTGCCACAACCAGTGTGCTGCAGGCTGC
gi|297256 240 T G P R E S D C L V C R K F R D E A T C
gi|413277 966 ACAGGCCCCCGGGAGAGCGACTGCCTGGTCTGCCGCAAATTCCGAGACGAAGCCACGTGC
gi|297256 260 K D T C P P L M L Y N P T T Y Q M D V N
gi|413277 1026 AAGGACACCTGCCCCCCACTCATGCTCTACAACCCCACCACGTACCAGATGGATGTGAAC
gi|297256 280 P E G K Y S F G A T C V K K C P R N Y V
gi|413277 1086 CCCGAGGGCAAATACAGCTTTGGTGCCACCTGCGTGAAGAAGTGTCCCCGTAATTATGTG
gi|297256 300 V T D H G S C V R A C G A D S Y E M E E
gi|413277 1146 GTGACAGATCACGGCTCGTGCGTCCGAGCCTGTGGGGCCGACAGCTATGAGATGGAGGAA
gi|297256 320 D G V R K C K K C E G P C R K V C N G I
gi|413277 1206 GACGGCGTCCGCAAGTGTAAGAAGTGCGAAGGGCCTTGCCGCAAAGTGTGTAACGGAATA
gi|297256 340 G I G E F K D S L S I N A T N I K H F K
gi|413277 1266 GGTATTGGTGAATTTAAAGACTCACTCTCCATAAATGCTACGAATATTAAACACTTCAAA
gi|297256 360 N C T S I S G D L H I L P V A F R G D S
gi|413277 1326 AACTGCACCTCCATCAGTGGCGATCTCCACATCCTGCCGGTGGCATTTAGGGGTGACTCC
gi|297256 380 F T H T P P L D P Q E L D I L K T V K E
gi|413277 1386 TTCACACATACTCCTCCTCTGGATCCACAGGAACTGGATATTCTGAAAACCGTAAAGGAA
gi|297256 400 I T G F L L I Q A W P E N R T D L H A F
gi|413277 1446 ATCACAGGGTTTTTGCTGATTCAGGCTTGGCCTGAAAACAGGACGGACCTCCATGCCTTT
gi|297256 420 E N L E I I R G R T K Q H G Q F S L A V
gi|413277 1506 GAGAACCTAGAAATCATACGCGGCAGGACCAAGCAACATGGTCAGTTTTCTCTTGCAGTC
gi|297256 440 V S L N I T S L G L R S L K E I S D G D
gi|413277 1566 GTCAGCCTGAACATAACATCCTTGGGATTACGCTCCCTCAAGGAGATAAGTGATGGAGAT
gi|297256 460 V I I S G N K N L C Y A N T I N W K K L
gi|413277 1626 GTGATAATTTCAGGAAACAAAAATTTGTGCTATGCAAATACAATAAACTGGAAAAAACTG
gi|297256 480 F G T S G Q K T K I I S N R G E N S C K
gi|413277 1686 TTTGGGACCTCCGGTCAGAAAACCAAAATTATAAGCAACAGAGGTGAAAACAGCTGCAAG
gi|297256 500 A T G Q V C H A L C S P E G C W G P E P
gi|413277 1746 GCCACAGGCCAGGTCTGCCATGCCTTGTGCTCCCCCGAGGGCTGCTGGGGCCCGGAGCCC
gi|297256 520 R D C V S C R N V S R G R E C V D K C N
gi|413277 1806 AGGGACTGCGTCTCTTGCCGGAATGTCAGCCGAGGCAGGGAATGCGTGGACAAGTGCAAC
gi|297256 540 L L E G E P R E F V E N S E C I Q C H P
gi|413277 1866 CTTCTGGAGGGTGAGCCAAGGGAGTTTGTGGAGAACTCTGAGTGCATACAGTGCCACCCA
gi|297256 560 E C L P Q A M N I T C T G R G P D N C I
gi|413277 1926 GAGTGCCTGCCTCAGGCCATGAACATCACCTGCACAGGACGGGGACCAGACAACTGTATC
gi|297256 580 Q C A H Y I D G P H C V K T C P A G V M
gi|413277 1986 CAGTGTGCCCACTACATTGACGGCCCCCACTGCGTCAAGACCTGCCCGGCAGGAGTCATG
gi|297256 600 G E N N T L V W K Y A D A G H V C H L C
gi|413277 2046 GGAGAAAACAACACCCTGGTCTGGAAGTACGCAGACGCCGGCCATGTGTGCCACCTGTGC
gi|297256 620 H P N C T Y G C T G P G L E G C P T N G
gi|413277 2106 CATCCAAACTGCACCTACGGATGCACTGGGCCAGGTCTTGAAGGCTGTCCAACGAATGGG
gi|297256 640 P K I P S I A T G M V G A L L L L L V V
gi|413277 2166 CCTAAGATCCCGTCCATCGCCACTGGGATGGTGGGGGCCCTCCTCTTGCTGCTGGTGGTG
gi|297256 660 A L G I G L F M R R R H I V R K R T L R
gi|413277 2226 GCCCTGGGGATCGGCCTCTTCATGCGAAGGCGCCACATCGTTCGGAAGCGCACGCTGCGG
gi|297256 680 R L L Q E R E L V E P L T P S G E A P N
gi|413277 2286 AGGCTGCTGCAGGAGAGGGAGCTTGTGGAGCCTCTTACACCCAGTGGAGAAGCTCCCAAC
gi|297256 700 Q A L L R I L K E T E F K K I K V L G S
gi|413277 2346 CAAGCTCTCTTGAGGATCTTGAAGGAAACTGAATTCAAAAAGATCAAAGTGCTGGGCTCC
gi|297256 720 G A F G T V Y K G L W I P E G E K V K I
gi|413277 2406 GGTGCGTTCGGCACGGTGTATAAGGGACTCTGGATCCCAGAAGGTGAGAAAGTTAAAATT
gi|297256 740 P V A I K E L R E A T S P K A N K E I L
gi|413277 2466 CCCGTCGCTATCAAGGAATTAAGAGAAGCAACATCTCCGAAAGCCAACAAGGAAATCCTC
gi|297256 760 D E A Y V M A S V D N P H V C R L L G I
gi|413277 2526 GATGAAGCCTACGTGATGGCCAGCGTGGACAACCCCCACGTGTGCCGCCTGCTGGGCATC
gi|297256 780 C L T S T V Q L I T Q L M P F G C L L D
gi|413277 2586 TGCCTCACCTCCACCGTGCAGCTCATCACGCAGCTCATGCCCTTCGGCTGCCTCCTGGAC
gi|297256 800 Y V R E H K D N I G S Q Y L L N W C V Q
gi|413277 2646 TATGTCCGGGAACACAAAGACAATATTGGCTCCCAGTACCTGCTCAACTGGTGTGTGCAG
gi|297256 820 I A K G M N Y L E D R R L V H R D L A A
gi|413277 2706 ATCGCAAAGGGCATGAACTACTTGGAGGACCGTCGCTTGGTGCACCGCGACCTGGCAGCC
gi|297256 840 R N V L V K T P Q H V K I T D F G L A K
gi|413277 2766 AGGAACGTACTGGTGAAAACACCGCAGCATGTCAAGATCACAGATTTTGGGCTGGCCAAA
gi|297256 860 L L G A E E K E Y H A E G G K V P I K W
gi|413277 2826 CTGCTGGGTGCGGAAGAGAAAGAATACCATGCAGAAGGAGGCAAAGTGCCTATCAAGTGG
gi|297256 880 M A L E S I L H R I Y T H Q S D V W S Y
gi|413277 2886 ATGGCATTGGAATCAATTTTACACAGAATCTATACCCACCAGAGTGATGTCTGGAGCTAC
gi|297256 900 G V T V W E L M T F G S K P Y D G I P A
gi|413277 2946 GGGGTGACCGTTTGGGAGTTGATGACCTTTGGATCCAAGCCATATGACGGAATCCCTGCC
gi|297256 920 S E I S S I L E K G E R L P Q P P I C T
gi|413277 3006 AGCGAGATCTCCTCCATCCTGGAGAAAGGAGAACGCCTCCCTCAGCCACCCATATGTACC
gi|297256 940 I D V Y M I M V K C W M I D A D S R P K
gi|413277 3066 ATCGATGTCTACATGATCATGGTCAAGTGCTGGATGATAGACGCAGATAGTCGCCCAAAG
gi|297256 960 F R E L I I E F S K M A R D P Q R Y L V
gi|413277 3126 TTCCGTGAGTTGATCATCGAATTCTCCAAAATGGCCCGAGACCCCCAGCGCTACCTTGTC
gi|297256 980 I Q G D E R M H L P S P T D S N F Y R A
gi|413277 3186 ATTCAGGGGGATGAAAGAATGCATTTGCCAAGTCCTACAGACTCCAACTTCTACCGTGCC
gi|297256 1000 L M D E E D M D D V V D A D E Y L I P Q
gi|413277 3246 CTGATGGATGAAGAAGACATGGACGACGTGGTGGATGCCGACGAGTACCTCATCCCACAG
gi|297256 1020 Q G F F S S P S T S R T P L L S S L S A
gi|413277 3306 CAGGGCTTCTTCAGCAGCCCCTCCACGTCACGGACTCCCCTCCTGAGCTCTCTGAGTGCA
gi|297256 1040 T S N N S T V A C I D R N G L Q S C P I
gi|413277 3366 ACCAGCAACAATTCCACCGTGGCTTGCATTGATAGAAATGGGCTGCAAAGCTGTCCCATC
gi|297256 1060 K E D S F L Q R Y S S D P T G A L T E D
gi|413277 3426 AAGGAAGACAGCTTCTTGCAGCGATACAGCTCAGACCCCACAGGCGCCTTGACTGAGGAC
gi|297256 1080 S I D D T F L P V P E Y I N Q S V P K R
gi|413277 3486 AGCATAGACGACACCTTCCTCCCAGTGCCTGAATACATAAACCAGTCCGTTCCCAAAAGG
gi|297256 1100 P A G S V Q N P V Y H N Q P L N P A P S
gi|413277 3546 CCCGCTGGCTCTGTGCAGAATCCTGTCTATCACAATCAGCCTCTGAACCCCGCGCCCAGC
gi|297256 1120 R D P H Y Q D P H S T A V G N P E Y L N
gi|413277 3606 AGAGACCCACACTACCAGGACCCCCACAGCACTGCAGTGGGCAACCCCGAGTATCTCAAC
gi|297256 1140 T V Q P T C V N S T F D S P A H W A Q K
gi|413277 3666 ACTGTCCAGCCCACCTGTGTCAACAGCACATTCGACAGCCCTGCCCACTGGGCCCAGAAA
gi|297256 1160 G S H Q I S L D N P D Y Q Q D F F P K E
gi|413277 3726 GGCAGCCACCAAATTAGCCTGGACAACCCTGACTACCAGCAGGACTTCTTTCCCAAGGAA
gi|297256 1180 A K P N G I F K G S T A E N A E Y L R V
gi|413277 3786 GCCAAGCCAAATGGCATCTTTAAGGGCTCCACAGCTGAAAATGCAGAATACCTAAGGGTC
gi|297256 1200 A P Q S S E F I G A 1210
gi|413277 3846 GCGCCACAAAGCAGTGAATTTATTGGAGCA 3876
""",
)
protein_record = protein_alignment.sequences[5]
self.assertEqual(protein_record.id, "gi|6478868|gb|AAF14008.1|")
nucleotide_record = nucleotide_records["gi|6478867|gb|M37394.2|RATEGFR"]
alignments = aligner.align(protein_record, nucleotide_record)
self.assertEqual(len(alignments), 1)
alignment = next(alignments)
codon_alignments.append(alignment)
self.assertTrue(
np.array_equal(alignment.coordinates, np.array([[0, 1209], [153, 3780]]))
)
self.assertEqual(
str(alignment),
"""\
gi|647886 0 M R P S G T A R T K L L L L L A A L C A
gi|647886 153 ATGCGACCCTCAGGGACTGCGAGAACCAAGCTACTGCTGCTGCTGGCTGCGCTCTGCGCC
gi|647886 20 A G G A L E E K K V C Q G T S N R L T Q
gi|647886 213 GCAGGTGGGGCGCTGGAGGAAAAGAAAGTTTGCCAAGGCACAAGTAACAGGCTCACCCAA
gi|647886 40 L G T F E D H F L S L Q R M F N N C E V
gi|647886 273 CTAGGCACCTTTGAAGACCACTTTCTGAGCCTCCAGAGGATGTTCAACAACTGTGAAGTG
gi|647886 60 V L G N L E I T Y V Q R N Y D L S F L K
gi|647886 333 GTCCTTGGAAACTTGGAAATCACCTATGTGCAAAGGAATTATGACCTTTCCTTCTTAAAG
gi|647886 80 T I Q E V A G Y V L I A L N T V E R I P
gi|647886 393 ACCATCCAGGAGGTGGCTGGCTATGTTCTCATTGCCCTGAACACCGTGGAGAGAATCCCT
gi|647886 100 L E N L Q I I R G N A L Y E N T Y A L A
gi|647886 453 TTGGAGAACCTGCAGATCATCAGGGGAAATGCTCTCTACGAAAACACCTACGCCTTAGCC
gi|647886 120 V L S N Y G T N K T G L R E L P M R N L
gi|647886 513 GTCCTGTCCAACTATGGAACCAACAAAACTGGGCTTAGGGAACTGCCCATGCGGAACTTA
gi|647886 140 Q E I L I G A V R F S N N P I L C N M E
gi|647886 573 CAGGAAATTCTGATCGGTGCTGTGCGATTTAGCAACAACCCCATCCTCTGCAATATGGAG
gi|647886 160 T I Q W R D I V Q D V F L S N M S M D V
gi|647886 633 ACCATCCAGTGGAGGGACATCGTCCAAGATGTCTTTCTGAGCAACATGTCAATGGACGTA
gi|647886 180 Q R H L T G C P K C D P S C P N G S C W
gi|647886 693 CAGCGCCACCTGACGGGCTGCCCGAAATGTGATCCGAGCTGTCCCAATGGAAGCTGCTGG
gi|647886 200 G R G E E N C Q K L T K I I C A Q Q C S
gi|647886 753 GGAAGAGGAGAGGAGAACTGCCAGAAATTGACCAAAATCATCTGCGCCCAGCAATGTTCC
gi|647886 220 R R C R G R S P S D C C H N Q C A A G C
gi|647886 813 CGGCGTTGTCGTGGCAGGTCCCCTAGCGACTGCTGCCACAACCAGTGTGCCGCAGGGTGT
gi|647886 240 T G P R E S D C L V C H R F R D E A T C
gi|647886 873 ACAGGGCCCAGAGAGAGTGACTGTCTGGTCTGCCACAGGTTCCGAGATGAAGCCACGTGC
gi|647886 260 K D T C P P L M L Y N P T T Y Q M D V N
gi|647886 933 AAAGACACCTGCCCACCACTCATGCTGTACAACCCCACCACGTACCAGATGGATGTCAAC
gi|647886 280 P E G K Y S F G A T C V K K C P R N Y V
gi|647886 993 CCTGAGGGGAAGTACAGCTTTGGTGCCACCTGTGTGAAGAAATGCCCCAGAAACTACGTG
gi|647886 300 V T D H G S C V R A C G P D Y Y E V E E
gi|647886 1053 GTGACAGATCACGGCTCGTGTGTCCGGGCCTGTGGGCCAGACTACTATGAAGTAGAAGAA
gi|647886 320 D G V S K C K K C D G P C R K V C N G I
gi|647886 1113 GATGGAGTCAGCAAGTGTAAAAAATGTGACGGGCCCTGCCGCAAAGTTTGCAATGGCATA
gi|647886 340 G I G E F K D T L S I N A T N I K H F K
gi|647886 1173 GGCATTGGTGAATTTAAAGACACACTCTCCATAAATGCTACAAACATCAAACACTTCAAG
gi|647886 360 Y C T A I S G D L H I L P V A F K G D S
gi|647886 1233 TACTGCACTGCCATCAGTGGGGACCTCCACATCCTGCCAGTGGCCTTTAAGGGGGATTCT
gi|647886 380 F T R T P P L D P R E L E I L K T V K E
gi|647886 1293 TTCACCCGCACTCCTCCTCTAGACCCACGGGAACTAGAAATTCTCAAAACTGTGAAGGAA
gi|647886 400 I T G F L L I Q A W P E N W T D L H A F
gi|647886 1353 ATAACAGGGTTTTTGCTGATTCAGGCTTGGCCTGAAAACTGGACTGACCTCCATGCTTTT
gi|647886 420 E N L E I I R G R T K Q H G Q F S L A V
gi|647886 1413 GAGAACCTAGAAATAATTCGTGGCAGAACAAAGCAACATGGTCAGTTTTCTCTGGCGGTT
gi|647886 440 V G L N I T S L G L R S L K E I S D G D
gi|647886 1473 GTCGGCCTGAACATAACATCGCTGGGGTTGCGTTCCCTCAAGGAGATCAGTGATGGGGAT
gi|647886 460 V I I S G N R N L C Y A N T I N W K K L
gi|647886 1533 GTGATTATTTCTGGGAACCGAAATTTGTGCTACGCAAACACTATAAACTGGAAAAAACTC
gi|647886 480 F G T P N Q K T K I M N N R A E K D C K
gi|647886 1593 TTCGGGACGCCCAATCAAAAGACCAAAATCATGAACAACAGAGCTGAAAAGGACTGCAAG
gi|647886 500 A T N H V C N P L C S S E G C W G P E P
gi|647886 1653 GCCACGAACCACGTCTGTAATCCTTTATGCTCCTCGGAAGGCTGCTGGGGCCCTGAGCCC
gi|647886 520 T D C V S C Q N V S R G R E C V D K C N
gi|647886 1713 ACGGACTGTGTCTCCTGCCAGAATGTGAGCAGAGGCAGGGAGTGCGTGGACAAGTGCAAC
gi|647886 540 I L E G E P R E F V E N S E C I Q C H P
gi|647886 1773 ATCCTGGAGGGGGAACCGAGGGAGTTTGTGGAAAATTCTGAATGCATCCAGTGCCATCCA
gi|647886 560 E C L P Q T M N I T C T G R G P D N C I
gi|647886 1833 GAATGTCTGCCCCAGACCATGAACATCACCTGTACAGGCCGGGGGCCAGACAACTGCATC
gi|647886 580 K C A H Y V D G P H C V K T C P S G I M
gi|647886 1893 AAGTGTGCCCACTATGTTGATGGTCCCCACTGTGTCAAGACCTGCCCTTCGGGCATCATG
gi|647886 600 G E N N T L V W K F A D A N N V C H L C
gi|647886 1953 GGGGAGAACAACACCCTGGTCTGGAAGTTTGCAGATGCCAATAACGTCTGCCACCTCTGC
gi|647886 620 H A N C T Y G C A G P G L K G C Q Q P E
gi|647886 2013 CATGCAAACTGTACCTATGGATGTGCTGGGCCAGGCCTTAAAGGATGTCAACAACCAGAA
gi|647886 640 G P K I P S I A T G I V G G L L F I V V
gi|647886 2073 GGGCCAAAGATCCCATCCATCGCCACTGGGATTGTGGGTGGCCTCCTCTTCATAGTAGTG
gi|647886 660 V A L G I G L F M R R R Q L V R K R T L
gi|647886 2133 GTGGCCCTTGGGATCGGCCTCTTCATGCGTCGACGTCAGCTTGTCCGAAAACGTACACTA
gi|647886 680 R R L L Q E R E L V E P L T P S G E A P
gi|647886 2193 CGCCGCCTGCTTCAAGAGAGAGAGCTCGTGGAACCTCTCACACCCAGCGGAGAAGCTCCG
gi|647886 700 N Q A H L R I L K E T E F K K I K V L G
gi|647886 2253 AACCAAGCCCACTTGAGGATATTAAAGGAAACAGAATTCAAAAAGATCAAAGTTCTGGGT
gi|647886 720 S G A F G T V Y K G L W I P E G E K V K
gi|647886 2313 TCAGGAGCATTTGGCACAGTGTATAAGGGTCTCTGGATCCCAGAAGGCGAGAAAGTGAAA
gi|647886 740 I P V A I K E L R E A T S P K A N K E I
gi|647886 2373 ATCCCTGTGGCCATCAAGGAGTTAAGAGAAGCCACATCTCCCAAAGCCAACAAGGAAATC
gi|647886 760 L D E A Y V M A S V D N P H V C R L L G
gi|647886 2433 CTTGATGAAGCCTACGTGATGGCCAGTGTGGACAACCCTCATGTATGCCGCCTCCTGGGC
gi|647886 780 I C L T S T V Q L I T Q L M P Y G C L L
gi|647886 2493 ATCTGTCTGACCTCCACTGTCCAGCTCATTACACAACTCATGCCCTATGGTTGCCTCCTG
gi|647886 800 D Y V R E H K D N I G S Q Y L L N W C V
gi|647886 2553 GACTATGTCCGAGAACATAAGGACAACATTGGCTCCCAGTACCTACTCAACTGGTGTGTG
gi|647886 820 Q I A K G M N Y L E D R R L V H R D L A
gi|647886 2613 CAGATTGCAAAGGGCATGAACTACCTGGAAGACCGGCGTTTGGTACACCGTGACTTGGCA
gi|647886 840 A R N V L V K T P Q H V K I T D F G L A
gi|647886 2673 GCCAGGAATGTACTGGTAAAGACACCACAGCATGTCAAGATCACAGATTTTGGACTGGCC
gi|647886 860 K L L G A E E K E Y H A E G G K V P I K
gi|647886 2733 AAACTGCTTGGTGCTGAGGAGAAAGAATACCATGCAGAGGGGGGCAAAGTGCCTATCAAG
gi|647886 880 W M A L E S I L H R I Y T H Q S D V W S
gi|647886 2793 TGGATGGCTTTGGAATCAATTTTACACCGAATTTATACACACCAAAGCGACGTCTGGAGC
gi|647886 900 Y G V T V W E L M T F G S K P Y D G I P
gi|647886 2853 TATGGAGTCACCGTGTGGGAACTGATGACCTTTGGGTCCAAGCCTTATGATGGGATCCCT
gi|647886 920 A S E I S S I L E K G E R L P Q P P I C
gi|647886 2913 GCAAGTGAGATCTCATCCATCCTAGAGAAAGGAGAGCGCCTTCCACAGCCACCTATCTGC
gi|647886 940 T I D V Y M I M V K C W M I D A D S R P
gi|647886 2973 ACCATCGACGTCTACATGATCATGGTCAAGTGCTGGATGATAGATGCTGATAGCCGCCCA
gi|647886 960 K F R E L I L E F S K M A R D P Q R Y L
gi|647886 3033 AAGTTCCGAGAGTTGATTCTCGAATTCTCCAAAATGGCCAGAGACCCACAGCGCTACCTT
gi|647886 980 V I Q G D E R M H L P S P T D S N F Y R
gi|647886 3093 GTTATCCAGGGGGATGAAAGGATGCATTTGCCGAGCCCTACAGACTCCAACTTTTACCGA
gi|647886 1000 A L M E E E D M E D V V D A D E Y L I P
gi|647886 3153 GCCCTGATGGAGGAGGAGGACATGGAAGACGTAGTTGATGCTGATGAATACCTCATCCCA
gi|647886 1020 Q Q G F F N S P S T S R T P L L S S L S
gi|647886 3213 CAGCAAGGCTTCTTCAACAGCCCATCCACGTCACGGACTCCACTCTTGAGCTCTCTGAGT
gi|647886 1040 A N S N S S T V A C I N R N G S C R V K
gi|647886 3273 GCAAATAGCAACAGTTCCACTGTGGCTTGCATTAATAGAAATGGGAGCTGCCGTGTCAAA
gi|647886 1060 E D A F L Q R Y S S D P T S V L T E D N
gi|647886 3333 GAAGACGCCTTCTTGCAACGGTATAGCTCCGATCCCACCAGCGTCCTGACAGAGGACAAC
gi|647886 1080 I D D T F L P V P E Y I N Q S V P K R P
gi|647886 3393 ATAGATGACACATTCCTTCCCGTGCCTGAATATATAAACCAATCTGTTCCCAAGAGGCCG
gi|647886 1100 A G S V Q N P V Y H N Q P L H P A P G R
gi|647886 3453 GCTGGCTCTGTGCAGAACCCAGTCTATCACAATCAGCCCCTGCATCCAGCTCCTGGAAGA
gi|647886 1120 D L H Y Q N P H S N A V S N P E Y L N T
gi|647886 3513 GACCTGCATTATCAAAATCCCCATAGCAATGCGGTGAGCAACCCTGAGTATCTCAACACT
gi|647886 1140 A Q P T C L S S G F D S S A L W I Q K G
gi|647886 3573 GCCCAGCCGACCTGCCTCAGTAGTGGGTTTGACAGCTCTGCCCTCTGGATCCAGAAAGGC
gi|647886 1160 S H Q M S L D N P D Y Q Q D F F P K E A
gi|647886 3633 AGCCACCAAATGAGCCTGGACAACCCTGACTACCAGCAGGACTTCTTTCCCAAAGAAGCC
gi|647886 1180 K P N G I F K G P T A E N A E Y L R V A
gi|647886 3693 AAGCCGAATGGCATCTTTAAGGGCCCCACAGCTGAAAATGCAGAGTACCTGCGGGTGGCA
gi|647886 1200 P P S S E F S G A 1209
gi|647886 3753 CCGCCAAGCAGTGAGTTTAGTGGAGCA 3780
""",
)
alignment = protein_alignment.mapall(codon_alignments)
self.assertTrue(
np.array_equal(
alignment.coordinates,
# fmt: off
np.array([[ 84, 105, 114, 129, 171, 183, 198, 198, 210,
234, 366, 369, 492, 507, 531, 531, 741, 741,
807, 810, 1038, 1038, 1089, 1089, 1107, 1107, 1161,
1161, 1245, 1260, 1281, 1290, 1443, 1446, 1779, 1779,
1821, 1821, 1902, 1953, 1986, 2085, 2097, 2151, 2175,
2301, 2319, 2319, 2355, 2358, 2373, 2394, 2418, 2559,
2610, 2613, 2655, 2661, 3585, 3594, 3642, 3645, 3765,
3765, 3777, 3777, 3777, 3777, 3843, 3843, 3858, 3864,
3894, 3900, 3921, 3921, 3969, 3975, 4038, 4038, 4215],
[ 22, 22, 31, 46, 88, 100, 115, 283, 295,
319, 451, 454, 577, 592, 616, 616, 826, 826,
892, 895, 1123, 1123, 1174, 1174, 1192, 1192, 1246,
1246, 1330, 1345, 1366, 1375, 1528, 1531, 1864, 1864,
1906, 1906, 1987, 2038, 2071, 2170, 2182, 2236, 2260,
2386, 2404, 2404, 2440, 2443, 2458, 2479, 2503, 2644,
2695, 2698, 2740, 2746, 3670, 3679, 3727, 3730, 3850,
3850, 3862, 3862, 3862, 3862, 3928, 3928, 3943, 3949,
3979, 3985, 4006, 4006, 4054, 4060, 4123, 4123, 4300],
[ 0, 0, 0, 15, 15, 15, 15, 15, 15,
15, 147, 147, 270, 270, 294, 312, 522, 525,
591, 591, 819, 822, 873, 879, 897, 903, 957,
981, 1065, 1065, 1086, 1086, 1239, 1239, 1572, 1578,
1620, 1638, 1719, 1719, 1752, 1752, 1764, 1764, 1788,
1788, 1806, 1809, 1845, 1845, 1860, 1860, 1884, 1884,
1935, 1935, 1977, 1977, 2901, 2901, 2949, 2949, 3069,
3081, 3093, 3093, 3093, 3099, 3165, 3183, 3198, 3198,
3228, 3228, 3249, 3258, 3306, 3306, 3369, 3378, 3555],
[ 126, 126, 126, 141, 183, 183, 198, 198, 210,
210, 342, 342, 465, 465, 489, 507, 717, 720,
786, 786, 1014, 1017, 1068, 1074, 1092, 1098, 1152,
1176, 1260, 1260, 1281, 1281, 1434, 1434, 1767, 1773,
1815, 1833, 1914, 1914, 1947, 1947, 1959, 1959, 1983,
1983, 2001, 2004, 2040, 2040, 2055, 2055, 2079, 2079,
2130, 2130, 2172, 2172, 3096, 3096, 3144, 3144, 3264,
3276, 3288, 3288, 3291, 3297, 3363, 3381, 3396, 3396,
3426, 3426, 3447, 3456, 3504, 3504, 3567, 3576, 3753],
[ 246, 246, 246, 261, 303, 303, 318, 318, 330,
330, 462, 462, 585, 585, 609, 627, 837, 840,
906, 906, 1134, 1137, 1188, 1194, 1212, 1218, 1272,
1296, 1380, 1380, 1401, 1401, 1554, 1554, 1887, 1893,
1935, 1953, 2034, 2034, 2067, 2067, 2079, 2079, 2103,
2103, 2121, 2124, 2160, 2160, 2175, 2175, 2199, 2199,
2250, 2250, 2292, 2292, 3216, 3216, 3264, 3264, 3384,
3396, 3408, 3411, 3414, 3420, 3486, 3504, 3519, 3519,
3549, 3549, 3570, 3579, 3627, 3627, 3690, 3699, 3876],
[ 153, 153, 153, 168, 210, 210, 225, 225, 237,
237, 369, 369, 492, 492, 516, 534, 744, 747,
813, 813, 1041, 1044, 1095, 1101, 1119, 1125, 1179,
1203, 1287, 1287, 1308, 1308, 1461, 1461, 1794, 1800,
1842, 1860, 1941, 1941, 1974, 1974, 1986, 1986, 2010,
2010, 2028, 2031, 2067, 2070, 2085, 2085, 2109, 2109,
2160, 2160, 2202, 2202, 3126, 3126, 3174, 3174, 3294,
3306, 3318, 3318, 3318, 3324, 3390, 3408, 3423, 3423,
3453, 3453, 3474, 3483, 3531, 3531, 3594, 3603, 3780]])
# fmt: on
)
)
self.assertEqual(
format(alignment, "clustal"),
"""\
gi|24657088|ref|NM_057410.3| ATGATGATTATCAGCATGTGGATGAGCATATCGCGAGGATTGTGGGACAG
gi|24657104|ref|NM_057411.3| ---------------------ATGCTGCTGCGACGGCGCAACGGCCCCTG
gi|302179500|gb|HM749883.1| ------------------------------ATGAAAAAGCACGAG-----
gi|47522839|ref|NM_214007.1| ------------------------------ATGCGACGCTCCTGGGCGGG
gi|41327737|ref|NM_005228.3| ------------------------------ATGCGACCCTCCGGGACGGC
gi|6478867|gb|M37394.2|RATEGFR ------------------------------ATGCGACCCTCAGGGACTGC
gi|24657088|ref|NM_057410.3| CAGCTCCATCTGGTCGGTGCTGCTGATCCTCGCCTGCATGGCATCCATCA
gi|24657104|ref|NM_057411.3| CCCCTTCCCCCTGCTGCTCCTGCTCCTGGCCCACTGCATTTGCATTTGGC
gi|302179500|gb|HM749883.1| --------------------------------------------------
gi|47522839|ref|NM_214007.1| CGGCGCCGCGCTCCTGGCGCTGCTGGCCGCGCACTTC------------C
gi|41327737|ref|NM_005228.3| CGGGGCAGCGCTCCTGGCGCTGCTGGCTGCGCTCTGC------------C
gi|6478867|gb|M37394.2|RATEGFR GAGAACCAAGCTACTGCTGCTGCTGGCTGCGCTCTGC------------G
gi|24657088|ref|NM_057410.3| CCACAAGCTCATCG------------------------------------
gi|24657104|ref|NM_057411.3| CCGCGTCGGCGGCCCGCGATCGCTACGCCCGCCAGAACAATCGCCAGCGC
gi|302179500|gb|HM749883.1| --------------------------------------------------
gi|47522839|ref|NM_214007.1| AGGCGAGTCCGGCG------------------------------------
gi|41327737|ref|NM_005228.3| CGGCGAGTCGGGCT------------------------------------
gi|6478867|gb|M37394.2|RATEGFR CCGCAGGTGGGGCG------------------------------------
gi|24657088|ref|NM_057410.3| --------------------------------------------------
gi|24657104|ref|NM_057411.3| CATCAGGATATAGATCGCGATCGGGATCGAGATCGATTCCTATACCGCAG
gi|302179500|gb|HM749883.1| --------------------------------------------------
gi|47522839|ref|NM_214007.1| --------------------------------------------------
gi|41327737|ref|NM_005228.3| --------------------------------------------------
gi|6478867|gb|M37394.2|RATEGFR --------------------------------------------------
gi|24657088|ref|NM_057410.3| --------------------------------------------------
gi|24657104|ref|NM_057411.3| CAGTTCGGCCCAAAATCGACAGAGGGGCGGGGCCAACTTCGCCCTGGGAC
gi|302179500|gb|HM749883.1| --------------------------------------------------
gi|47522839|ref|NM_214007.1| --------------------------------------------------
gi|41327737|ref|NM_005228.3| --------------------------------------------------
gi|6478867|gb|M37394.2|RATEGFR --------------------------------------------------
gi|24657088|ref|NM_057410.3| --------------------------------GTCAGCAATGCCGGCTAT
gi|24657104|ref|NM_057411.3| TGGGAGCCAACGGAGTCACCATTCCCACCAGTCTGGAGGATAAGAACAAG
gi|302179500|gb|HM749883.1| --------------------------------------------------
gi|47522839|ref|NM_214007.1| --------------------------------CTGGAGGAGAAG------
gi|41327737|ref|NM_005228.3| --------------------------------CTGGAGGAAAAG------
gi|6478867|gb|M37394.2|RATEGFR --------------------------------CTGGAGGAAAAG------
gi|24657088|ref|NM_057410.3| GTGGATAATGGCAATATGAAAGTCTGCATCGGCACTAAATCTCGGCTCTC
gi|24657104|ref|NM_057411.3| AACGAGTTCGTCAAGGGGAAAATCTGCATCGGCACTAAATCTCGGCTCTC
gi|302179500|gb|HM749883.1| ------------------TTACTTTGCCAAGGGACAAGTAACAAGCTCAC
gi|47522839|ref|NM_214007.1| ------------------AAAGTTTGCCAAGGTACAAGTAACAAGCTCAC
gi|41327737|ref|NM_005228.3| ------------------AAAGTTTGCCAAGGCACGAGTAACAAGCTCAC
gi|6478867|gb|M37394.2|RATEGFR ------------------AAAGTTTGCCAAGGCACAAGTAACAGGCTCAC
gi|24657088|ref|NM_057410.3| CGTGCCCTCCAACAAGGAACATCATTACCGGAACCTCAGAGATCGGTACA
gi|24657104|ref|NM_057411.3| CGTGCCCTCCAACAAGGAACATCATTACCGGAACCTCAGAGATCGGTACA
gi|302179500|gb|HM749883.1| CCAGTTGGGCACTTTTGAAGACCACTTTCTGAGCCTACAGAGGATGTTCA
gi|47522839|ref|NM_214007.1| CCAGCTGGGCACTTTCGAAGACCACTTTCTGAGCCTCCAGAGGATGTTCA
gi|41327737|ref|NM_005228.3| GCAGTTGGGCACTTTTGAAGATCATTTTCTCAGCCTCCAGAGGATGTTCA
gi|6478867|gb|M37394.2|RATEGFR CCAACTAGGCACCTTTGAAGACCACTTTCTGAGCCTCCAGAGGATGTTCA
gi|24657088|ref|NM_057410.3| CGAACTGTACGTATGTGGATGGCAACCTGGAGCTGACCTGGCTGCCCAAC
gi|24657104|ref|NM_057411.3| CGAACTGTACGTATGTGGATGGCAACCTGGAGCTGACCTGGCTGCCCAAC
gi|302179500|gb|HM749883.1| ACAACTGTGAGGTGGTCCTTGGGAATTTGGAAATTACCTACATGCAGAGT
gi|47522839|ref|NM_214007.1| ATAACTGCGAGGTGGTCCTTGGGAACTTGGAGATCACCTACATGCAGAAC
gi|41327737|ref|NM_005228.3| ATAACTGTGAGGTGGTCCTTGGGAATTTGGAAATTACCTATGTGCAGAGG
gi|6478867|gb|M37394.2|RATEGFR ACAACTGTGAAGTGGTCCTTGGAAACTTGGAAATCACCTATGTGCAAAGG
gi|24657088|ref|NM_057410.3| GAGAATTTGGACCTCAGCTTCCTGGACAACATACGGGAGGTCACCGGCTA
gi|24657104|ref|NM_057411.3| GAGAATTTGGACCTCAGCTTCCTGGACAACATACGGGAGGTCACCGGCTA
gi|302179500|gb|HM749883.1| ---AGTTACAACCTTTCTTTTCTCAAGACCATCCAGGAGGTTGCCGGCTA
gi|47522839|ref|NM_214007.1| ---AGCTACAACCTGTCTTTCCTAAAGACCATTCAGGAGGTCGCCGGCTA
gi|41327737|ref|NM_005228.3| ---AATTATGATCTTTCCTTCTTAAAGACCATCCAGGAGGTGGCTGGTTA
gi|6478867|gb|M37394.2|RATEGFR ---AATTATGACCTTTCCTTCTTAAAGACCATCCAGGAGGTGGCTGGCTA
gi|24657088|ref|NM_057410.3| TATTCTGATCAGTCATGTGGACGTTAAGAAAGTGGTATTTCCCAAACTAC
gi|24657104|ref|NM_057411.3| TATTCTGATCAGTCATGTGGACGTTAAGAAAGTGGTATTTCCCAAACTAC
gi|302179500|gb|HM749883.1| TGTACTCATTGCCCTCAACACAGTGGAGAAGATTCCGCTGGAAAACCTGC
gi|47522839|ref|NM_214007.1| CGTGCTCATCGCCCTCAACACCGTGGAGAAGATCCCTTTGGAAAACCTGC
gi|41327737|ref|NM_005228.3| TGTCCTCATTGCCCTCAACACAGTGGAGCGAATTCCTTTGGAAAACCTGC
gi|6478867|gb|M37394.2|RATEGFR TGTTCTCATTGCCCTGAACACCGTGGAGAGAATCCCTTTGGAGAACCTGC
gi|24657088|ref|NM_057410.3| AAATCATTCGCGGACGCACGCTGTTCAGCTTATCCGTGGAGGAGGAGAAG
gi|24657104|ref|NM_057411.3| AAATCATTCGCGGACGCACGCTGTTCAGCTTATCCGTGGAGGAGGAGAAG
gi|302179500|gb|HM749883.1| AGATCATCCGAGGAAATGTGCTTTAT---------------GAAAACACC
gi|47522839|ref|NM_214007.1| AGATCATCCGAGGAAATGTACTGTAT---------------GAAAACACC
gi|41327737|ref|NM_005228.3| AGATCATCAGAGGAAATATGTACTAC---------------GAAAATTCC
gi|6478867|gb|M37394.2|RATEGFR AGATCATCAGGGGAAATGCTCTCTAC---------------GAAAACACC
gi|24657088|ref|NM_057410.3| TATGCCTTGTTCGTC------------------ACTTATTCCAAAATGTA
gi|24657104|ref|NM_057411.3| TATGCCTTGTTCGTC------------------ACTTATTCCAAAATGTA
gi|302179500|gb|HM749883.1| CATGCCTTAGCCGTCTTATCCAACTATGGAGCAAACAAAACCGGACTGAG
gi|47522839|ref|NM_214007.1| CATGCCTTAGCCGTCTTATCCAACTACGGGGCCAATAAAACCGGCCTGAG
gi|41327737|ref|NM_005228.3| TATGCCTTAGCAGTCTTATCTAACTATGATGCAAATAAAACCGGACTGAA
gi|6478867|gb|M37394.2|RATEGFR TACGCCTTAGCCGTCCTGTCCAACTATGGAACCAACAAAACTGGGCTTAG
gi|24657088|ref|NM_057410.3| CACGCTGGAGATTCCCGATCTACGCGATGTCTTAAATGGCCAAGTGGGCT
gi|24657104|ref|NM_057411.3| CACGCTGGAGATTCCCGATCTACGCGATGTCTTAAATGGCCAAGTGGGCT
gi|302179500|gb|HM749883.1| GGAGCTGCCCTTGAGAAACTTACAGGAAATTCTGCAAGGTGCCGTGAGAT
gi|47522839|ref|NM_214007.1| GGAGCTGCCCATGAGGAACTTACAAGAGATCCTGCAAGGCGCCGTGCGCT
gi|41327737|ref|NM_005228.3| GGAGCTGCCCATGAGAAATTTACAGGAAATCCTGCATGGCGCCGTGCGGT
gi|6478867|gb|M37394.2|RATEGFR GGAACTGCCCATGCGGAACTTACAGGAAATTCTGATCGGTGCTGTGCGAT
gi|24657088|ref|NM_057410.3| TCCACAACAACTACAATCTCTGCCACATGCGAACGATCCAGTGGTCGGAG
gi|24657104|ref|NM_057411.3| TCCACAACAACTACAATCTCTGCCACATGCGAACGATCCAGTGGTCGGAG
gi|302179500|gb|HM749883.1| TCAGCAACAACCCTGTCCTCTGCAACGTGGAGACCATCCAGTGGCGGGAC
gi|47522839|ref|NM_214007.1| TCAGCAACAACCCTGCCCTCTGTCACGCGGAGTCCATCCAGTGGAGGGAC
gi|41327737|ref|NM_005228.3| TCAGCAACAACCCTGCCCTGTGCAACGTGGAGAGCATCCAGTGGCGGGAC
gi|6478867|gb|M37394.2|RATEGFR TTAGCAACAACCCCATCCTCTGCAATATGGAGACCATCCAGTGGAGGGAC
gi|24657088|ref|NM_057410.3| ATTGTATCCAACGGCACGGATGCATACTACAACTACGACTTTACTGCTCC
gi|24657104|ref|NM_057411.3| ATTGTATCCAACGGCACGGATGCATACTACAACTACGACTTTACTGCTCC
gi|302179500|gb|HM749883.1| ATCGTCAACCCTGATTTTCTAAGCAACATGACAGGGGACTTTCAGAACCA
gi|47522839|ref|NM_214007.1| ATTGTCAACAGCGACTTTCTAAGCAACATGTCCATGGACTTTCAGAGCCA
gi|41327737|ref|NM_005228.3| ATAGTCAGCAGTGACTTTCTCAGCAACATGTCGATGGACTTCCAGAACCA
gi|6478867|gb|M37394.2|RATEGFR ATCGTCCAAGATGTCTTTCTGAGCAACATGTCAATGGACGTACAGCGCCA
gi|24657088|ref|NM_057410.3| GGAGCGCGAGTGTCCCAAGTGCCACGAGAGCTGCACGCACGGA---TGTT
gi|24657104|ref|NM_057411.3| GGAGCGCGAGTGTCCCAAGTGCCACGAGAGCTGCACGCACGGA---TGTT
gi|302179500|gb|HM749883.1| GCAGGGCAACTGCCCAAAGTGTGATCCAGCCTGTCTCAACAGAAGCTGCT
gi|47522839|ref|NM_214007.1| GCTGGGCAGCTGCCCGAAGTGTGATCCAGGCTGTCTCAATGGGAGCTGCT
gi|41327737|ref|NM_005228.3| CCTGGGCAGCTGCCAAAAGTGTGATCCAAGCTGTCCCAATGGGAGCTGCT
gi|6478867|gb|M37394.2|RATEGFR CCTGACGGGCTGCCCGAAATGTGATCCGAGCTGTCCCAATGGAAGCTGCT
gi|24657088|ref|NM_057410.3| GGGGCGAGGGTCCCAAGAATTGCCAGAAGTTCAGCAAGCTCACCTGCTCG
gi|24657104|ref|NM_057411.3| GGGGCGAGGGTCCCAAGAATTGCCAGAAGTTCAGCAAGCTCACCTGCTCG
gi|302179500|gb|HM749883.1| GGGGTGCCGGGGAGGAGAACTGTCAGAAATTGACCAAAATCATCTGTGCC
gi|47522839|ref|NM_214007.1| GGGGTGCTGGGAAGGAGAACTGCCAGAAATTGACCAAAGTCATCTGTGCC
gi|41327737|ref|NM_005228.3| GGGGTGCAGGAGAGGAGAACTGCCAGAAACTGACCAAAATCATCTGTGCC
gi|6478867|gb|M37394.2|RATEGFR GGGGAAGAGGAGAGGAGAACTGCCAGAAATTGACCAAAATCATCTGCGCC
gi|24657088|ref|NM_057410.3| CCACAGTGTGCCGGAGGTCGTTGCTATGGACCAAAGCCGCGGGAGTGTTG
gi|24657104|ref|NM_057411.3| CCACAGTGTGCCGGAGGTCGTTGCTATGGACCAAAGCCGCGGGAGTGTTG
gi|302179500|gb|HM749883.1| CAGCAGTGTTCC---GGGCGCTGCCGTGGCAGGTCCCCCAGTGACTGCTG
gi|47522839|ref|NM_214007.1| CAGCAGTGCTCC---GGGCGCTGCCGCGGCCGGTCGCCCAGTGACTGCTG
gi|41327737|ref|NM_005228.3| CAGCAGTGCTCC---GGGCGCTGCCGTGGCAAGTCCCCCAGTGACTGCTG
gi|6478867|gb|M37394.2|RATEGFR CAGCAATGTTCC---CGGCGTTGTCGTGGCAGGTCCCCTAGCGACTGCTG
gi|24657088|ref|NM_057410.3| TCACCTCTTCTGCGCCGGAGGATGCACTGGTCCCACGCAAAAGGATTGCA
gi|24657104|ref|NM_057411.3| TCACCTCTTCTGCGCCGGAGGATGCACTGGTCCCACGCAAAAGGATTGCA
gi|302179500|gb|HM749883.1| CCACAACCAGTGTGCCGCTGGCTGCACAGGGCCACGGGAGAGCGACTGCC
gi|47522839|ref|NM_214007.1| CCACAACCAGTGCGCCGCTGGCTGCACGGGGCCGCGGGAGAGCGACTGCC
gi|41327737|ref|NM_005228.3| CCACAACCAGTGTGCTGCAGGCTGCACAGGCCCCCGGGAGAGCGACTGCC
gi|6478867|gb|M37394.2|RATEGFR CCACAACCAGTGTGCCGCAGGGTGTACAGGGCCCAGAGAGAGTGACTGTC
gi|24657088|ref|NM_057410.3| TCGCCTGCAAGAACTTCTTCGACGAGGGCGTATGCAAGGAGGAATGCCCG
gi|24657104|ref|NM_057411.3| TCGCCTGCAAGAACTTCTTCGACGAGGGCGTATGCAAGGAGGAATGCCCG
gi|302179500|gb|HM749883.1| TGGTCTGCCGCAGGTTCCGTGATGAAGCCACCTGCAAGGACACGTGTCCG
gi|47522839|ref|NM_214007.1| TGGTTTGCCGCAGATTCCGTGACGAGGCCACCTGCAAGGACACATGCCCG
gi|41327737|ref|NM_005228.3| TGGTCTGCCGCAAATTCCGAGACGAAGCCACGTGCAAGGACACCTGCCCC
gi|6478867|gb|M37394.2|RATEGFR TGGTCTGCCACAGGTTCCGAGATGAAGCCACGTGCAAAGACACCTGCCCA
gi|24657088|ref|NM_057410.3| CCCATGCGCAAGTACAATCCCACCACCTATGTTCTTGAAACGAATCCTGA
gi|24657104|ref|NM_057411.3| CCCATGCGCAAGTACAATCCCACCACCTATGTTCTTGAAACGAATCCTGA
gi|302179500|gb|HM749883.1| CCACTCATGCTCTATGACCCTACCACCTACGAAATGAAGGTCAACCCGCT
gi|47522839|ref|NM_214007.1| CCGCTCATGCTCTACAACCCCACCACCTACCAGATGGACGTCAACCCGCT
gi|41327737|ref|NM_005228.3| CCACTCATGCTCTACAACCCCACCACGTACCAGATGGATGTGAACCCCGA
gi|6478867|gb|M37394.2|RATEGFR CCACTCATGCTGTACAACCCCACCACGTACCAGATGGATGTCAACCCTGA
gi|24657088|ref|NM_057410.3| GGGAAAGTATGCCTATGGTGCCACCTGCGTCAAGGAGTGTCCC---GGTC
gi|24657104|ref|NM_057411.3| GGGAAAGTATGCCTATGGTGCCACCTGCGTCAAGGAGTGTCCC---GGTC
gi|302179500|gb|HM749883.1| GGGGAAGTACAGCTTTGGCGCCACCTGTGTCAAGAAGTGTCCCCGTAACT
gi|47522839|ref|NM_214007.1| GGGGAAGTACAGCTTTGGCGCCACCTGTGTCAAGAAGTGCCCTCGTAACT
gi|41327737|ref|NM_005228.3| GGGCAAATACAGCTTTGGTGCCACCTGCGTGAAGAAGTGTCCCCGTAATT
gi|6478867|gb|M37394.2|RATEGFR GGGGAAGTACAGCTTTGGTGCCACCTGTGTGAAGAAATGCCCCAGAAACT
gi|24657088|ref|NM_057410.3| ATCTGTTGCGTGATAATGGCGCCTGCGTGCGCAGCTGTCCCCAGGAC---
gi|24657104|ref|NM_057411.3| ATCTGTTGCGTGATAATGGCGCCTGCGTGCGCAGCTGTCCCCAGGAC---
gi|302179500|gb|HM749883.1| ACGTGGTGACAGACCACGGCTCCTGCGTCCGCGCCTGCAGTTCTGACAGC
gi|47522839|ref|NM_214007.1| ACGTGGTGACAGACCATGGCTCCTGTGTCCGTGCCTGCAGCTCCGACAGC
gi|41327737|ref|NM_005228.3| ATGTGGTGACAGATCACGGCTCGTGCGTCCGAGCCTGTGGGGCCGACAGC
gi|6478867|gb|M37394.2|RATEGFR ACGTGGTGACAGATCACGGCTCGTGTGTCCGGGCCTGTGGGCCAGACTAC
gi|24657088|ref|NM_057410.3| ---AAGATGGACAAGGGGGGC------GAGTGTGTGCCCTGCAATGGACC
gi|24657104|ref|NM_057411.3| ---AAGATGGACAAGGGGGGC------GAGTGTGTGCCCTGCAATGGACC
gi|302179500|gb|HM749883.1| CAGGAGGTAGAGGAAGACGGTGTCCGCAAGTGTAAAAAGTGTGACGGGCC
gi|47522839|ref|NM_214007.1| TACGAGGTGGAGGAGGACGGCGTCCGCAAGTGTAAAAAGTGTGACGGGCC
gi|41327737|ref|NM_005228.3| TATGAGATGGAGGAAGACGGCGTCCGCAAGTGTAAGAAGTGCGAAGGGCC
gi|6478867|gb|M37394.2|RATEGFR TATGAAGTAGAAGAAGATGGAGTCAGCAAGTGTAAAAAATGTGACGGGCC
gi|24657088|ref|NM_057410.3| GTGCCCCAAAACCTGCCCGGGCGTTACTGTC-------------------
gi|24657104|ref|NM_057411.3| GTGCCCCAAAACCTGCCCGGGCGTTACTGTC-------------------
gi|302179500|gb|HM749883.1| TTGTGGCAAAGTTTGTAACGGAATAGGAATCGGTGAGTTTAAAGACACAC
gi|47522839|ref|NM_214007.1| CTGCGGCAAAGTTTGTAACGGGATAGGGATTGGCGAGTTTAAAGACACAC
gi|41327737|ref|NM_005228.3| TTGCCGCAAAGTGTGTAACGGAATAGGTATTGGTGAATTTAAAGACTCAC
gi|6478867|gb|M37394.2|RATEGFR CTGCCGCAAAGTTTGCAATGGCATAGGCATTGGTGAATTTAAAGACACAC
gi|24657088|ref|NM_057410.3| -----CTGCATGCCGGCAACATTGACTCGTTCCGGAATTGTACGGTGATC
gi|24657104|ref|NM_057411.3| -----CTGCATGCCGGCAACATTGACTCGTTCCGGAATTGTACGGTGATC
gi|302179500|gb|HM749883.1| TTTCCATAAATGCTACAAACATTAAACACTTCAGAAACTGCACATCCATC
gi|47522839|ref|NM_214007.1| TTTCCATAAATGCTACGAATATCAAGCACTTCAGGAACTGCACCTCGATC
gi|41327737|ref|NM_005228.3| TCTCCATAAATGCTACGAATATTAAACACTTCAAAAACTGCACCTCCATC
gi|6478867|gb|M37394.2|RATEGFR TCTCCATAAATGCTACAAACATCAAACACTTCAAGTACTGCACTGCCATC
gi|24657088|ref|NM_057410.3| GATGGCAACATTCGCATTTTGGATCAGACCTTCTCGGGCTTCCAGGATGT
gi|24657104|ref|NM_057411.3| GATGGCAACATTCGCATTTTGGATCAGACCTTCTCGGGCTTCCAGGATGT
gi|302179500|gb|HM749883.1| AGTGGAGATCTTCATATCCTGCCAGTAGCATTTAGGGGT-----------
gi|47522839|ref|NM_214007.1| AGCGGAGATCTTCATATCCTGCCGGTAGCATTTAGGGGT-----------
gi|41327737|ref|NM_005228.3| AGTGGCGATCTCCACATCCTGCCGGTGGCATTTAGGGGT-----------
gi|6478867|gb|M37394.2|RATEGFR AGTGGGGACCTCCACATCCTGCCAGTGGCCTTTAAGGGG-----------
gi|24657088|ref|NM_057410.3| CTATGCCAACTACACGATGGGACCACGATACATACCGCTGGATCCCGAGC
gi|24657104|ref|NM_057411.3| CTATGCCAACTACACGATGGGACCACGATACATACCGCTGGATCCCGAGC
gi|302179500|gb|HM749883.1| ----GACTCCTTCACACGTACTGCA---------CCTCTGGACCCGAAAG
gi|47522839|ref|NM_214007.1| ----GACTCCTTCACACGCACGCCG---------CCTCTGGACCCCAAGG
gi|41327737|ref|NM_005228.3| ----GACTCCTTCACACATACTCCT---------CCTCTGGATCCACAGG
gi|6478867|gb|M37394.2|RATEGFR ----GATTCTTTCACCCGCACTCCT---------CCTCTAGACCCACGGG
gi|24657088|ref|NM_057410.3| GACTGGAGGTGTTCTCCACGGTGAAGGAGATCACCGGGTATCTGAATATC
gi|24657104|ref|NM_057411.3| GACTGGAGGTGTTCTCCACGGTGAAGGAGATCACCGGGTATCTGAATATC
gi|302179500|gb|HM749883.1| AACTGGACATTCTAAGAACTGTAAAAGAAATAACAGGGTTTTTGCTGATT
gi|47522839|ref|NM_214007.1| AACTGGACATCCTGAAAACCGTGAAGGAAATAACAGGGTTTTTACTGATT
gi|41327737|ref|NM_005228.3| AACTGGATATTCTGAAAACCGTAAAGGAAATCACAGGGTTTTTGCTGATT
gi|6478867|gb|M37394.2|RATEGFR AACTAGAAATTCTCAAAACTGTGAAGGAAATAACAGGGTTTTTGCTGATT
gi|24657088|ref|NM_057410.3| GAGGGAACCCACCCGCAGTTCCGGAATCTGTCGTACTTCCGCAATCTGGA
gi|24657104|ref|NM_057411.3| GAGGGAACCCACCCGCAGTTCCGGAATCTGTCGTACTTCCGCAATCTGGA
gi|302179500|gb|HM749883.1| CAGGCCTGGCCCGAAAACAGGACTGACCTCCATGCTTTTGAGAACCTGGA
gi|47522839|ref|NM_214007.1| CAGGCCTGGCCTGAAAACAGGACTGGCCTCCATGCTTTTGAGAACCTGGA
gi|41327737|ref|NM_005228.3| CAGGCTTGGCCTGAAAACAGGACGGACCTCCATGCCTTTGAGAACCTAGA
gi|6478867|gb|M37394.2|RATEGFR CAGGCTTGGCCTGAAAACTGGACTGACCTCCATGCTTTTGAGAACCTAGA
gi|24657088|ref|NM_057410.3| AACAATTCATGGCCGCCAGCTGATGGAGAGCATGTTTGCCGCTTTGGCGA
gi|24657104|ref|NM_057411.3| AACAATTCATGGCCGCCAGCTGATGGAGAGCATGTTTGCCGCTTTGGCGA
gi|302179500|gb|HM749883.1| AATCATACGTGGCAGAACGAAGCAGCATGGCCAGTTT---TCTCTTGCGG
gi|47522839|ref|NM_214007.1| AATCATACGTGGCAGGACGAAGCAACATGGTCAGTTT---TCCCTCGCGG
gi|41327737|ref|NM_005228.3| AATCATACGCGGCAGGACCAAGCAACATGGTCAGTTT---TCTCTTGCAG
gi|6478867|gb|M37394.2|RATEGFR AATAATTCGTGGCAGAACAAAGCAACATGGTCAGTTT---TCTCTGGCGG
gi|24657088|ref|NM_057410.3| TCGTTAAGTCATCCCTGTACAGCCTGGAGATGCGCAATCTGAAGCAGATT
gi|24657104|ref|NM_057411.3| TCGTTAAGTCATCCCTGTACAGCCTGGAGATGCGCAATCTGAAGCAGATT
gi|302179500|gb|HM749883.1| TTGTCGGCCTGGATATAACATCTTTGGGATTACGCTCCCTCAAGGAGATA
gi|47522839|ref|NM_214007.1| TTGTTGGCCTGGACATAGCGTCCTTGGGGATGCGCTCCCTCAAGGAGATC
gi|41327737|ref|NM_005228.3| TCGTCAGCCTGAACATAACATCCTTGGGATTACGCTCCCTCAAGGAGATA
gi|6478867|gb|M37394.2|RATEGFR TTGTCGGCCTGAACATAACATCGCTGGGGTTGCGTTCCCTCAAGGAGATC
gi|24657088|ref|NM_057410.3| AGTTCCGGCAGTGTGGTCATCCAGCATAATAGAGACCTCTGCTACGTAAG
gi|24657104|ref|NM_057411.3| AGTTCCGGCAGTGTGGTCATCCAGCATAATAGAGACCTCTGCTACGTAAG
gi|302179500|gb|HM749883.1| AGTGATGGTGATGTGATAATTTCAGGAAATCGAAACTTGTGCTATGCAGA
gi|47522839|ref|NM_214007.1| AGCGACGGAGACGTGATCGTCTCAGGAAACCGAAACCTGTGCTATGCAAA
gi|41327737|ref|NM_005228.3| AGTGATGGAGATGTGATAATTTCAGGAAACAAAAATTTGTGCTATGCAAA
gi|6478867|gb|M37394.2|RATEGFR AGTGATGGGGATGTGATTATTTCTGGGAACCGAAATTTGTGCTACGCAAA
gi|24657088|ref|NM_057410.3| CAATATCCGTTGGCCGGCCATTCAGAAGGAGCCCGAACAGAAGGTGTGGG
gi|24657104|ref|NM_057411.3| CAATATCCGTTGGCCGGCCATTCAGAAGGAGCCCGAACAGAAGGTGTGGG
gi|302179500|gb|HM749883.1| TACAATACGCTGGAAAAAACTTTTTGGGACCTCAACTCAGAAAACCAAAA
gi|47522839|ref|NM_214007.1| TACAATCAGCTGGAAAAAACTATTTGGGACCGCAAGTCAGAAAACCAAAA
gi|41327737|ref|NM_005228.3| TACAATAAACTGGAAAAAACTGTTTGGGACCTCCGGTCAGAAAACCAAAA
gi|6478867|gb|M37394.2|RATEGFR CACTATAAACTGGAAAAAACTCTTCGGGACGCCCAATCAAAAGACCAAAA
gi|24657088|ref|NM_057410.3| TCAACGAGAATCTCAGGGCGGATCTATGCGAGAAAAATGGAACCATTTGC
gi|24657104|ref|NM_057411.3| TCAACGAGAATCTCAGGGCGGATCTATGCGAGAAAAATGGAACCATTTGC
gi|302179500|gb|HM749883.1| TTTTAAACAACAGGAGTGAAAAACAGTGCAAGGCCGCAGGCCACATCTGT
gi|47522839|ref|NM_214007.1| TTATAAACAACAGGAGCGAAAAAGAGTGCAAAGCCATGGGCCACATCTGT
gi|41327737|ref|NM_005228.3| TTATAAGCAACAGAGGTGAAAACAGCTGCAAGGCCACAGGCCAGGTCTGC
gi|6478867|gb|M37394.2|RATEGFR TCATGAACAACAGAGCTGAAAAGGACTGCAAGGCCACGAACCACGTCTGT
gi|24657088|ref|NM_057410.3| TCGGATCAGTGCAACGAGGACGGCTGCTGGGGAGCTGGCACGGATCAGTG
gi|24657104|ref|NM_057411.3| TCGGATCAGTGCAACGAGGACGGCTGCTGGGGAGCTGGCACGGATCAGTG
gi|302179500|gb|HM749883.1| CACCCGCTGTGCTCATCAGAGGGCTGCTGGGGACCGGGACCCAAATACTG
gi|47522839|ref|NM_214007.1| AACCCGCTGTGCTCATCAGAGGGCTGCTGGGGCCCTGAACCCAGAGACTG
gi|41327737|ref|NM_005228.3| CATGCCTTGTGCTCCCCCGAGGGCTGCTGGGGCCCGGAGCCCAGGGACTG
gi|6478867|gb|M37394.2|RATEGFR AATCCTTTATGCTCCTCGGAAGGCTGCTGGGGCCCTGAGCCCACGGACTG
gi|24657088|ref|NM_057410.3| CCTTACCTGCAAGAACTTCAATTTCAATGGCACCTGCATCGCCGACTGTG
gi|24657104|ref|NM_057411.3| CCTTACCTGCAAGAACTTCAATTTCAATGGCACCTGCATCGCCGACTGTG
gi|302179500|gb|HM749883.1| CATGTCCTGCCAGAACTTCAGTCGTGGCAAGGAGTGTGTGGGAAAGTGCA
gi|47522839|ref|NM_214007.1| CATGTCCTGTCGAAACTTTAGCCGCGGCAAGGAATGTGTGGAGAAGTGCA
gi|41327737|ref|NM_005228.3| CGTCTCTTGCCGGAATGTCAGCCGAGGCAGGGAATGCGTGGACAAGTGCA
gi|6478867|gb|M37394.2|RATEGFR TGTCTCCTGCCAGAATGTGAGCAGAGGCAGGGAGTGCGTGGACAAGTGCA
gi|24657088|ref|NM_057410.3| GTTATATATCCAATGCCTACAAG------TTTGACAATAGAACGTGCAAG
gi|24657104|ref|NM_057411.3| GTTATATATCCAATGCCTACAAG------TTTGACAATAGAACGTGCAAG
gi|302179500|gb|HM749883.1| ACATTCTAGAGGGAGAGCCCAGAGAATTCGTGGAGAACTCCGAGTGTGTG
gi|47522839|ref|NM_214007.1| ACGTTCTGGAGGGGGAGCCGAGAGAGTTCGTGGAGAATGCCGAGTGTGTG
gi|41327737|ref|NM_005228.3| ACCTTCTGGAGGGTGAGCCAAGGGAGTTTGTGGAGAACTCTGAGTGCATA
gi|6478867|gb|M37394.2|RATEGFR ACATCCTGGAGGGGGAACCGAGGGAGTTTGTGGAAAATTCTGAATGCATC
gi|24657088|ref|NM_057410.3| ATATGCCATCCAGAGTGCCGG------------------ACTTGCAATGG
gi|24657104|ref|NM_057411.3| ATATGCCATCCAGAGTGCCGG------------------ACTTGCAATGG
gi|302179500|gb|HM749883.1| CAGTGCCATCCAGAATGCCTGCCCCAGGCCATGAACGTGACCTGCACTGG
gi|47522839|ref|NM_214007.1| CAGTGCCACCCGGAGTGCCTGCCCCAGGCCAAGAACGTGACCTGCATGGG
gi|41327737|ref|NM_005228.3| CAGTGCCACCCAGAGTGCCTGCCTCAGGCCATGAACATCACCTGCACAGG
gi|6478867|gb|M37394.2|RATEGFR CAGTGCCATCCAGAATGTCTGCCCCAGACCATGAACATCACCTGTACAGG
gi|24657088|ref|NM_057410.3| AGCTGGAGCAGATCACTGCCAGGAGTGCGTCCATGTGAGGGACGGTCAGC
gi|24657104|ref|NM_057411.3| AGCTGGAGCAGATCACTGCCAGGAGTGCGTCCATGTGAGGGACGGTCAGC
gi|302179500|gb|HM749883.1| ACGCGGACCAGGCAACTGTGTAAAGTGCGCCCACTACATTGATGGCCCTC
gi|47522839|ref|NM_214007.1| ACGCGGACCGGACAGCTGTGTCCGGTGTGCTCACTACATCGACGGCCCTC
gi|41327737|ref|NM_005228.3| ACGGGGACCAGACAACTGTATCCAGTGTGCCCACTACATTGACGGCCCCC
gi|6478867|gb|M37394.2|RATEGFR CCGGGGGCCAGACAACTGCATCAAGTGTGCCCACTATGTTGATGGTCCCC
gi|24657088|ref|NM_057410.3| ACTGTGTGTCCGAGTGCCCGAAGAACAAGTACAACGATCGTGGTGTCTGC
gi|24657104|ref|NM_057411.3| ACTGTGTGTCCGAGTGCCCGAAGAACAAGTACAACGATCGTGGTGTCTGC
gi|302179500|gb|HM749883.1| ACTGCGTCAAGACCTGCCCT------------------------------
gi|47522839|ref|NM_214007.1| ACTGTGTCAAGACCTGCCCC------------------------------
gi|41327737|ref|NM_005228.3| ACTGCGTCAAGACCTGCCCG------------------------------
gi|6478867|gb|M37394.2|RATEGFR ACTGTGTCAAGACCTGCCCT------------------------------
gi|24657088|ref|NM_057410.3| CGAGAGTGCCACGCCACCTGCGATGGATGCACTGGGCCCAAGGACACCAT
gi|24657104|ref|NM_057411.3| CGAGAGTGCCACGCCACCTGCGATGGATGCACTGGGCCCAAGGACACCAT
gi|302179500|gb|HM749883.1| ---------------------GCTGGAGTCGCGGGAGAGAATGGCACCCT
gi|47522839|ref|NM_214007.1| ---------------------GCGGGAATCGCAGGAGAAAACAGCACCCT
gi|41327737|ref|NM_005228.3| ---------------------GCAGGAGTCATGGGAGAAAACAACACCCT
gi|6478867|gb|M37394.2|RATEGFR ---------------------TCGGGCATCATGGGGGAGAACAACACCCT
gi|24657088|ref|NM_057410.3| CGGCATTGGAGCGTGTACAACGTGCAATTTGGCCATTATCAACAATGACG
gi|24657104|ref|NM_057411.3| CGGCATTGGAGCGTGTACAACGTGCAATTTGGCCATTATCAACAATGACG
gi|302179500|gb|HM749883.1| GATC----------------------------------------------
gi|47522839|ref|NM_214007.1| CATC----------------------------------------------
gi|41327737|ref|NM_005228.3| GGTC----------------------------------------------
gi|6478867|gb|M37394.2|RATEGFR GGTC----------------------------------------------
gi|24657088|ref|NM_057410.3| CCACAGTAAAACGCTGCCTGCTGAAGGACGACAAGTGCCCCGATGGGTAC
gi|24657104|ref|NM_057411.3| CCACAGTAAAACGCTGCCTGCTGAAGGACGACAAGTGCCCCGATGGGTAC
gi|302179500|gb|HM749883.1| --------------------------------------------------
gi|47522839|ref|NM_214007.1| --------------------------------------------------
gi|41327737|ref|NM_005228.3| --------------------------------------------------
gi|6478867|gb|M37394.2|RATEGFR --------------------------------------------------
gi|24657088|ref|NM_057410.3| TTCTGGGAGTATGTGCATCCACAAGAGCAGGGATCGCTAAAGCCATTGGC
gi|24657104|ref|NM_057411.3| TTCTGGGAGTATGTGCATCCACAAGAGCAGGGATCGCTAAAGCCATTGGC
gi|302179500|gb|HM749883.1| ---TGGAAGTTTGCA-----------------------------------
gi|47522839|ref|NM_214007.1| ---TGGAAGTTTGCG-----------------------------------
gi|41327737|ref|NM_005228.3| ---TGGAAGTACGCA-----------------------------------
gi|6478867|gb|M37394.2|RATEGFR ---TGGAAGTTTGCA-----------------------------------
gi|24657088|ref|NM_057410.3| CGGCAGAGCAGTTTGCCGAAAGTGCCATCCCCTTTGCGAGCTGTGCACCA
gi|24657104|ref|NM_057411.3| CGGCAGAGCAGTTTGCCGAAAGTGCCATCCCCTTTGCGAGCTGTGCACCA
gi|302179500|gb|HM749883.1| -------------------GATGCCAACCACGTGTGTCTCCTG-------
gi|47522839|ref|NM_214007.1| -------------------GATGCCAACCACGTGTGTCACCTG-------
gi|41327737|ref|NM_005228.3| -------------------GACGCCGGCCATGTGTGCCACCTG-------
gi|6478867|gb|M37394.2|RATEGFR -------------------GATGCCAATAACGTCTGCCACCTC-------
gi|24657088|ref|NM_057410.3| ACTACGGATACCATGAACAGGTGTGCTCCAAGTGCACCCACTACAAGCGA
gi|24657104|ref|NM_057411.3| ACTACGGATACCATGAACAGGTGTGCTCCAAGTGCACCCACTACAAGCGA
gi|302179500|gb|HM749883.1| --------------------------------------------------
gi|47522839|ref|NM_214007.1| --------------------------------------------------
gi|41327737|ref|NM_005228.3| --------------------------------------------------
gi|6478867|gb|M37394.2|RATEGFR --------------------------------------------------
gi|24657088|ref|NM_057410.3| CGAGAGCAGTGCGAGACCGAGTGTCCGGCCGATCACTACACGGATGAGGA
gi|24657104|ref|NM_057411.3| CGAGAGCAGTGCGAGACCGAGTGTCCGGCCGATCACTACACGGATGAGGA
gi|302179500|gb|HM749883.1| --------------------------------------------------
gi|47522839|ref|NM_214007.1| --------------------------------------------------
gi|41327737|ref|NM_005228.3| --------------------------------------------------
gi|6478867|gb|M37394.2|RATEGFR --------------------------------------------------
gi|24657088|ref|NM_057410.3| GCAGCGCGAGTGCTTCCAGTGCCACCCAGAATGCAAC---GGTTGCACTG
gi|24657104|ref|NM_057411.3| GCAGCGCGAGTGCTTCCAGTGCCACCCAGAATGCAAC---GGTTGCACTG
gi|302179500|gb|HM749883.1| -------------------TGCCACCCCAACTGCACCTATGGCTGTGAAG
gi|47522839|ref|NM_214007.1| -------------------TGCCACCCCAACTGCACCTACGGCTGTGTCG
gi|41327737|ref|NM_005228.3| -------------------TGCCATCCAAACTGCACCTACGGATGCACTG
gi|6478867|gb|M37394.2|RATEGFR -------------------TGCCATGCAAACTGTACCTATGGATGTGCTG
gi|24657088|ref|NM_057410.3| GTCCGGGTGCCGACGATTGCAAGTCTTGTCGCAACTTCAAGTTGTTCGAC
gi|24657104|ref|NM_057411.3| GTCCGGGTGCCGACGATTGCAAGTCTTGTCGCAACTTCAAGTTGTTCGAC
gi|302179500|gb|HM749883.1| GGCCAGGTCTCGAAGGCTGTCCACAA---AAAGGGCCCAAGATC------
gi|47522839|ref|NM_214007.1| GACCAGGTCTCGAGGGCTGTGCGGTG---GACAGGCCCAAGATC------
gi|41327737|ref|NM_005228.3| GGCCAGGTCTTGAAGGCTGTCCAACG---AATGGGCCTAAGATC------
gi|6478867|gb|M37394.2|RATEGFR GGCCAGGCCTTAAAGGATGTCAACAACCAGAAGGGCCAAAGATC------
gi|24657088|ref|NM_057410.3| GCGAATGAGACGGGTCCCTATGTGAACTCCACGATGTTCAATTGCACCTC
gi|24657104|ref|NM_057411.3| GCGAATGAGACGGGTCCCTATGTGAACTCCACGATGTTCAATTGCACCTC
gi|302179500|gb|HM749883.1| ---------------CCGTCCATTGCCACGGGCATCGTG-----------
gi|47522839|ref|NM_214007.1| ---------------CCGTCCATCGCCACCGGGATAGTG-----------
gi|41327737|ref|NM_005228.3| ---------------CCGTCCATCGCCACTGGGATGGTG-----------
gi|6478867|gb|M37394.2|RATEGFR ---------------CCATCCATCGCCACTGGGATTGTG-----------
gi|24657088|ref|NM_057410.3| GAAGTGTCCCTTGGAGATGCGACATGTGAACTATCAGTACACGGCCATTG
gi|24657104|ref|NM_057411.3| GAAGTGTCCCTTGGAGATGCGACATGTGAACTATCAGTACACGGCCATTG
gi|302179500|gb|HM749883.1| --------------------------------------------------
gi|47522839|ref|NM_214007.1| --------------------------------------------------
gi|41327737|ref|NM_005228.3| --------------------------------------------------
gi|6478867|gb|M37394.2|RATEGFR --------------------------------------------------
gi|24657088|ref|NM_057410.3| GACCCTACTGTGCAGCTAGTCCGCCGAGGAGCAGCAAGATAACTGCCAAT
gi|24657104|ref|NM_057411.3| GACCCTACTGTGCAGCTAGTCCGCCGAGGAGCAGCAAGATAACTGCCAAT
gi|302179500|gb|HM749883.1| --------------------------------------------------
gi|47522839|ref|NM_214007.1| --------------------------------------------------
gi|41327737|ref|NM_005228.3| --------------------------------------------------
gi|6478867|gb|M37394.2|RATEGFR --------------------------------------------------
gi|24657088|ref|NM_057410.3| CTGGATGTGAACATGATCTTCATTATCACTGGTGCTGTTCTGGTGCCGAC
gi|24657104|ref|NM_057411.3| CTGGATGTGAACATGATCTTCATTATCACTGGTGCTGTTCTGGTGCCGAC
gi|302179500|gb|HM749883.1| ------------------------------GGCGGCCTGCTGCTGGTGGT
gi|47522839|ref|NM_214007.1| ------------------------------GGGGGCCTGCTTCTGGCCGT
gi|41327737|ref|NM_005228.3| ------------------------------GGGGCCCTCCTCTTGCTGCT
gi|6478867|gb|M37394.2|RATEGFR ------------------------------GGTGGCCTCCTCTTCATAGT
gi|24657088|ref|NM_057410.3| GATCTGCATCCTCTGCGTGGTCACATACATTTGTCGGCAAAAGCAAAAGG
gi|24657104|ref|NM_057411.3| GATCTGCATCCTCTGCGTGGTCACATACATTTGTCGGCAAAAGCAAAAGG
gi|302179500|gb|HM749883.1| GGTGCTGGCCCTGAGCGTCGGCCTCTTCATG---CGCAGGCGCCACATCG
gi|47522839|ref|NM_214007.1| GGTGCTGGCCCTGGGGGTCGGCCTCTTTCTG---CGCAGGCGCCACATCG
gi|41327737|ref|NM_005228.3| GGTGGTGGCCCTGGGGATCGGCCTCTTCATG---CGAAGGCGCCACATCG
gi|6478867|gb|M37394.2|RATEGFR AGTGGTGGCCCTTGGGATCGGCCTCTTCATG---CGTCGACGTCAGCTTG
gi|24657088|ref|NM_057410.3| CCAAGAAAGAAACAGTGAAGATGACCATGGCTCTGTCCGGCTGTGAGGAT
gi|24657104|ref|NM_057411.3| CCAAGAAAGAAACAGTGAAGATGACCATGGCTCTGTCCGGCTGTGAGGAT
gi|302179500|gb|HM749883.1| TGCGCAAGCGCACACTGCGCCGGCTG------CTGCAGGAGCGTGAGCTC
gi|47522839|ref|NM_214007.1| TCCGCAAGCGCACGCTGCGCCGGCTG------CTGCAGGAGCGGGAGCTG
gi|41327737|ref|NM_005228.3| TTCGGAAGCGCACGCTGCGGAGGCTG------CTGCAGGAGAGGGAGCTT
gi|6478867|gb|M37394.2|RATEGFR TCCGAAAACGTACACTACGCCGCCTG------CTTCAAGAGAGAGAGCTC
gi|24657088|ref|NM_057410.3| TCCGAGCCGCTGCGTCCCTCGAACATTGGAGCCAATCTATGCAAGTTGCG
gi|24657104|ref|NM_057411.3| TCCGAGCCGCTGCGTCCCTCGAACATTGGAGCCAATCTATGCAAGTTGCG
gi|302179500|gb|HM749883.1| GTGGAGCCTCTGACGCCCAGCGGAGAAGCTCCCAACCAAGCTCTCTTGAG
gi|47522839|ref|NM_214007.1| GTTGAGCCTCTCACACCCAGTGGAGAAGCTCCCAACCAAGCTCTCTTGAG
gi|41327737|ref|NM_005228.3| GTGGAGCCTCTTACACCCAGTGGAGAAGCTCCCAACCAAGCTCTCTTGAG
gi|6478867|gb|M37394.2|RATEGFR GTGGAACCTCTCACACCCAGCGGAGAAGCTCCGAACCAAGCCCACTTGAG
gi|24657088|ref|NM_057410.3| CATTGTCAAGGACGCCGAGTTGCGCAAGGGCGGAGTCCTCGGAATGGGAG
gi|24657104|ref|NM_057411.3| CATTGTCAAGGACGCCGAGTTGCGCAAGGGCGGAGTCCTCGGAATGGGAG
gi|302179500|gb|HM749883.1| GATCCTAAAGGAAACAGAATTCAAGAAGGTCAAGGTGCTGGGCTCGGGAG
gi|47522839|ref|NM_214007.1| GATCCTGAAGGAGACGGAATTCAAAAAGGTCAAGGTGCTGGGCTCCGGCG
gi|41327737|ref|NM_005228.3| GATCTTGAAGGAAACTGAATTCAAAAAGATCAAAGTGCTGGGCTCCGGTG
gi|6478867|gb|M37394.2|RATEGFR GATATTAAAGGAAACAGAATTCAAAAAGATCAAAGTTCTGGGTTCAGGAG
gi|24657088|ref|NM_057410.3| CCTTTGGACGAGTGTACAAGGGCGTTTGGGTGCCGGAGGGTGAGAACGTC
gi|24657104|ref|NM_057411.3| CCTTTGGACGAGTGTACAAGGGCGTTTGGGTGCCGGAGGGTGAGAACGTC
gi|302179500|gb|HM749883.1| CATTTGGCACCGTGTACAAGGGACTCTGGATCCCAGAAGGCGAGAAGGTT
gi|47522839|ref|NM_214007.1| CGTTCGGCACGGTGTACAAGGGCCTCTGGATCCCAGAAGGTGAGAAGGTG
gi|41327737|ref|NM_005228.3| CGTTCGGCACGGTGTATAAGGGACTCTGGATCCCAGAAGGTGAGAAAGTT
gi|6478867|gb|M37394.2|RATEGFR CATTTGGCACAGTGTATAAGGGTCTCTGGATCCCAGAAGGCGAGAAAGTG
gi|24657088|ref|NM_057410.3| AAGATTCCAGTGGCCATTAAGGAGCTGCTCAAGTCCACAGGCGCCGAGTC
gi|24657104|ref|NM_057411.3| AAGATTCCAGTGGCCATTAAGGAGCTGCTCAAGTCCACAGGCGCCGAGTC
gi|302179500|gb|HM749883.1| AAAATTCCTGTAGCTATCAAGGAATTAAGAGAAGCCACATCTCCAAAAGC
gi|47522839|ref|NM_214007.1| AAAATTCCTGTGGCTATCAAGGAATTAAGAGAAGCCACTTCTCCAAAAGC
gi|41327737|ref|NM_005228.3| AAAATTCCCGTCGCTATCAAGGAATTAAGAGAAGCAACATCTCCGAAAGC
gi|6478867|gb|M37394.2|RATEGFR AAAATCCCTGTGGCCATCAAGGAGTTAAGAGAAGCCACATCTCCCAAAGC
gi|24657088|ref|NM_057410.3| AAGCGAAGAGTTCCTCCGCGAAGCCTACATCATGGCCTCTGTGGAGCACG
gi|24657104|ref|NM_057411.3| AAGCGAAGAGTTCCTCCGCGAAGCCTACATCATGGCCTCTGTGGAGCACG
gi|302179500|gb|HM749883.1| CAACAAGGAAATTCTTGATGAGGCCTACGTGATGGCCAGTGTGGACAACC
gi|47522839|ref|NM_214007.1| CAACAAGGAAATTCTTGACGAAGCCTACGTGATGGCCAGTGTGGACAATC
gi|41327737|ref|NM_005228.3| CAACAAGGAAATCCTCGATGAAGCCTACGTGATGGCCAGCGTGGACAACC
gi|6478867|gb|M37394.2|RATEGFR CAACAAGGAAATCCTTGATGAAGCCTACGTGATGGCCAGTGTGGACAACC
gi|24657088|ref|NM_057410.3| TTAATCTGCTGAAGCTCCTGGCCGTCTGCATGTCCTCACAAATGATGCTA
gi|24657104|ref|NM_057411.3| TTAATCTGCTGAAGCTCCTGGCCGTCTGCATGTCCTCACAAATGATGCTA
gi|302179500|gb|HM749883.1| CCCATGTGTGCCGCCTCCTGGGCATCTGCCTGACCTCCACCGTGCAGCTC
gi|47522839|ref|NM_214007.1| CTCATGTGTGCCGCCTCCTGGGCATCTGCCTGACCTCCACGGTGCAGCTC
gi|41327737|ref|NM_005228.3| CCCACGTGTGCCGCCTGCTGGGCATCTGCCTCACCTCCACCGTGCAGCTC
gi|6478867|gb|M37394.2|RATEGFR CTCATGTATGCCGCCTCCTGGGCATCTGTCTGACCTCCACTGTCCAGCTC
gi|24657088|ref|NM_057410.3| ATCACGCAACTGATGCCGCTTGGCTGCCTGTTGGACTATGTGCGAAATAA
gi|24657104|ref|NM_057411.3| ATCACGCAACTGATGCCGCTTGGCTGCCTGTTGGACTATGTGCGAAATAA
gi|302179500|gb|HM749883.1| ATCACACAGCTCATGCCCTTCGGCTGCCTGCTGGACTACGTCCGCGAGCA
gi|47522839|ref|NM_214007.1| ATCACGCAGCTCATGCCCTTCGGCTGCCTCCTGGACTACGTCCGCGAGCA
gi|41327737|ref|NM_005228.3| ATCACGCAGCTCATGCCCTTCGGCTGCCTCCTGGACTATGTCCGGGAACA
gi|6478867|gb|M37394.2|RATEGFR ATTACACAACTCATGCCCTATGGTTGCCTCCTGGACTATGTCCGAGAACA
gi|24657088|ref|NM_057410.3| CCGGGACAAGATCGGCTCTAAGGCTCTGCTCAACTGGAGCACGCAAATCG
gi|24657104|ref|NM_057411.3| CCGGGACAAGATCGGCTCTAAGGCTCTGCTCAACTGGAGCACGCAAATCG
gi|302179500|gb|HM749883.1| CAAGGACAATGTCGGCTCCCAGTACCTGCTCAACTGGTGTGTGCAGATCG
gi|47522839|ref|NM_214007.1| CAAGGACAACATCGGCTCCCAGCACCTGCTCAACTGGTGTGTGCAGATCG
gi|41327737|ref|NM_005228.3| CAAAGACAATATTGGCTCCCAGTACCTGCTCAACTGGTGTGTGCAGATCG
gi|6478867|gb|M37394.2|RATEGFR TAAGGACAACATTGGCTCCCAGTACCTACTCAACTGGTGTGTGCAGATTG
gi|24657088|ref|NM_057410.3| CCAAGGGCATGTCGTATCTGGAGGAGAAGCGACTGGTCCACAGAGACTTG
gi|24657104|ref|NM_057411.3| CCAAGGGCATGTCGTATCTGGAGGAGAAGCGACTGGTCCACAGAGACTTG
gi|302179500|gb|HM749883.1| CAAAGGGCATGAATTACCTGGAAGACCGGCGCTTGGTGCATAGGGACCTG
gi|47522839|ref|NM_214007.1| CAAAGGGCATGAACTATCTGGAAGACCGGCGCTTGGTGCACCGAGACCTG
gi|41327737|ref|NM_005228.3| CAAAGGGCATGAACTACTTGGAGGACCGTCGCTTGGTGCACCGCGACCTG
gi|6478867|gb|M37394.2|RATEGFR CAAAGGGCATGAACTACCTGGAAGACCGGCGTTTGGTACACCGTGACTTG
gi|24657088|ref|NM_057410.3| GCTGCCCGCAATGTCCTGGTGCAGACTCCCTCGCTGGTGAAGATCACCGA
gi|24657104|ref|NM_057411.3| GCTGCCCGCAATGTCCTGGTGCAGACTCCCTCGCTGGTGAAGATCACCGA
gi|302179500|gb|HM749883.1| GCAGCCAGGAACGTGCTGGTGAAGACGCCGCAGCACGTGAAGATCACAGA
gi|47522839|ref|NM_214007.1| GCGGCCAGGAATGTGCTGGTGAAGACACCGCAGCATGTCAAGATCACTGA
gi|41327737|ref|NM_005228.3| GCAGCCAGGAACGTACTGGTGAAAACACCGCAGCATGTCAAGATCACAGA
gi|6478867|gb|M37394.2|RATEGFR GCAGCCAGGAATGTACTGGTAAAGACACCACAGCATGTCAAGATCACAGA
gi|24657088|ref|NM_057410.3| CTTTGGGCTGGCCAAGTTGCTGAGCAGCGATTCCAATGAGTACAAGGCTG
gi|24657104|ref|NM_057411.3| CTTTGGGCTGGCCAAGTTGCTGAGCAGCGATTCCAATGAGTACAAGGCTG
gi|302179500|gb|HM749883.1| CTTCGGGCTGGCCAAGCTGCTGGGTGCCGAGGAGAAGGAGTATCATGCAG
gi|47522839|ref|NM_214007.1| CTTTGGGCTGGCCAAGCTGCTGGGCGCCGAGGAGAAAGAGTACCACGCGG
gi|41327737|ref|NM_005228.3| TTTTGGGCTGGCCAAACTGCTGGGTGCGGAAGAGAAAGAATACCATGCAG
gi|6478867|gb|M37394.2|RATEGFR TTTTGGACTGGCCAAACTGCTTGGTGCTGAGGAGAAAGAATACCATGCAG
gi|24657088|ref|NM_057410.3| CTGGCGGCAAGATGCCCATCAAGTGGTTGGCACTGGAGTGCATTCGCAAT
gi|24657104|ref|NM_057411.3| CTGGCGGCAAGATGCCCATCAAGTGGTTGGCACTGGAGTGCATTCGCAAT
gi|302179500|gb|HM749883.1| AAGGAGGCAAGGTCCCTATCAAATGGATGGCTTTGGAATCAATTTTACAC
gi|47522839|ref|NM_214007.1| AAGGAGGCAAAGTGCCCATCAAGTGGCTGGCTCTAGAGTCAATCCTGCAC
gi|41327737|ref|NM_005228.3| AAGGAGGCAAAGTGCCTATCAAGTGGATGGCATTGGAATCAATTTTACAC
gi|6478867|gb|M37394.2|RATEGFR AGGGGGGCAAAGTGCCTATCAAGTGGATGGCTTTGGAATCAATTTTACAC
gi|24657088|ref|NM_057410.3| CGTGTATTCACCAGCAAGTCCGATGTCTGGGCCTTTGGTGTGACAATTTG
gi|24657104|ref|NM_057411.3| CGTGTATTCACCAGCAAGTCCGATGTCTGGGCCTTTGGTGTGACAATTTG
gi|302179500|gb|HM749883.1| CGAATTTATACCCATCAGAGTGATGTCTGGAGCTATGGAGTCACTGTTTG
gi|47522839|ref|NM_214007.1| CGTGTATACACCCACCAGAGTGACGTCTGGAGCTACGGAGTCACCGTTTG
gi|41327737|ref|NM_005228.3| AGAATCTATACCCACCAGAGTGATGTCTGGAGCTACGGGGTGACCGTTTG
gi|6478867|gb|M37394.2|RATEGFR CGAATTTATACACACCAAAGCGACGTCTGGAGCTATGGAGTCACCGTGTG
gi|24657088|ref|NM_057410.3| GGAACTGCTGACCTTTGGCCAGCGTCCACACGAGAACATCCCCGCTAAGG
gi|24657104|ref|NM_057411.3| GGAACTGCTGACCTTTGGCCAGCGTCCACACGAGAACATCCCCGCTAAGG
gi|302179500|gb|HM749883.1| GGAGTTGATGACCTTTGGATCCAAGCCTTACGATGGAATCCCTGCGAGTG
gi|47522839|ref|NM_214007.1| GGAGCTGATGACCTTTGGGTCCAAGCCTTATGACGGGATCCCCGCGAGTG
gi|41327737|ref|NM_005228.3| GGAGTTGATGACCTTTGGATCCAAGCCATATGACGGAATCCCTGCCAGCG
gi|6478867|gb|M37394.2|RATEGFR GGAACTGATGACCTTTGGGTCCAAGCCTTATGATGGGATCCCTGCAAGTG
gi|24657088|ref|NM_057410.3| ATATTCCCGATCTTATTGAAGTCGGTCTGAAGCTGGAGCAGCCGGAGATT
gi|24657104|ref|NM_057411.3| ATATTCCCGATCTTATTGAAGTCGGTCTGAAGCTGGAGCAGCCGGAGATT
gi|302179500|gb|HM749883.1| AGATCTCGACTGTCCTGGAGAAAGGAGAGCGCCTCCCACAGCCACCCATC
gi|47522839|ref|NM_214007.1| AGATCTCGACCGTCCTGGAGAAGGGAGAGCGCCTCCCGCAGCCCCCCATC
gi|41327737|ref|NM_005228.3| AGATCTCCTCCATCCTGGAGAAAGGAGAACGCCTCCCTCAGCCACCCATA
gi|6478867|gb|M37394.2|RATEGFR AGATCTCATCCATCCTAGAGAAAGGAGAGCGCCTTCCACAGCCACCTATC
gi|24657088|ref|NM_057410.3| TGTTCGCTGGACATTTACTGCACACTTCTCTCGTGCTGGCACTTGGATGC
gi|24657104|ref|NM_057411.3| TGTTCGCTGGACATTTACTGCACACTTCTCTCGTGCTGGCACTTGGATGC
gi|302179500|gb|HM749883.1| TGCACCATCGACGTCTACATGATCATGGTCAAGTGCTGGATGATAGATGC
gi|47522839|ref|NM_214007.1| TGCACCATTGATGTCTACATGATCATGGTCAAGTGCTGGATGATAGATGC
gi|41327737|ref|NM_005228.3| TGTACCATCGATGTCTACATGATCATGGTCAAGTGCTGGATGATAGACGC
gi|6478867|gb|M37394.2|RATEGFR TGCACCATCGACGTCTACATGATCATGGTCAAGTGCTGGATGATAGATGC
gi|24657088|ref|NM_057410.3| CGCCATGCGTCCAACCTTCAAGCAGCTGACTACGGTCTTTGCTGAGTTCG
gi|24657104|ref|NM_057411.3| CGCCATGCGTCCAACCTTCAAGCAGCTGACTACGGTCTTTGCTGAGTTCG
gi|302179500|gb|HM749883.1| AGACAGTCGCCCAAAGTTCCGTGAGTTGATCCTTGAATTCTCCAAGATGG
gi|47522839|ref|NM_214007.1| TGATAGTCGCCCAAAGTTCCGTGAGCTGATCATCGAATTCTCCAAAATGG
gi|41327737|ref|NM_005228.3| AGATAGTCGCCCAAAGTTCCGTGAGTTGATCATCGAATTCTCCAAAATGG
gi|6478867|gb|M37394.2|RATEGFR TGATAGCCGCCCAAAGTTCCGAGAGTTGATTCTCGAATTCTCCAAAATGG
gi|24657088|ref|NM_057410.3| CCAGAGATCCGGGTCGCTATCTGGCCATTCCCGGGGATAAGTTCACCCGG
gi|24657104|ref|NM_057411.3| CCAGAGATCCGGGTCGCTATCTGGCCATTCCCGGGGATAAGTTCACCCGG
gi|302179500|gb|HM749883.1| CCCGAGACCCCCAGCGCTACCTTGTCATCCAGGGGGACGAGAGAATGCAT
gi|47522839|ref|NM_214007.1| CCCGAGACCCCCAGCGCTACCTTGTCATCCAGGGAGACGAGCGAATGCAC
gi|41327737|ref|NM_005228.3| CCCGAGACCCCCAGCGCTACCTTGTCATTCAGGGGGATGAAAGAATGCAT
gi|6478867|gb|M37394.2|RATEGFR CCAGAGACCCACAGCGCTACCTTGTTATCCAGGGGGATGAAAGGATGCAT
gi|24657088|ref|NM_057410.3| CTGCCGGCCTACACGAGTCAGGATGAGAAGGATCTCATCCGAAAATTGGC
gi|24657104|ref|NM_057411.3| CTGCCGGCCTACACGAGTCAGGATGAGAAGGATCTCATCCGAAAATTGGC
gi|302179500|gb|HM749883.1| TTGCCA---------AGCCCTACGGACTCCAACTTCTACCGCGCCCTGAT
gi|47522839|ref|NM_214007.1| TTGCCA---------AGCCCTACGGACTCCAACTTCTACCGCGCCCTGAT
gi|41327737|ref|NM_005228.3| TTGCCA---------AGTCCTACAGACTCCAACTTCTACCGTGCCCTGAT
gi|6478867|gb|M37394.2|RATEGFR TTGCCG---------AGCCCTACAGACTCCAACTTTTACCGAGCCCTGAT
gi|24657088|ref|NM_057410.3| TCCCACCACCGATGGGTCCGAAGCCATTGCGGAACCCGATGACTACCTGC
gi|24657104|ref|NM_057411.3| TCCCACCACCGATGGGTCCGAAGCCATTGCGGAACCCGATGACTACCTGC
gi|302179500|gb|HM749883.1| GGATGAGGAGGAC---ATGGAGGATGTTGTGGATGCCGATGAGTACCTCG
gi|47522839|ref|NM_214007.1| GGACGAGGAGGAC---ATGGAGGATGTGGTGGACGCCGACGAGTACCTCG
gi|41327737|ref|NM_005228.3| GGATGAAGAAGAC---ATGGACGACGTGGTGGATGCCGACGAGTACCTCA
gi|6478867|gb|M37394.2|RATEGFR GGAGGAGGAGGAC---ATGGAAGACGTAGTTGATGCTGATGAATACCTCA
gi|24657088|ref|NM_057410.3| AACCCAAGGCAGCACCTGGTCCTAGTCACAGAACCGACTGCACGGATGAG
gi|24657104|ref|NM_057411.3| AACCCAAGGCAGCACCTGGTCCTAGTCACAGAACCGACTGCACGGATGAG
gi|302179500|gb|HM749883.1| TCCCCCAGCAGGGCTTCTTCCACAGCCCCACCACCTCCCGGACACCCCTC
gi|47522839|ref|NM_214007.1| TCCCCCAGCAGGGCTTCTTCCACAGCCCCGCCACCTCCCGGACGCCGCTG
gi|41327737|ref|NM_005228.3| TCCCACAGCAGGGCTTCTTCAGCAGCCCCTCCACGTCACGGACTCCCCTC
gi|6478867|gb|M37394.2|RATEGFR TCCCACAGCAAGGCTTCTTCAACAGCCCATCCACGTCACGGACTCCACTC
gi|24657088|ref|NM_057410.3| ATACCCAAGCTGAACCGCTACTGCAAGGATCCTAGC------------AA
gi|24657104|ref|NM_057411.3| ATACCCAAGCTGAACCGCTACTGCAAGGATCCTAGC------------AA
gi|302179500|gb|HM749883.1| CTCAGCTCGCTGAGCACCTCCAGCAACACTCCCACTGTGACTTGCGTTGA
gi|47522839|ref|NM_214007.1| CTCAGCTCTCTGAGCGCCACCAGCAGCACCCCCGCTGTGGCTTGCGTTGA
gi|41327737|ref|NM_005228.3| CTGAGCTCTCTGAGTGCAACCAGCAACAATTCCACCGTGGCTTGCATTGA
gi|6478867|gb|M37394.2|RATEGFR TTGAGCTCTCTGAGTGCAAATAGCAACAGTTCCACTGTGGCTTGCATTAA
gi|24657088|ref|NM_057410.3| CAAGAATTCG------------AGTACCGGAGACGATGAGACGGATTCGA
gi|24657104|ref|NM_057411.3| CAAGAATTCG------------AGTACCGGAGACGATGAGACGGATTCGA
gi|302179500|gb|HM749883.1| TAGAAATGGG------AGCTACCCTCTCAAGGAAGACAGCTTCCTGCAGC
gi|47522839|ref|NM_214007.1| CAGAAACGGG---CAGAGTTATCCCCTCAAGGAAGACAGCTTCCTGCAGC
gi|41327737|ref|NM_005228.3| TAGAAATGGGCTGCAAAGCTGTCCCATCAAGGAAGACAGCTTCTTGCAGC
gi|6478867|gb|M37394.2|RATEGFR TAGAAATGGG------AGCTGCCGTGTCAAAGAAGACGCCTTCTTGCAAC
gi|24657088|ref|NM_057410.3| GTGCCCGGGAAGTGGGCGTGGGTAATCTGCGCCTCGAT------------
gi|24657104|ref|NM_057411.3| GTGCCCGGGAAGTGGGCGTGGGTAATCTGCGCCTCGAT------------
gi|302179500|gb|HM749883.1| GCTACAGCTCAGACCCCACTGGTGCCCTCATCGAGGACAGCATGGACGAC
gi|47522839|ref|NM_214007.1| GGTACAGCTCCGACCCCACTGGCGCCCTGACCGAGGACAGCCTAGACGAC
gi|41327737|ref|NM_005228.3| GATACAGCTCAGACCCCACAGGCGCCTTGACTGAGGACAGCATAGACGAC
gi|6478867|gb|M37394.2|RATEGFR GGTATAGCTCCGATCCCACCAGCGTCCTGACAGAGGACAACATAGATGAC
gi|24657088|ref|NM_057410.3| ------CTACCAGTCGATGAGGATGATTACCTGATGCCCACATGCCAACC
gi|24657104|ref|NM_057411.3| ------CTACCAGTCGATGAGGATGATTACCTGATGCCCACATGCCAACC
gi|302179500|gb|HM749883.1| GCTTTCCTCCCAGTACCCGAA------TATGTAAACCAATCTGTTCCCAA
gi|47522839|ref|NM_214007.1| ACTTTTCTCCCAGCACCCGAA------TATGTAAACCAGTCTGTTCCCAA
gi|41327737|ref|NM_005228.3| ACCTTCCTCCCAGTGCCTGAA------TACATAAACCAGTCCGTTCCCAA
gi|6478867|gb|M37394.2|RATEGFR ACATTCCTTCCCGTGCCTGAA------TATATAAACCAATCTGTTCCCAA
gi|24657088|ref|NM_057410.3| GGGGCCCAACAACAACAACAACATAAATAATCCC---------AATCAAA
gi|24657104|ref|NM_057411.3| GGGGCCCAACAACAACAACAACATAAATAATCCC---------AATCAAA
gi|302179500|gb|HM749883.1| AAGACCC------GCAGGCTCTGTCCAGAACCCTGTCTATCACAATCAGC
gi|47522839|ref|NM_214007.1| GAGGCCC------GCGGGCTCCGTCCAGAACCCTGTCTACCACAATCAGC
gi|41327737|ref|NM_005228.3| AAGGCCC------GCTGGCTCTGTGCAGAATCCTGTCTATCACAATCAGC
gi|6478867|gb|M37394.2|RATEGFR GAGGCCG------GCTGGCTCTGTGCAGAACCCAGTCTATCACAATCAGC
gi|24657088|ref|NM_057410.3| ACAATATGGCAGCTGTGGGCGTGGCTGCCGGCTACATGGATCTCATCGGA
gi|24657104|ref|NM_057411.3| ACAATATGGCAGCTGTGGGCGTGGCTGCCGGCTACATGGATCTCATCGGA
gi|302179500|gb|HM749883.1| CTCTATATCCAGCTCCTGGCAGAGACCCTCAGTACCAAAAT------TCA
gi|47522839|ref|NM_214007.1| CTCTCAGTGCAGCTCCTGGCCGGGACCCCCACTACCAGAAC------TCC
gi|41327737|ref|NM_005228.3| CTCTGAACCCCGCGCCCAGCAGAGACCCACACTACCAGGAC------CCC
gi|6478867|gb|M37394.2|RATEGFR CCCTGCATCCAGCTCCTGGAAGAGACCTGCATTATCAAAAT------CCC
gi|24657088|ref|NM_057410.3| GTGCCCGTTAGTGTGGACAATCCGGAGTATCTGCTAAACGCGCAGACACT
gi|24657104|ref|NM_057411.3| GTGCCCGTTAGTGTGGACAATCCGGAGTATCTGCTAAACGCGCAGACACT
gi|302179500|gb|HM749883.1| CTCAGCAACGCCGTGGACAACCCTGAGTATCTCAACACCACCCATCCTGC
gi|47522839|ref|NM_214007.1| CACAGCAATGCCGTGGGCAACCCTGAGTATCTCAACACCCCCCGCCCCGC
gi|41327737|ref|NM_005228.3| CACAGCACTGCAGTGGGCAACCCCGAGTATCTCAACACTGTCCAGCCCAC
gi|6478867|gb|M37394.2|RATEGFR CATAGCAATGCGGTGAGCAACCCTGAGTATCTCAACACTGCCCAGCCGAC
gi|24657088|ref|NM_057410.3| GGGTGTTGGG---------GAGTCGCCGATACCCACCCAGACCATCGGGA
gi|24657104|ref|NM_057411.3| GGGTGTTGGG---------GAGTCGCCGATACCCACCCAGACCATCGGGA
gi|302179500|gb|HM749883.1| CTGTATCAATGGTGTGCTCGACGGCCCTGCCCTCTGGGCTCAGAAGGGCA
gi|47522839|ref|NM_214007.1| CTGCATCAACGGAGGACTGGACGGCCCTGCCTTCTGGGCACAGACAGGCA
gi|41327737|ref|NM_005228.3| CTGTGTCAACAGCACATTCGACAGCCCTGCCCACTGGGCCCAGAAAGGCA
gi|6478867|gb|M37394.2|RATEGFR CTGCCTCAGTAGTGGGTTTGACAGCTCTGCCCTCTGGATCCAGAAAGGCA
gi|24657088|ref|NM_057410.3| TACCGGTGATGGGAGTCCCGGGCACCATGGAGGTCAAGGTGCCAATGCCA
gi|24657104|ref|NM_057411.3| TACCGGTGATGGGAGTCCCGGGCACCATGGAGGTCAAGGTGCCAATGCCA
gi|302179500|gb|HM749883.1| GTCACCAATTTAGCCTAGACAACCCTGACTACCAGCAGGCCTTCTTTCCC
gi|47522839|ref|NM_214007.1| GCCACCAGATTAATCTGGACAACCCAGACTACCAGCAGGCCTTCTTCCCC
gi|41327737|ref|NM_005228.3| GCCACCAAATTAGCCTGGACAACCCTGACTACCAGCAGGACTTCTTTCCC
gi|6478867|gb|M37394.2|RATEGFR GCCACCAAATGAGCCTGGACAACCCTGACTACCAGCAGGACTTCTTTCCC
gi|24657088|ref|NM_057410.3| GGCAGTGAGCCAACGAGCTCCGATCACGAGTACTACAATGATACCCAACG
gi|24657104|ref|NM_057411.3| GGCAGTGAGCCAACGAGCTCCGATCACGAGTACTACAATGATACCCAACG
gi|302179500|gb|HM749883.1| AAGGAAGCCAAGTCGAATGGCATCTTTAAGGGGCCTGCAGCTGAAAATGC
gi|47522839|ref|NM_214007.1| AAGGAAGCCAAGTCAAACGGCATCTGTAAGGGTCCCGCCGCCGAAAACGC
gi|41327737|ref|NM_005228.3| AAGGAAGCCAAGCCAAATGGCATCTTTAAGGGCTCCACAGCTGAAAATGC
gi|6478867|gb|M37394.2|RATEGFR AAAGAAGCCAAGCCGAATGGCATCTTTAAGGGCCCCACAGCTGAAAATGC
gi|24657088|ref|NM_057410.3| GGAGTTGCAGCCACTGCATCGAAACCGCAACACGGAGACGAGGGTG
gi|24657104|ref|NM_057411.3| GGAGTTGCAGCCACTGCATCGAAACCGCAACACGGAGACGAGGGTG
gi|302179500|gb|HM749883.1| AGAATACCTGCGGGCAGCACCAGCAGGCAGTGACTTTACTGGGGCC
gi|47522839|ref|NM_214007.1| AGAGTACCTAAGGGCGGCACCAGCCAGCAGTGACCTTACTGGGGCA
gi|41327737|ref|NM_005228.3| AGAATACCTAAGGGTCGCGCCACAAAGCAGTGAATTTATTGGAGCA
gi|6478867|gb|M37394.2|RATEGFR AGAGTACCTGCGGGTGGCACCGCCAAGCAGTGAGTTTAGTGGAGCA
""",
)
pairwise_alignment = alignment[:2]
dN, dS = calculate_dn_ds(pairwise_alignment, method="NG86")
self.assertAlmostEqual(dN, 0.0209, places=4)
self.assertAlmostEqual(dS, 0.0178, places=4)
dN, dS = calculate_dn_ds(pairwise_alignment, method="LWL85")
self.assertAlmostEqual(dN, 0.0203, places=4)
self.assertAlmostEqual(dS, 0.0164, places=4)
try:
import scipy
except ImportError:
# Silently skip the rest of the test
return
# This should be present:
from scipy.linalg import expm
dN, dS = calculate_dn_ds(pairwise_alignment, method="YN00")
self.assertAlmostEqual(dN, 0.0198, places=4)
self.assertAlmostEqual(dS, 0.0222, places=4)
try:
# New in scipy v0.11
from scipy.optimize import minimize
dN, dS = calculate_dn_ds(pairwise_alignment, method="ML")
self.assertAlmostEqual(dN, 0.0194, places=4)
self.assertAlmostEqual(dS, 0.0217, places=4)
except ImportError:
pass
# NG86 method with default codon table
dn_correct = [
0,
0.02090783050583131,
0,
0.6115239249238438,
0.6102203266798018,
0,
0.6140350835631757,
0.6040168621204747,
0.041180350405913294,
0,
0.6141532531400524,
0.6018263135601294,
0.06701051445629494,
0.061470360954086874,
0,
0.6187088340904762,
0.6068687248870475,
0.07386903034833081,
0.07357890927918581,
0.05179847072570129,
0,
]
ds_correct = [
0,
0.01783718763890243,
0,
2.9382055377913687,
3.0375115405379267,
0,
2.008913071877126,
2.0182088023715616,
0.5638033197005285,
0,
2.771425931736778,
2.7353083173058295,
0.6374483799734671,
0.723542095485497,
0,
-1,
-1,
0.953865978141643,
1.182154857347706,
0.843182957978177,
0,
]
dn, ds = calculate_dn_ds_matrix(alignment)
dn_list = []
for i in dn.matrix:
dn_list.extend(i)
for dn_cal, dn_corr in zip(dn_list, dn_correct):
self.assertAlmostEqual(dn_cal, dn_corr, places=4)
ds_list = []
for i in ds.matrix:
ds_list.extend(i)
for ds_cal, ds_corr in zip(ds_list, ds_correct):
self.assertAlmostEqual(ds_cal, ds_corr, places=4)
# YN00 method with user specified codon table
dn_correct = [
0,
0.019701773284646867,
0,
0.6109649819852769,
0.6099903856901369,
0,
0.6114499930666559,
0.6028068208599121,
0.045158286242251426,
0,
0.6151835071687592,
0.6053227393422296,
0.07034397741651377,
0.06956967795096626,
0,
0.6103850655769698,
0.5988716898831496,
0.07905930042150053,
0.08203052937107111,
0.05659346894088538,
0,
]
ds_correct = [
0,
0.01881718550096053,
0,
1.814457265482046,
1.8417575124882066,
0,
1.5627041719628896,
1.563930819079887,
0.4748890153032888,
0,
1.6754828466084355,
1.6531212012501901,
0.5130923627791538,
0.5599667707191436,
0,
2.0796114236540943,
2.1452591651827304,
0.7243066372971764,
0.8536617406770075,
0.6509203399899367,
0,
]
dn, ds = calculate_dn_ds_matrix(
alignment, method="LWL85", codon_table=CodonTable.unambiguous_dna_by_id[3]
)
dn_list = []
for i in dn.matrix:
dn_list.extend(i)
for dn_cal, dn_corr in zip(dn_list, dn_correct):
self.assertAlmostEqual(dn_cal, dn_corr, places=4)
ds_list = []
for i in ds.matrix:
ds_list.extend(i)
for ds_cal, ds_corr in zip(ds_list, ds_correct):
self.assertAlmostEqual(ds_cal, ds_corr, places=4)
class Test_MK(unittest.TestCase):
def test_mk(self):
aligner = CodonAligner()
nucleotide_records = SeqIO.index("codonalign/drosophila.fasta", "fasta")
protein_alignment = Align.read("codonalign/adh.aln", "clustal")
self.assertEqual(len(protein_alignment.sequences), 27)
codon_alignments = []
protein_record = protein_alignment.sequences[0]
nucleotide_record = nucleotide_records[protein_record.id]
self.assertEqual(nucleotide_record.id, protein_record.id)
alignments = aligner.align(protein_record, nucleotide_record)
self.assertEqual(len(alignments), 1)
alignment = next(alignments)
codon_alignments.append(alignment)
self.assertTrue(
np.array_equal(alignment.coordinates, np.array([[0, 256], [0, 768]]))
)
self.assertEqual(
str(alignment),
"""\
gi|9217|e 0 M A F T L T N K N V V F V A G L G G I G
gi|9217|e 0 ATGGCGTTTACCTTGACCAACAAGAACGTGGTTTTCGTGGCCGGTCTGGGAGGCATTGGT
gi|9217|e 20 L D T S K E L V K R D L K N L V I L D R
gi|9217|e 60 CTGGACACCAGCAAGGAGCTGGTCAAGCGGGACCTGAAGAACCTGGTGATCCTCGACCGC
gi|9217|e 40 I E N P A A I A E L K A I N P K V T V T
gi|9217|e 120 ATTGAGAACCCGGCTGCCATCGCCGAGCTGAAGGCAATCAATCCAAAGGTGACCGTCACC
gi|9217|e 60 F Y P Y D V T V P I A E T T K L L K T I
gi|9217|e 180 TTCTACCCCTATGATGTGACCGTGCCCATTGCCGAGACCACCAAGCTGCTGAAGACCATC
gi|9217|e 80 F A Q L K T I D V L I N G A G I L D D H
gi|9217|e 240 TTCGCCCAGCTGAAGACCATCGATGTCCTGATCAACGGAGCTGGCATCCTGGACGATCAC
gi|9217|e 100 Q I E R T I A V N Y T G L V N T T T A I
gi|9217|e 300 CAGATCGAGCGCACCATCGCCGTCAACTACACCGGCCTGGTGAACACCACGACTGCCATC
gi|9217|e 120 L D F W D K R K G G P G G I I C N I G S
gi|9217|e 360 CTGGACTTCTGGGACAAGCGCAAGGGTGGACCCGGTGGTATCATCTGCAACATTGGATCC
gi|9217|e 140 V T G F N A I Y Q V P V Y S G T K A A V
gi|9217|e 420 GTGACTGGATTCAACGCCATCTACCAGGTGCCCGTTTACTCCGGCACCAAGGCTGCCGTG
gi|9217|e 160 V N F T S S L A K L A P I T G V T A Y T
gi|9217|e 480 GTCAACTTCACCAGCTCCCTGGCGAAACTGGCCCCCATCACCGGCGTGACCGCTTACACC
gi|9217|e 180 V N P G I T R T T L V H K F N S W L D V
gi|9217|e 540 GTGAACCCCGGCATCACCCGCACCACCCTGGTGCACAAGTTCAACTCCTGGCTGGATGTT
gi|9217|e 200 E P Q V A E K L L A H P T Q P S L A C A
gi|9217|e 600 GAGCCCCAGGTGGCCGAGAAGCTCCTGGCTCACCCCACCCAGCCCTCGTTGGCCTGCGCC
gi|9217|e 220 Q N F V K A I E L N Q N G A I W K L D L
gi|9217|e 660 CAGAACTTTGTGAAGGCCATCGAGCTGAACCAGAACGGTGCCATCTGGAAACTGGACTTG
gi|9217|e 240 G T L E A I Q W S K H W D S G I 256
gi|9217|e 720 GGCACCCTGGAGGCCATCCAGTGGTCCAAGCACTGGGACTCCGGCATC 768
""",
)
protein_record = protein_alignment.sequences[1]
nucleotide_record = nucleotide_records[protein_record.id]
self.assertEqual(nucleotide_record.id, protein_record.id)
alignments = aligner.align(protein_record, nucleotide_record)
self.assertEqual(len(alignments), 1)
alignment = next(alignments)
codon_alignments.append(alignment)
self.assertTrue(
np.array_equal(alignment.coordinates, np.array([[0, 256], [0, 768]]))
)
self.assertEqual(
str(alignment),
"""\
gi|9219|e 0 M A F T L T N K N V V F V A G L G G I G
gi|9219|e 0 ATGGCGTTTACCTTGACCAACAAGAACGTGGTTTTCGTGGCCGGTCTGGGAGGCATTGGT
gi|9219|e 20 L D T S K E L V K R D L K N L V I L D R
gi|9219|e 60 CTGGACACCAGCAAGGAGCTGGTCAAGCGGGACCTGAAGAACCTGGTGATCCTCGACCGC
gi|9219|e 40 I E N P A A I A E L K A I N P K V T V T
gi|9219|e 120 ATTGAGAACCCGGCTGCCATCGCCGAGCTGAAGGCAATCAATCCAAAGGTGACCGTCACC
gi|9219|e 60 F Y P Y D V T V P I A E T T K L L K T I
gi|9219|e 180 TTCTACCCCTATGATGTGACCGTGCCCATTGCCGAGACCACCAAGCTGCTGAAGACCATC
gi|9219|e 80 F A Q L K T I D V L I N G A G I L D D H
gi|9219|e 240 TTCGCCCAGCTGAAGACCATCGATGTCCTGATCAACGGAGCTGGCATCCTGGACGATCAC
gi|9219|e 100 Q I E R T I A V N Y T G L V N T T T A I
gi|9219|e 300 CAGATCGAGCGCACCATCGCCGTCAACTACACCGGCCTGGTGAACACCACGACTGCCATC
gi|9219|e 120 L D F W D K R K G G P G G I I C N I G S
gi|9219|e 360 CTGGACTTCTGGGACAAGCGCAAGGGTGGACCCGGTGGTATCATCTGCAACATTGGATCC
gi|9219|e 140 V T G F N A I Y Q V P V Y S G T K A A V
gi|9219|e 420 GTGACTGGATTCAACGCCATCTACCAGGTGCCCGTTTACTCCGGCACCAAGGCTGCCGTG
gi|9219|e 160 V N F T S S L A K L A P I T G V T A Y T
gi|9219|e 480 GTCAACTTCACCAGCTCCCTGGCGAAACTGGCCCCCATCACCGGCGTGACCGCTTACACC
gi|9219|e 180 V N P G I T R T T L V H K F N S W L D V
gi|9219|e 540 GTGAACCCCGGCATCACCCGCACCACCCTGGTGCACAAGTTCAACTCCTGGCTGGATGTT
gi|9219|e 200 E P Q V A E K L L A H P T Q P S L A C A
gi|9219|e 600 GAGCCCCAGGTGGCCGAGAAGCTCCTGGCTCACCCCACCCAGCCCTCGTTGGCCTGCGCC
gi|9219|e 220 Q N F V K A I E L N Q N G A I W K L D L
gi|9219|e 660 CAGAACTTTGTGAAGGCCATCGAGCTGAACCAGAACGGTGCCATCTGGAAACTGGACTTG
gi|9219|e 240 G T L E A I Q W S K H W D S G I 256
gi|9219|e 720 GGCACCCTGGAGGCCATCCAGTGGTCCAAGCACTGGGACTCCGGCATC 768
""",
)
protein_record = protein_alignment.sequences[2]
nucleotide_record = nucleotide_records[protein_record.id]
self.assertEqual(nucleotide_record.id, protein_record.id)
alignments = aligner.align(protein_record, nucleotide_record)
self.assertEqual(len(alignments), 1)
alignment = next(alignments)
codon_alignments.append(alignment)
self.assertTrue(
np.array_equal(alignment.coordinates, np.array([[0, 256], [0, 768]]))
)
self.assertEqual(
str(alignment),
"""\
gi|9221|e 0 M A F T L T N K N V V F V A G L G G I G
gi|9221|e 0 ATGGCGTTTACCTTGACCAACAAGAACGTGGTTTTCGTGGCCGGTCTGGGAGGCATTGGT
gi|9221|e 20 L D T S K E L V K R D L K N L V I L D R
gi|9221|e 60 CTGGACACCAGCAAGGAGCTGGTCAAGCGCGACCTGAAGAACCTGGTGATCCTCGACCGC
gi|9221|e 40 I E N P A A I A E L K A I N P K V T V T
gi|9221|e 120 ATTGAGAACCCGGCTGCCATCGCCGAGCTGAAGGCAATCAATCCAAAGGTGACCGTCACC
gi|9221|e 60 F Y P Y D V T V P I A E T T K L L K T I
gi|9221|e 180 TTCTACCCCTATGATGTGACCGTGCCCATTGCCGAGACCACCAAGCTGCTGAAGACCATC
gi|9221|e 80 F A Q L K T I D V L I N G A G I L D D H
gi|9221|e 240 TTCGCCCAGCTGAAGACCATCGATGTCCTGATCAACGGAGCTGGCATCCTGGACGATCAC
gi|9221|e 100 Q I E R T I A V N Y T G L V N T T T A I
gi|9221|e 300 CAGATCGAGCGCACCATCGCCGTCAACTACACCGGCCTGGTGAACACAACGACGGCCATC
gi|9221|e 120 L D F W D K R K G G P G G I I C N I G S
gi|9221|e 360 CTGGACTTCTGGGACAAGCGCAAGGGTGGACCCGGTGGTATAATCTGCAACATTGGATCC
gi|9221|e 140 V T G F N A I Y Q V P V Y S G T K A A V
gi|9221|e 420 GTGACTGGATTCAACGCCATCTACCAGGTGCCCGTTTACTCCGGCACCAAGGCTGCCGTG
gi|9221|e 160 V N F T S S L A K L A P I T G V T A Y T
gi|9221|e 480 GTCAACTTCACCAGCTCCCTGGCGAAACTGGCCCCCATCACCGGCGTGACCGCTTACACC
gi|9221|e 180 V N P G I T R T T L V H K F N S W L D V
gi|9221|e 540 GTGAACCCCGGCATCACCCGCACCACCCTGGTGCACAAGTTCAACTCCTGGCTGGATGTT
gi|9221|e 200 E P Q V A E K L L A H P T Q P S L A C A
gi|9221|e 600 GAGCCCCAGGTGGCCGAGAAGCTCCTGGCTCACCCCACCCAGCCCTCGTTGGCCTGCGCC
gi|9221|e 220 Q N F V K A I E L N Q N G A I W K L D L
gi|9221|e 660 CAGAACTTTGTCAAGGCCATCGAGCTGAACCAGAACGGTGCCATCTGGAAACTGGACTTG
gi|9221|e 240 G T L E A I Q W S K H W D S G I 256
gi|9221|e 720 GGTACCCTGGAGGCCATCCAGTGGTCCAAGCACTGGGACTCCGGCATC 768
""",
)
protein_record = protein_alignment.sequences[3]
nucleotide_record = nucleotide_records[protein_record.id]
self.assertEqual(nucleotide_record.id, protein_record.id)
alignments = aligner.align(protein_record, nucleotide_record)
self.assertEqual(len(alignments), 1)
alignment = next(alignments)
codon_alignments.append(alignment)
self.assertTrue(
np.array_equal(alignment.coordinates, np.array([[0, 256], [0, 768]]))
)
self.assertEqual(
str(alignment),
"""\
gi|9223|e 0 M A F T L T N K N V V F V A G L G G I G
gi|9223|e 0 ATGGCGTTTACCTTGACCAACAAGAACGTGGTTTTCGTGGCCGGTCTGGGAGGCATTGGT
gi|9223|e 20 L D T S K E L V K R D L K N L V I L D R
gi|9223|e 60 CTGGACACCAGCAAGGAGCTGGTCAAGCGGGACCTGAAGAACCTGGTGATCCTCGACCGC
gi|9223|e 40 I E N P A A I A E L K A I N P K V T V T
gi|9223|e 120 ATTGAGAACCCGGCTGCCATCGCCGAGCTGAAGGCAATCAATCCAAAGGTGACCGTCACC
gi|9223|e 60 F Y P Y D V T V P I A E T T K L L K T I
gi|9223|e 180 TTCTACCCCTATGATGTGACCGTGCCCATTGCCGAGACCACCAAGCTGCTGAAGACCATC
gi|9223|e 80 F A Q L K T I D V L I N G A G I L D D H
gi|9223|e 240 TTCGCCCAGCTGAAGACCATCGATGTCCTGATCAACGGAGCTGGCATCCTGGACGATCAC
gi|9223|e 100 Q I E R T I A V N Y T G L V N T T T A I
gi|9223|e 300 CAGATCGAGCGCACCATCGCCGTCAACTACACCGGCCTGGTGAACACCACGACTGCCATC
gi|9223|e 120 L D F W D K R K G G P G G I I C N I G S
gi|9223|e 360 CTGGACTTCTGGGACAAGCGCAAGGGTGGACCCGGTGGTATCATCTGCAACATTGGATCC
gi|9223|e 140 V T G F N A I Y Q V P V Y S G T K A A V
gi|9223|e 420 GTGACTGGATTCAACGCCATCTACCAGGTGCCCGTTTACTCCGGCACCAAGGCTGCCGTG
gi|9223|e 160 V N F T S S L A K L A P I T G V T A Y T
gi|9223|e 480 GTCAACTTCACCAGCTCCCTGGCGAAACTGGCCCCCATCACCGGCGTGACCGCTTACACC
gi|9223|e 180 V N P G I T R T T L V H K F N S W L D V
gi|9223|e 540 GTGAACCCCGGCATCACCCGCACCACCCTGGTGCACAAGTTCAACTCCTGGCTGGATGTT
gi|9223|e 200 E P Q V A E K L L A H P T Q P S L A C A
gi|9223|e 600 GAGCCCCAGGTGGCCGAGAAGCTCCTGGCTCACCCCACCCAGCCCTCGTTGGCCTGCGCC
gi|9223|e 220 Q N F V K A I E L N Q N G A I W K L D L
gi|9223|e 660 CAGAACTTTGTGAAGGCCATCGAGCTGAACCAGAACGGTGCCATCTGGAAACTGGACTTG
gi|9223|e 240 G T L E A I Q W S K H W D S G I 256
gi|9223|e 720 GGCACCCTGGAGGCCATCCAGTGGTCCAAGCACTGGGACTCCGGCATC 768
""",
)
protein_record = protein_alignment.sequences[4]
nucleotide_record = nucleotide_records[protein_record.id]
self.assertEqual(nucleotide_record.id, protein_record.id)
alignments = aligner.align(protein_record, nucleotide_record)
self.assertEqual(len(alignments), 1)
alignment = next(alignments)
codon_alignments.append(alignment)
self.assertTrue(
np.array_equal(alignment.coordinates, np.array([[0, 256], [0, 768]]))
)
self.assertEqual(
str(alignment),
"""\
gi|9225|e 0 M A F T L T N K N V V F V A G L G G I G
gi|9225|e 0 ATGGCGTTTACCTTGACCAACAAGAACGTGGTTTTCGTGGCCGGTCTGGGAGGCATTGGT
gi|9225|e 20 L D T S K E L V K R D L K N L V I L D R
gi|9225|e 60 CTGGACACCAGCAAGGAGCTGGTCAAGCGGGACCTGAAGAACCTGGTGATCCTCGACCGC
gi|9225|e 40 I E N P A A I A E L K A I N P K V T V T
gi|9225|e 120 ATTGAGAACCCGGCTGCCATCGCCGAGCTGAAGGCAATCAATCCAAAGGTGACCGTAACC
gi|9225|e 60 F Y P Y D V T V P I A E T T K L L K T I
gi|9225|e 180 TTCTACCCCTATGATGTGACAGTGCCCATTGCCGAGACCACCAAGCTGCTGAAGACCATC
gi|9225|e 80 F A Q L K T I D V L I N G A G I L D D H
gi|9225|e 240 TTCGCCCAGCTGAAGACCATCGATGTCCTGATCAACGGAGCTGGCATCTTGGACGATCAC
gi|9225|e 100 Q I E R T I A V N Y T G L V N T T T A I
gi|9225|e 300 CAGATCGAGCGCACCATCGCCGTCAACTACACCGGCCTGGTGAACACCACGACGGCCATC
gi|9225|e 120 L D F W D K R K G G P G G I I C N I G S
gi|9225|e 360 CTGGACTTCTGGGACAAGCGCAAGGGTGGACCCGGTGGTATCATCTGCAACATTGGATCC
gi|9225|e 140 V T G F N A I Y Q V P V Y S G T K A A V
gi|9225|e 420 GTGACTGGATTCAACGCCATCTACCAGGTGCCCGTTTACTCCGGCACCAAGGCTGCCGTG
gi|9225|e 160 V N F T S S L A K L A P I T G V T A Y T
gi|9225|e 480 GTCAACTTCACCAGCTCCCTGGCGAAACTGGCCCCCATCACCGGCGTGACCGCTTACACC
gi|9225|e 180 V N P G I T R T T L V H K F N S W L D V
gi|9225|e 540 GTGAACCCCGGCATCACCCGCACCACCCTGGTGCACAAGTTCAACTCCTGGCTGGATGTT
gi|9225|e 200 E P Q V A E K L L A H P T Q P S L A C A
gi|9225|e 600 GAGCCCCAGGTGGCTGAGAAGCTCCTGGCTCACCCAACCCAGCCCTCGTTGGCCTGCGCC
gi|9225|e 220 Q N F V K A I E L N Q N G A I W K L D L
gi|9225|e 660 CAGAACTTTGTCAAGGCCATCGAGCTGAACCAGAACGGTGCCATCTGGAAACTGGACTTG
gi|9225|e 240 G T L E A I Q W S K H W D S G I 256
gi|9225|e 720 GGTACCCTGGAGGCCATCCAGTGGTCCAAGCACTGGGACTCCGGCATC 768
""",
)
protein_record = protein_alignment.sequences[5]
nucleotide_record = nucleotide_records[protein_record.id]
self.assertEqual(nucleotide_record.id, protein_record.id)
alignments = aligner.align(protein_record, nucleotide_record)
self.assertEqual(len(alignments), 1)
alignment = next(alignments)
codon_alignments.append(alignment)
self.assertTrue(
np.array_equal(alignment.coordinates, np.array([[0, 256], [0, 768]]))
)
self.assertEqual(
str(alignment),
"""\
gi|9227|e 0 M A F T L T N K N V V F V A G L G G I G
gi|9227|e 0 ATGGCGTTTACCTTGACCAACAAGAACGTGGTTTTCGTGGCCGGTCTGGGAGGCATTGGT
gi|9227|e 20 L D T S K E L V K R D L K N L V I L D R
gi|9227|e 60 CTGGACACCAGCAAGGAGCTGGTCAAGCGAGACCTGAAGAACCTGGTGATCCTCGACCGC
gi|9227|e 40 I E N P A A I A E L K A I N P K V T V T
gi|9227|e 120 ATTGAGAACCCGGCTGCCATCGCCGAGCTGAAGGCAATCAATCCAAAGGTGACCGTCACC
gi|9227|e 60 F Y P Y D V T V P I A E T T K L L K T I
gi|9227|e 180 TTCTACCCCTATGATGTGACCGTGCCCATTGCCGAGACCACCAAGCTGCTGAAGACCATC
gi|9227|e 80 F A Q L K T I D V L I N G A G I L D D H
gi|9227|e 240 TTCGCCCAGCTGAAGACCATCGATGTCCTGATCAACGGAGCTGGCATCCTGGACGATCAC
gi|9227|e 100 Q I E R T I A V N Y T G L V N T T T A I
gi|9227|e 300 CAGATCGAGCGCACCATCGCCGTCAACTACACCGGCCTGGTGAACACCACGACGGCCATC
gi|9227|e 120 L D F W D K R K G G P G G I I C N I G S
gi|9227|e 360 CTGGACTTCTGGGACAAGCGCAAGGGTGGACCCGGTGGTATCATCTGCAACATTGGATCC
gi|9227|e 140 V T G F N A I Y Q V P V Y S G T K A A V
gi|9227|e 420 GTGACTGGATTCAACGCCATCTACCAGGTGCCCGTTTACTCCGGCACCAAGGCTGCCGTG
gi|9227|e 160 V N F T S S L A K L A P I T G V T A Y T
gi|9227|e 480 GTCAACTTCACCAGCTCCCTGGCGAAACTGGCCCCCATTACCGGCGTGACCGCTTACACC
gi|9227|e 180 V N P G I T R T T L V H K F N S W L D V
gi|9227|e 540 GTGAACCCCGGCATCACCCGCACCACCCTGGTGCACAAGTTCAACTCCTGGCTGGATGTT
gi|9227|e 200 E P Q V A E K L L A H P T Q P S L A C A
gi|9227|e 600 GAGCCCCAGGTGGCCGAGAAGCTCCTGGCTCACCCCACCCAGCCCTCGTTGGCCTGCGCC
gi|9227|e 220 Q N F V K A I E L N Q N G A I W K L D L
gi|9227|e 660 CAGAACTTTGTGAAGGCCATCGAGCTGAACCAGAACGGTGCCATCTGGAAACTGGACTTG
gi|9227|e 240 G T L E A I Q W S K H W D S G I 256
gi|9227|e 720 GGCACCCTGGAGGCCATCCAGTGGTCCAAGCACTGGGACTCCGGCATC 768
""",
)
protein_record = protein_alignment.sequences[6]
nucleotide_record = nucleotide_records[protein_record.id]
self.assertEqual(nucleotide_record.id, protein_record.id)
alignments = aligner.align(protein_record, nucleotide_record)
self.assertEqual(len(alignments), 1)
alignment = next(alignments)
codon_alignments.append(alignment)
self.assertTrue(
np.array_equal(alignment.coordinates, np.array([[0, 256], [0, 768]]))
)
self.assertEqual(
str(alignment),
"""\
gi|9229|e 0 M A F T L T N K N V V F V A G L G G I G
gi|9229|e 0 ATGGCGTTTACCTTGACCAACAAGAACGTGGTTTTCGTGGCCGGTCTGGGAGGCATTGGT
gi|9229|e 20 L D T S K E L V K R D L K N L V I L D R
gi|9229|e 60 CTGGACACCAGCAAGGAGCTGGTCAAGCGGGACCTGAAGAACCTGGTGATCCTCGACCGC
gi|9229|e 40 I E N P A A I A E L K A I N P K V T V T
gi|9229|e 120 ATTGAGAACCCGGCTGCCATCGCCGAGCTGAAGGCAATCAATCCAAAGGTGACCGTCACC
gi|9229|e 60 F Y P Y D V T V P I A E T T K L L K T I
gi|9229|e 180 TTCTACCCCTATGATGTGACCGTGCCCATTGCCGAGACCACCAAGCTGCTGAAGACCATC
gi|9229|e 80 F A Q L K T I D V L I N G A G I L D D H
gi|9229|e 240 TTCGCCCAGCTGAAGACCATCGATGTCCTGATCAACGGAGCTGGCATCCTGGACGATCAC
gi|9229|e 100 Q I E R T I A V N Y T G L V N T T T A I
gi|9229|e 300 CAGATCGAGCGCACCATCGCCGTCAACTACACCGGCCTGGTGAACACCACGACTGCCATC
gi|9229|e 120 L D F W D K R K G G P G G I I C N I G S
gi|9229|e 360 CTGGACTTCTGGGACAAGCGCAAGGGTGGACCCGGTGGTATCATCTGCAACATTGGATCC
gi|9229|e 140 V T G F N A I Y Q V P V Y S G T K A A V
gi|9229|e 420 GTGACTGGATTCAACGCCATCTACCAGGTGCCCGTTTACTCCGGCACCAAGGCTGCCGTG
gi|9229|e 160 V N F T S S L A K L A P I T G V T A Y T
gi|9229|e 480 GTCAACTTCACCAGCTCCCTGGCGAAACTGGCCCCCATCACCGGCGTGACCGCTTACACC
gi|9229|e 180 V N P G I T R T T L V H K F N S W L D V
gi|9229|e 540 GTGAACCCCGGCATCACCCGCACCACCCTGGTGCACAAGTTCAACTCCTGGCTGGATGTT
gi|9229|e 200 E P Q V A E K L L A H P T Q P S L A C A
gi|9229|e 600 GAGCCCCAGGTGGCCGAGAAGCTCCTGGCTCACCCCACCCAGCCCTCGTTGGCCTGCGCC
gi|9229|e 220 Q N F V K A I E L N Q N G A I W K L D L
gi|9229|e 660 CAGAACTTTGTGAAGGCCATCGAGCTGAACCAGAACGGTGCCATCTGGAAACTGGACTTG
gi|9229|e 240 G T L E A I Q W S K H W D S G I 256
gi|9229|e 720 GGCACCCTGGAGGCCATCCAGTGGTCCAAGCACTGGGACTCCGGCATC 768
""",
)
protein_record = protein_alignment.sequences[7]
nucleotide_record = nucleotide_records[protein_record.id]
self.assertEqual(nucleotide_record.id, protein_record.id)
alignments = aligner.align(protein_record, nucleotide_record)
self.assertEqual(len(alignments), 1)
alignment = next(alignments)
codon_alignments.append(alignment)
self.assertTrue(
np.array_equal(alignment.coordinates, np.array([[0, 256], [0, 768]]))
)
self.assertEqual(
str(alignment),
"""\
gi|9231|e 0 M A F T L T N K N V V F V A G L G G I G
gi|9231|e 0 ATGGCGTTTACCTTGACCAACAAGAACGTGGTTTTCGTGGCCGGTCTGGGAGGCATTGGT
gi|9231|e 20 L D T S K E L V K R D L K N L V I L D R
gi|9231|e 60 CTGGACACCAGCAAGGAGCTGGTCAAGCGCGACCTGAAGAACCTGGTGATCCTCGACCGC
gi|9231|e 40 I E N P A A I A E L K A I N P K V T V T
gi|9231|e 120 ATTGAGAACCCGGCTGCCATCGCCGAGCTGAAGGCAATCAATCCAAAGGTGACCGTCACC
gi|9231|e 60 F Y P Y D V T V P I A E T T K L L K T I
gi|9231|e 180 TTCTACCCCTATGATGTGACCGTGCCCATTGCCGAGACCACCAAGCTGCTGAAGACCATC
gi|9231|e 80 F A Q L K T I D V L I N G A G I L D D H
gi|9231|e 240 TTCGCCCAGCTGAAGACCATCGATGTCCTGATCAACGGAGCTGGCATCCTGGACGATCAC
gi|9231|e 100 Q I E R T I A V N Y T G L V N T T T A I
gi|9231|e 300 CAGATCGAGCGCACCATCGCCGTCAACTACACCGGCCTGGTGAACACCACGACTGCCATC
gi|9231|e 120 L D F W D K R K G G P G G I I C N I G S
gi|9231|e 360 CTGGACTTCTGGGACAAGCGCAAGGGTGGACCCGGTGGTATCATCTGCAACATTGGATCC
gi|9231|e 140 V T G F N A I Y Q V P V Y S G T K A A V
gi|9231|e 420 GTGACTGGATTCAACGCCATCTACCAGGTGCCCGTTTACTCCGGCACCAAGGCTGCCGTG
gi|9231|e 160 V N F T S S L A K L A P I T G V T A Y T
gi|9231|e 480 GTCAACTTCACCAGCTCCCTGGCGAAACTGGCCCCCATCACCGGCGTGACCGCTTACACC
gi|9231|e 180 V N P G I T R T T L V H K F N S W L D V
gi|9231|e 540 GTGAACCCCGGCATCACCCGCACCACCCTGGTGCACAAGTTCAACTCCTGGCTGGATGTT
gi|9231|e 200 E P Q V A E K L L A H P T Q P S L A C A
gi|9231|e 600 GAGCCCCAGGTGGCCGAGAAGCTCCTGGCTCACCCCACCCAGCCCTCGTTGGCCTGCGCC
gi|9231|e 220 Q N F V K A I E L N Q N G A I W K L D L
gi|9231|e 660 CAGAACTTTGTGAAGGCCATCGAGCTGAACCAGAACGGTGCTATCTGGAAACTGGACTTG
gi|9231|e 240 G T L E A I Q W S K H W D S G I 256
gi|9231|e 720 GGCACCCTGGAGGCCATCCAGTGGTCCAAGCACTGGGACTCCGGCATC 768
""",
)
protein_record = protein_alignment.sequences[8]
nucleotide_record = nucleotide_records[protein_record.id]
self.assertEqual(nucleotide_record.id, protein_record.id)
alignments = aligner.align(protein_record, nucleotide_record)
self.assertEqual(len(alignments), 1)
alignment = next(alignments)
codon_alignments.append(alignment)
self.assertTrue(
np.array_equal(alignment.coordinates, np.array([[0, 256], [0, 768]]))
)
self.assertEqual(
str(alignment),
"""\
gi|9233|e 0 M A F T L T N K N V V F V A G L G G I G
gi|9233|e 0 ATGGCGTTTACCTTGACCAACAAGAACGTGGTTTTCGTGGCCGGTCTGGGAGGCATTGGT
gi|9233|e 20 L D T S K E L V K R D L K N L V I L D R
gi|9233|e 60 CTGGACACCAGCAAGGAGCTGGTCAAGCGGGACCTGAAGAACCTGGTGATCCTCGACCGC
gi|9233|e 40 I E N P A A I A E L K A I N P K V T V T
gi|9233|e 120 ATTGAGAACCCGGCTGCCATCGCCGAGCTGAAGGCAATCAATCCAAAGGTGACCGTCACC
gi|9233|e 60 F Y P Y D V T V P I A E T T K L L K T I
gi|9233|e 180 TTCTACCCATACGATGTGACCGTGCCCATTGCCGAGACCACCAAGCTGCTGAAGACCATC
gi|9233|e 80 F A Q L K T I D V L I N G A G I L D D H
gi|9233|e 240 TTCGCCCAGCTGAAGACCATCGATGTCCTGATCAACGGAGCTGGCATCCTGGACGATCAC
gi|9233|e 100 Q I E R T I A V N Y T G L V N T T T A I
gi|9233|e 300 CAGATCGAGCGCACCATCGCCGTCAACTACACCGGCCTGGTGAACACCACGACGGCCATC
gi|9233|e 120 L D F W D K R K G G P G G I I C N I G S
gi|9233|e 360 CTGGACTTCTGGGACAAGCGCAAGGGTGGACCCGGTGGTATCATCTGCAACATTGGATCC
gi|9233|e 140 V T G F N A I Y Q V P V Y S G T K A A V
gi|9233|e 420 GTGACTGGATTCAACGCCATCTACCAGGTGCCCGTTTACTCCGGCACCAAGGCTGCCGTG
gi|9233|e 160 V N F T S S L A K L A P I T G V T A Y T
gi|9233|e 480 GTCAACTTCACCAGCTCCCTGGCGAAACTGGCCCCCATCACCGGCGTGACCGCTTACACC
gi|9233|e 180 V N P G I T R T T L V H K F N S W L D V
gi|9233|e 540 GTGAACCCCGGCATCACCCGCACCACCCTGGTGCACAAGTTCAACTCCTGGCTGGATGTT
gi|9233|e 200 E P Q V A E K L L A H P T Q P S L A C A
gi|9233|e 600 GAGCCCCAGGTGGCCGAGAAGCTCCTGGCTCACCCCACCCAGCCCTCGTTGGCCTGCGCC
gi|9233|e 220 Q N F V K A I E L N Q N G A I W K L D L
gi|9233|e 660 CAGAACTTTGTGAAGGCCATCGAGCTGAACCAGAACGGTGCCATCTGGAAACTGGACTTG
gi|9233|e 240 G T L E A I Q W S K H W D S G I 256
gi|9233|e 720 GGCACCCTGGAGGCCATCCAGTGGTCCAAGCACTGGGACTCCGGCATC 768
""",
)
protein_record = protein_alignment.sequences[9]
nucleotide_record = nucleotide_records[protein_record.id]
self.assertEqual(nucleotide_record.id, protein_record.id)
alignments = aligner.align(protein_record, nucleotide_record)
self.assertEqual(len(alignments), 1)
alignment = next(alignments)
codon_alignments.append(alignment)
self.assertTrue(
np.array_equal(alignment.coordinates, np.array([[0, 256], [0, 768]]))
)
self.assertEqual(
str(alignment),
"""\
gi|9235|e 0 M A F T L T N K N V V F V A G L G G I G
gi|9235|e 0 ATGGCGTTTACCTTGACCAACAAGAACGTGGTTTTCGTGGCCGGTCTGGGAGGCATTGGT
gi|9235|e 20 L D T S K E L V K R D L K N L V I L D R
gi|9235|e 60 CTGGACACCAGCAAGGAGCTGGTCAAGCGGGACCTGAAGAACCTGGTGATCCTCGACCGC
gi|9235|e 40 I E N P A A I A E L K A I N P K V T V T
gi|9235|e 120 ATTGAGAACCCGGCTGCCATCGCCGAGCTGAAGGCAATCAATCCAAAGGTGACCGTCACC
gi|9235|e 60 F Y P Y D V T V P I A E T T K L L K T I
gi|9235|e 180 TTCTACCCCTATGATGTGACCGTGCCCATTGCCGAGACCACCAAGCTGCTGAAGACCATC
gi|9235|e 80 F A Q L K T I D V L I N G A G I L D D H
gi|9235|e 240 TTCGCCCAGCTGAAGACCATCGATGTCCTGATCAACGGAGCTGGCATCCTGGACGATCAC
gi|9235|e 100 Q I E R T I A V N Y T G L V N T T T A I
gi|9235|e 300 CAGATCGAGCGCACCATCGCCGTCAACTACACCGGCCTGGTGAACACCACGACTGCCATC
gi|9235|e 120 L D F W D K R K G G P G G I I C N I G S
gi|9235|e 360 CTGGACTTCTGGGACAAGCGCAAGGGTGGACCCGGTGGTATCATCTGCAACATTGGATCC
gi|9235|e 140 V T G F N A I Y Q V P V Y S G T K A A V
gi|9235|e 420 GTGACTGGATTCAACGCCATCTACCAGGTGCCCGTTTACTCCGGCACCAAGGCTGCCGTG
gi|9235|e 160 V N F T S S L A K L A P I T G V T A Y T
gi|9235|e 480 GTCAACTTCACCAGCTCCCTGGCGAAACTGGCCCCCATCACCGGCGTGACCGCTTACACC
gi|9235|e 180 V N P G I T R T T L V H K F N S W L D V
gi|9235|e 540 GTGAACCCCGGCATCACCCGCACCACCCTGGTGCACAAGTTCAACTCCTGGCTGGATGTT
gi|9235|e 200 E P Q V A E K L L A H P T Q P S L A C A
gi|9235|e 600 GAGCCCCAGGTGGCCGAGAAGCTCCTGGCTCACCCCACCCAGCCCTCGTTGGCCTGCGCC
gi|9235|e 220 Q N F V K A I E L N Q N G A I W K L D L
gi|9235|e 660 CAGAACTTTGTGAAGGCCATCGAGCTGAACCAGAACGGTGCCATCTGGAAACTGGACTTG
gi|9235|e 240 G T L E A I Q W S K H W D S G I 256
gi|9235|e 720 GGCACCCTGGAGGCCATCCAGTGGTCCAAGCATTGGGACTCCGGCATC 768
""",
)
protein_record = protein_alignment.sequences[10]
nucleotide_record = nucleotide_records[protein_record.id]
self.assertEqual(nucleotide_record.id, protein_record.id)
alignments = aligner.align(protein_record, nucleotide_record)
self.assertEqual(len(alignments), 1)
alignment = next(alignments)
codon_alignments.append(alignment)
self.assertTrue(
np.array_equal(alignment.coordinates, np.array([[0, 256], [0, 768]]))
)
self.assertEqual(
str(alignment),
"""\
gi|9237|e 0 M A F T L T N K N V V F V A G L G G I G
gi|9237|e 0 ATGGCGTTTACCTTGACCAACAAGAACGTGGTTTTCGTGGCCGGTCTGGGAGGCATTGGT
gi|9237|e 20 L D T S K E L V K R D L K N L V I L D R
gi|9237|e 60 CTGGACACCAGCAAGGAGCTGGTCAAGCGGGACCTGAAGAACCTGGTGATCCTCGACCGC
gi|9237|e 40 I E N P A A I A E L K A I N P K V T V T
gi|9237|e 120 ATTGAGAACCCGGCTGCCATCGCCGAGCTGAAGGCAATCAATCCAAAGGTGACCGTCACC
gi|9237|e 60 F Y P Y D V T V P I A E T T K L L K T I
gi|9237|e 180 TTCTACCCCTACGATGTGACCGTGCCCATTGCCGAGACCACCAAGCTGCTGAAGACCATC
gi|9237|e 80 F A Q L K T I D V L I N G A G I L D D H
gi|9237|e 240 TTCGCCCAGCTGAAGACCATCGATGTCCTGATCAACGGAGCTGGCATCCTGGACGATCAC
gi|9237|e 100 Q I E R T I A V N Y T G L V N T T T A I
gi|9237|e 300 CAGATCGAGCGCACCATCGCCGTCAACTACACCGGACTGGTGAACACCACGACGGCCATC
gi|9237|e 120 L D F W D K R K G G P G G I I C N I G S
gi|9237|e 360 CTGGACTTCTGGGACAAGCGCAAGGGTGGACCCGGTGGTATCATCTGCAACATTGGATCC
gi|9237|e 140 V T G F N A I Y Q V P V Y S G T K A A V
gi|9237|e 420 GTGACTGGATTCAACGCCATCTACCAGGTGCCCGTTTACTCCGGCACCAAGGCTGCCGTG
gi|9237|e 160 V N F T S S L A K L A P I T G V T A Y T
gi|9237|e 480 GTCAACTTCACCAGCTCCCTGGCGAAACTGGCCCCCATCACCGGCGTGACCGCTTACACC
gi|9237|e 180 V N P G I T R T T L V H K F N S W L D V
gi|9237|e 540 GTGAACCCCGGCATCACCCGCACCACCCTGGTGCACAAGTTCAACTCCTGGCTGGATGTT
gi|9237|e 200 E P Q V A E K L L A H P T Q P S L A C A
gi|9237|e 600 GAGCCCCAGGTGGCCGAGAAGCTCCTGGCTCACCCCACCCAGCCCTCGTTGGCCTGCGCC
gi|9237|e 220 Q N F V K A I E L N Q N G A I W K L D L
gi|9237|e 660 CAGAACTTTGTGAAGGCCATCGAGCTGAACCAGAACGGTGCCATCTGGAAACTGGACTTG
gi|9237|e 240 G T L E A I Q W S K H W D S G I 256
gi|9237|e 720 GGCACCCTGGAGGCCATCCAGTGGTCCAAGCACTGGGACTCCGGCATC 768
""",
)
protein_record = protein_alignment.sequences[11]
nucleotide_record = nucleotide_records[protein_record.id]
self.assertEqual(nucleotide_record.id, protein_record.id)
alignments = aligner.align(protein_record, nucleotide_record)
self.assertEqual(len(alignments), 1)
alignment = next(alignments)
codon_alignments.append(alignment)
self.assertTrue(
np.array_equal(alignment.coordinates, np.array([[0, 256], [0, 768]]))
)
self.assertEqual(
str(alignment),
"""\
gi|9239|e 0 M A F T L T N K N V V F V A G L G G I G
gi|9239|e 0 ATGGCGTTTACCTTGACCAACAAGAACGTGGTTTTCGTGGCCGGTCTGGGAGGCATTGGT
gi|9239|e 20 L D T S K E L V K R D L K N L V I L D R
gi|9239|e 60 CTGGACACCAGCAAGGAGCTGGTCAAGCGGGACCTGAAGAACCTGGTGATCCTCGACCGC
gi|9239|e 40 I E N P A A I A E L K A I N P K V T V T
gi|9239|e 120 ATTGAGAACCCGGCTGCCATCGCCGAGCTGAAGGCAATCAATCCAAAGGTGACCGTCACC
gi|9239|e 60 F Y P Y D V T V P I A E T T K L L K T I
gi|9239|e 180 TTCTACCCCTACGATGTGACCGTGCCCATTGCCGAGACCACCAAGCTGCTGAAGACCATC
gi|9239|e 80 F A Q L K T I D V L I N G A G I L D D H
gi|9239|e 240 TTCGCCCAGCTGAAGACCATCGATGTCCTGATCAACGGAGCTGGCATCCTGGACGATCAC
gi|9239|e 100 Q I E R T I A V N Y T G L V N T T T A I
gi|9239|e 300 CAGATCGAGCGCACCATCGCCGTCAACTACACCGGCCTGGTGAACACCACGACGGCCATC
gi|9239|e 120 L D F W D K R K G G P G G I I C N I G S
gi|9239|e 360 CTGGACTTCTGGGACAAGCGCAAGGGTGGACCCGGTGGTATCATCTGCAACATTGGATCC
gi|9239|e 140 V T G F N A I Y Q V P V Y S G T K A A V
gi|9239|e 420 GTGACTGGATTCAACGCCATCTACCAGGTGCCCGTTTACTCCGGCACCAAGGCTGCCGTG
gi|9239|e 160 V N F T S S L A K L A P I T G V T A Y T
gi|9239|e 480 GTCAACTTCACCAGCTCCCTGGCGAAACTGGCCCCCATCACCGGCGTGACCGCTTACACC
gi|9239|e 180 V N P G I T R T T L V H K F N S W L D V
gi|9239|e 540 GTGAACCCCGGCATCACCCGCACCACCCTGGTGCACAAGTTCAACTCCTGGCTGGATGTT
gi|9239|e 200 E P Q V A E K L L A H P T Q P S L A C A
gi|9239|e 600 GAGCCCCAGGTGGCCGAGAAGCTCCTGGCTCACCCCACCCAGCCCTCGTTGGCCTGCGCC
gi|9239|e 220 Q N F V K A I E L N Q N G A I W K L D L
gi|9239|e 660 CAGAACTTTGTCAAGGCCATCGAGCTGAACCAGAACGGTGCCATCTGGAAACTGGACTTG
gi|9239|e 240 G T L E A I Q W S K H W D S G I 256
gi|9239|e 720 GGCACCCTGGAGGCCATCCAGTGGTCCAAGCACTGGGACTCCGGCATC 768
""",
)
protein_record = protein_alignment.sequences[12]
nucleotide_record = nucleotide_records[protein_record.id]
self.assertEqual(nucleotide_record.id, protein_record.id)
alignments = aligner.align(protein_record, nucleotide_record)
self.assertEqual(len(alignments), 1)
alignment = next(alignments)
codon_alignments.append(alignment)
self.assertTrue(
np.array_equal(alignment.coordinates, np.array([[0, 256], [0, 768]]))
)
self.assertEqual(
str(alignment),
"""\
gi|9097|e 0 M A F T L T N K N V I F V A G L G G I G
gi|9097|e 0 ATGGCGTTTACTTTGACCAACAAGAACGTGATTTTCGTTGCCGGTCTGGGAGGCATTGGT
gi|9097|e 20 L D T S K E L L K R D L K N L V I L D R
gi|9097|e 60 CTGGACACCAGCAAGGAGCTGCTCAAGCGCGACCTGAAGAACCTGGTGATCCTCGACCGC
gi|9097|e 40 I E N P A A I A E L K A I N P K V T V T
gi|9097|e 120 ATTGAGAACCCTGCTGCCATTGCCGAGCTGAAGGCAATCAATCCAAAGGTGACCGTCACC
gi|9097|e 60 F Y P Y D V T V P I A E T T K L L K T I
gi|9097|e 180 TTCTACCCCTATGATGTGACCGTGCCCATTGCCGAGACCACCAAGCTGCTGAAGACCATC
gi|9097|e 80 F A K L K T V D V L I N G A G I L D D H
gi|9097|e 240 TTCGCCAAGCTGAAGACCGTCGATGTCCTGATCAACGGAGCTGGTATCCTGGACGATCAC
gi|9097|e 100 Q I E R T I A V N Y T G L V N T T T A I
gi|9097|e 300 CAGATCGAGCGCACCATTGCCGTCAACTACACTGGCCTGGTCAACACCACGACGGCCATT
gi|9097|e 120 L D F W D K R K G G P G G I I C N I G S
gi|9097|e 360 TTGGACTTCTGGGACAAGCGCAAGGGTGGTCCCGGTGGTATCATCTGCAACATTGGATCC
gi|9097|e 140 V T G F N A I Y Q V P V Y S G T K A A V
gi|9097|e 420 GTCACTGGATTCAATGCCATCTACCAGGTGCCCGTCTACTCCGGCACCAAGGCTGCCGTG
gi|9097|e 160 V N F T S S L A K L A P I T G V T A Y T
gi|9097|e 480 GTCAACTTCACCAGCTCCCTGGCGAAACTGGCCCCCATTACCGGCGTGACCGCTTACACC
gi|9097|e 180 V N P G I T R T T L V H K F N S W L D V
gi|9097|e 540 GTGAACCCCGGCATCACCCGCACCACCCTGGTGCACAAGTTCAACTCCTGGCTGGATGTT
gi|9097|e 200 E P Q V A E K L L A H P T Q P S L A C A
gi|9097|e 600 GAGCCCCAGGTTGCCGAGAAGCTCCTGGCTCATCCCACCCAGCCCTCGTTGGCCTGCGCC
gi|9097|e 220 E N F V K A I E L N Q N G A I W K L D L
gi|9097|e 660 GAGAACTTCGTCAAGGCTATCGAGCTGAACCAGAACGGAGCCATCTGGAAACTGGACTTG
gi|9097|e 240 G T L E A I Q W T K H W D S G I 256
gi|9097|e 720 GGCACCCTGGAGGCCATCCAGTGGACCAAGCACTGGGACTCCGGCATC 768
""",
)
protein_record = protein_alignment.sequences[13]
nucleotide_record = nucleotide_records[protein_record.id]
self.assertEqual(nucleotide_record.id, protein_record.id)
alignments = aligner.align(protein_record, nucleotide_record)
self.assertEqual(len(alignments), 1)
alignment = next(alignments)
codon_alignments.append(alignment)
self.assertTrue(
np.array_equal(alignment.coordinates, np.array([[0, 256], [0, 768]]))
)
self.assertEqual(
str(alignment),
"""\
gi|9099|e 0 M A F T L T N K N V I F V A G L G G I G
gi|9099|e 0 ATGGCGTTTACTTTGACCAACAAGAACGTGATTTTCGTTGCCGGTCTGGGAGGCATTGGT
gi|9099|e 20 L D T S K E L L K R D L K N L V I L D R
gi|9099|e 60 CTGGACACCAGCAAGGAGCTGCTCAAGCGCGACCTGAAGAACCTGGTGATCCTCGACCGC
gi|9099|e 40 I E N P A A I A E L K A I N P K V T V T
gi|9099|e 120 ATTGAGAACCCTGCTGCCATTGCCGAGCTGAAGGCAATCAATCCAAAGGTGACCGTCACC
gi|9099|e 60 F Y P Y D V T V P I A E T T K L L K T I
gi|9099|e 180 TTCTACCCCTATGATGTGACCGTGCCCATTGCCGAGACCACCAAGCTGCTGAAGACCATC
gi|9099|e 80 F A K L K T V D V L I N G A G I L D D H
gi|9099|e 240 TTCGCCAAGCTGAAGACCGTCGATGTCCTGATCAACGGAGCTGGTATCCTGGACGATCAC
gi|9099|e 100 Q I E R T I A V N Y T G L V N T T T A I
gi|9099|e 300 CAGATCGAGCGCACCATTGCCGTCAACTACACTGGCCTGGTCAACACCACGACGGCCATT
gi|9099|e 120 L D F W D K R K G G P G G I I C N I G S
gi|9099|e 360 CTGGACTTCTGGGACAAGCGCAAGGGTGGTCCCGGTGGTATCATCTGCAACATTGGATCC
gi|9099|e 140 V T G F N A I Y Q V P V Y S G T K A A V
gi|9099|e 420 GTCACTGGTTTCAATGCCATCTACCAGGTGCCCGTCTACTCCGGCACCAAGGCTGCCGTG
gi|9099|e 160 V N F T S S L A K L A P I T G V T A Y T
gi|9099|e 480 GTCAACTTCACCAGCTCCCTGGCGAAACTGGCCCCCATTACCGGCGTGACCGCTTACACC
gi|9099|e 180 V N P G I T R T T L V H K F N S W L D V
gi|9099|e 540 GTGAACCCCGGCATCACCCGCACCACCCTGGTGCACAAGTTCAACTCCTGGCTGGATGTT
gi|9099|e 200 E P Q V A E K L L A H P T Q P S L A C A
gi|9099|e 600 GAGCCCCAGGTTGCCGAGAAGCTCCTGGCTCATCCCACTCAGCCCTCATTGGCCTGCGCC
gi|9099|e 220 E N F V K A I E L N Q N G A I W K L D L
gi|9099|e 660 GAGAACTTCGTCAAGGCCATCGAGCTGAACCAGAACGGAGCCATCTGGAAACTGGACTTG
gi|9099|e 240 G T L E A I Q W T K H W D S G I 256
gi|9099|e 720 GGCACCCTGGAGGCCATCCAGTGGACCAAGCACTGGGACTCCGGCATC 768
""",
)
protein_record = protein_alignment.sequences[14]
nucleotide_record = nucleotide_records[protein_record.id]
self.assertEqual(nucleotide_record.id, protein_record.id)
alignments = aligner.align(protein_record, nucleotide_record)
self.assertEqual(len(alignments), 1)
alignment = next(alignments)
codon_alignments.append(alignment)
self.assertTrue(
np.array_equal(alignment.coordinates, np.array([[0, 256], [0, 768]]))
)
self.assertEqual(
str(alignment),
"""\
gi|9101|e 0 M A F T L T N K N V I F V A G L G G I G
gi|9101|e 0 ATGGCGTTTACTTTGACCAACAAGAACGTGATTTTCGTTGCCGGTCTGGGAGGCATTGGT
gi|9101|e 20 L D T S K E L L K R D L K N L V I L D R
gi|9101|e 60 CTGGACACCAGCAAGGAGCTGCTCAAGCGCGACCTGAAGAACCTGGTGATCCTCGACCGC
gi|9101|e 40 I E N P A A I A E L K A I N P K V T V T
gi|9101|e 120 ATTGAGAACCCTGCTGCCATTGCCGAGCTGAAGGCAATCAATCCAAAGGTGACCGTCACC
gi|9101|e 60 F Y P Y D V T V P I A E T T K L L K T I
gi|9101|e 180 TTCTACCCCTATGATGTGACCGTGCCCATTGCCGAGACCACCAAGCTGCTGAAGACCATC
gi|9101|e 80 F A K L K T V D V L I N G A G I L D D H
gi|9101|e 240 TTCGCCAAGCTGAAGACCGTCGATGTCCTGATCAACGGAGCTGGTATCCTGGACGATCAC
gi|9101|e 100 Q I E R T I A V N Y T G L V N T T T A I
gi|9101|e 300 CAGATCGAGCGCACCATTGCCGTCAACTACACTGGCCTGGTCAACACCACGACGGCCATT
gi|9101|e 120 L D F W D K R K G G P G G I I C N I G S
gi|9101|e 360 CTGGACTTCTGGGACAAGCGCAAGGGTGGTCCCGGTGGTATCATCTGCAACATTGGATCC
gi|9101|e 140 V T G F N A I Y Q V P V Y S G T K A A V
gi|9101|e 420 GTCACTGGATTCAATGCCATCTACCAGGTGCCCGTCTACTCTGGCACCAAGGCCGCCGTG
gi|9101|e 160 V N F T S S L A K L A P I T G V T A Y T
gi|9101|e 480 GTCAACTTCACCAGCTCCCTGGCGAAACTGGCCCCCATTACCGGCGTGACCGCTTACACC
gi|9101|e 180 V N P G I T R T T L V H K F N S W L D V
gi|9101|e 540 GTGAACCCCGGCATCACCCGCACCACCCTGGTGCACAAGTTCAACTCCTGGCTGGATGTT
gi|9101|e 200 E P Q V A E K L L A H P T Q P S L A C A
gi|9101|e 600 GAGCCCCAGGTTGCCGAGAAGCTCCTGGCTCATCCCACCCAGCCCTCGTTGGCCTGCGCC
gi|9101|e 220 E N F V K A I E L N Q N G A I W K L D L
gi|9101|e 660 GAGAACTTCGTCAAGGCCATCGAGCTGAACCAGAACGGAGCCATCTGGAAACTGGACTTG
gi|9101|e 240 G T L E A I Q W T K H W D S G I 256
gi|9101|e 720 GGCACCCTGGAGGCCATCCAGTGGACCAAGCACTGGGACTCCGGCATC 768
""",
)
protein_record = protein_alignment.sequences[15]
nucleotide_record = nucleotide_records[protein_record.id]
self.assertEqual(nucleotide_record.id, protein_record.id)
alignments = aligner.align(protein_record, nucleotide_record)
self.assertEqual(len(alignments), 1)
alignment = next(alignments)
codon_alignments.append(alignment)
self.assertTrue(
np.array_equal(alignment.coordinates, np.array([[0, 256], [0, 768]]))
)
self.assertEqual(
str(alignment),
"""\
gi|9103|e 0 M A F T L T N K N V I F V A G L G G I G
gi|9103|e 0 ATGGCGTTTACTTTGACCAACAAGAACGTGATTTTCGTTGCCGGTCTGGGAGGCATCGGT
gi|9103|e 20 L D T S K E L L K R D L K N L V I L D R
gi|9103|e 60 CTGGACACCAGCAAGGAGCTGCTCAAGCGCGACCTGAAGAACCTGGTGATCCTCGACCGC
gi|9103|e 40 I E N P A A I A E L K A I N P K V T V T
gi|9103|e 120 ATTGAGAACCCTGCTGCCATTGCCGAGCTGAAGGCAATCAATCCAAAGGTGACCGTCACC
gi|9103|e 60 F Y P Y D V T V P I A E T T K L L K T I
gi|9103|e 180 TTCTACCCCTATGATGTGACCGTGCCCATTGCCGAGACCACCAAGCTGCTGAAGACCATC
gi|9103|e 80 F A K L K T V D V L I N G A G I L D D H
gi|9103|e 240 TTCGCCAAGCTGAAGACCGTCGATGTCCTGATCAACGGAGCTGGTATCCTGGACGATCAC
gi|9103|e 100 Q I E R T I A V N Y T G L V N T T T A I
gi|9103|e 300 CAGATCGAGCGCACCATTGCCGTCAACTACACTGGCCTGGTCAACACCACGACGGCCATT
gi|9103|e 120 L D F W D K R K G G P G G I I C N I G S
gi|9103|e 360 CTGGACTTCTGGGACAAGCGCAAGGGTGGTCCCGGTGGTATCATCTGCAACATTGGATCC
gi|9103|e 140 V T G F N A I Y Q V P V Y S G T K A A V
gi|9103|e 420 GTCACTGGATTCAATGCCATCTACCAGGTGCCCGTCTACTCCGGCACCAAGGCCGCCGTG
gi|9103|e 160 V N F T S S L A K L A P I T G V T A Y T
gi|9103|e 480 GTCAACTTCACCAGCTCCCTGGCGAAACTGGCCCCCATTACCGGCGTGACCGCTTACACC
gi|9103|e 180 V N P G I T R T T L V H K F N S W L D V
gi|9103|e 540 GTGAACCCCGGCATCACCCGCACCACCCTGGTGCACAAGTTCAACTCCTGGCTGGATGTT
gi|9103|e 200 E P Q V A E K L L A H P T Q P S L A C A
gi|9103|e 600 GAGCCCCAGGTTGCCGAGAAGCTCCTGGCTCATCCCACCCAGCCCTCGTTGGCCTGCGCC
gi|9103|e 220 E N F V K A I E L N Q N G A I W K L D L
gi|9103|e 660 GAGAACTTCGTCAAGGCCATCGAGCTGAACCAGAACGGAGCCATCTGGAAACTGGACTTG
gi|9103|e 240 G T L E A I Q W T K H W D S G I 256
gi|9103|e 720 GGCACCCTGGAGGCCATCCAGTGGACCAAGCACTGGGACTCCGGCATC 768
""",
)
protein_record = protein_alignment.sequences[16]
nucleotide_record = nucleotide_records[protein_record.id]
self.assertEqual(nucleotide_record.id, protein_record.id)
alignments = aligner.align(protein_record, nucleotide_record)
self.assertEqual(len(alignments), 1)
alignment = next(alignments)
codon_alignments.append(alignment)
self.assertTrue(
np.array_equal(alignment.coordinates, np.array([[0, 256], [0, 768]]))
)
self.assertEqual(
str(alignment),
"""\
gi|156879 0 M S F T L T N K N V I F V A G L G G I G
gi|156879 0 ATGTCGTTTACTTTGACCAACAAGAACGTGATTTTCGTGGCCGGTCTGGGAGGCATTGGT
gi|156879 20 L D T S K E L L K R D L K N L V I L D R
gi|156879 60 CTGGACACCAGCAAGGAGCTGCTCAAGCGCGATCTGAAGAACCTGGTGATCCTCGACCGC
gi|156879 40 I E N P A A I A E L K A I N P K V T V T
gi|156879 120 ATTGAGAACCCGGCTGCCATTGCCGAGCTGAAGGCAATCAATCCAAAGGTGACCGTCACC
gi|156879 60 F Y P Y D V T V P I A E T T K L L K T I
gi|156879 180 TTCTACCCCTATGATGTGACCGTGCCCATTGCCGAGACCACCAAGCTGCTGAAGACCATC
gi|156879 80 F A Q L K T V D V L I N G A G I L D D H
gi|156879 240 TTCGCCCAGCTGAAGACCGTCGATGTCCTGATCAACGGAGCTGGTATCCTGGACGATCAC
gi|156879 100 Q I E R T I A V N Y T G L V N T T T A I
gi|156879 300 CAGATCGAGCGCACCATTGCCGTCAACTACACTGGCCTGGTCAACACCACGACGGCCATT
gi|156879 120 L D F W D K R K G G P G G I I C N I G S
gi|156879 360 CTGGACTTCTGGGACAAGCGCAAGGGCGGTCCAGGTGGTATCATCTGCAACATTGGATCC
gi|156879 140 V T G F N A I Y Q V P V Y S G T K A A V
gi|156879 420 GTCACTGGATTCAATGCCATCTACCAGGTGCCCGTCTACTCCGGCACCAAGGCCGCCGTG
gi|156879 160 V N F T S S L A K L A P I T G V T A Y T
gi|156879 480 GTCAACTTCACCAGCTCCCTGGCGAAACTGGCCCCCATTACCGGCGTGACGGCTTACACT
gi|156879 180 V N P G I T R T T L V H T F N S W L D V
gi|156879 540 GTGAACCCCGGCATCACCCGCACCACCCTGGTGCACACGTTCAACTCCTGGTTGGATGTT
gi|156879 200 E P Q V A E K L L A H P T Q P S L A C A
gi|156879 600 GAGCCTCAGGTTGCCGAGAAGCTCCTGGCTCATCCCACCCAGCCCTCGTTGGCCTGCGCC
gi|156879 220 E N F V K A I E L N Q N G A I W K L D L
gi|156879 660 GAGAACTTCGTCAAGGCTATCGAGCTGAACCAGAACGGAGCCATCTGGAAACTGGACTTG
gi|156879 240 G T L E A I Q W T K H W D S G I 256
gi|156879 720 GGCACCCTGGAGGCCATCCAGTGGACCAAGCACTGGGACTCCGGCATC 768
""",
)
protein_record = protein_alignment.sequences[17]
nucleotide_record = nucleotide_records[protein_record.id]
self.assertEqual(nucleotide_record.id, protein_record.id)
alignments = aligner.align(protein_record, nucleotide_record)
self.assertEqual(len(alignments), 1)
alignment = next(alignments)
codon_alignments.append(alignment)
self.assertTrue(
np.array_equal(alignment.coordinates, np.array([[0, 256], [0, 768]]))
)
self.assertEqual(
str(alignment),
"""\
gi|156877 0 M S F T L T N K N V I F V A G L G G I G
gi|156877 0 ATGTCGTTTACTTTGACCAACAAGAACGTGATTTTCGTGGCCGGTCTGGGAGGCATTGGT
gi|156877 20 L D T S K E L L K R D L K N L V I L D R
gi|156877 60 CTGGACACCAGCAAGGAGCTGCTCAAGCGCGATCTGAAGAACCTGGTGATCCTCGACCGC
gi|156877 40 I E N P A A I A E L K A I N P K V T V T
gi|156877 120 ATTGAGAACCCGGCTGCCATTGCCGAGCTGAAGGCAATCAATCCAAAGGTGACCGTCACC
gi|156877 60 F Y P Y D V T V P I A E T T K L L K T I
gi|156877 180 TTCTACCCCTATGATGTGACCGTGCCCATTGCCGAGACCACCAAGCTGCTGAAGACCATC
gi|156877 80 F A Q L K T V D V L I N G A G I L D D H
gi|156877 240 TTCGCCCAGCTGAAGACCGTCGATGTCCTGATCAACGGAGCTGGTATCCTGGACGATCAC
gi|156877 100 Q I E R T I A V N Y T G L V N T T T A I
gi|156877 300 CAGATCGAGCGCACCATTGCCGTCAACTACACTGGCCTGGTCAACACCACGACGGCCATT
gi|156877 120 L D F W D K R K G G P G G I I C N I G S
gi|156877 360 CTGGACTTCTGGGACAAGCGCAAGGGCGGTCCCGGTGGTATCATCTGCAACATTGGATCC
gi|156877 140 V T G F N A I Y Q V P V Y S G T K A A V
gi|156877 420 GTCACTGGATTCAATGCCATCTACCAGGTGCCCGTCTACTCCGGCACCAAGGCCGCCGTG
gi|156877 160 V N F T S S L A K L A P I T G V T A Y T
gi|156877 480 GTCAACTTCACCAGCTCCCTGGCGAAACTGGCCCCCATTACCGGCGTGACGGCTTACACT
gi|156877 180 V N P G I T R T T L V H T F N S W L D V
gi|156877 540 GTGAACCCCGGCATCACCCGCACCACCCTGGTGCACACGTTCAACTCCTGGTTGGATGTT
gi|156877 200 E P Q V A E K L L A H P T Q P S L A C A
gi|156877 600 GAGCCTCAGGTTGCCGAGAAGCTCCTGGCTCATCCCACCCAGCCCTCGTTGGCCTGCGCC
gi|156877 220 E N F V K A I E L N Q N G A I W K L D L
gi|156877 660 GAGAACTTCGTCAAGGCTATCGAGCTGAACCAGAACGGAGCCATCTGGAAACTGGACTTG
gi|156877 240 G T L E A I Q W T K H W D S G I 256
gi|156877 720 GGCACCCTGGAGGCCATCCAGTGGACCAAGCACTGGGACTCCGGCATC 768
""",
)
protein_record = protein_alignment.sequences[18]
nucleotide_record = nucleotide_records[protein_record.id]
self.assertEqual(nucleotide_record.id, protein_record.id)
alignments = aligner.align(protein_record, nucleotide_record)
self.assertEqual(len(alignments), 1)
alignment = next(alignments)
codon_alignments.append(alignment)
self.assertTrue(
np.array_equal(alignment.coordinates, np.array([[0, 256], [0, 768]]))
)
self.assertEqual(
str(alignment),
"""\
gi|156875 0 M S F T L T N K N V I F V A G L G G I G
gi|156875 0 ATGTCGTTTACTTTGACCAACAAGAACGTGATTTTCGTGGCCGGTCTGGGAGGCATTGGT
gi|156875 20 L D T S K E L L K R D L K N L V I L D R
gi|156875 60 CTGGACACCAGCAAGGAGCTGCTCAAGCGCGATCTGAAGAACCTGGTGATCCTCGACCGC
gi|156875 40 I E N P A A I A E L K A I N P K V T V T
gi|156875 120 ATTGAGAACCCGGCTGCCATTGCCGAGCTGAAGGCAATCAATCCAAAGGTGACCGTCACC
gi|156875 60 F Y P Y D V T V P I A E T T K L L K T I
gi|156875 180 TTCTACCCCTATGATGTGACCGTGCCCATTGCCGAGACCACCAAGCTGCTGAAGACCATC
gi|156875 80 F A Q L K T V D V L I N G A G I L D D H
gi|156875 240 TTCGCCCAGCTGAAGACCGTCGATGTCCTGATCAACGGAGCTGGTATCCTGGACGATCAC
gi|156875 100 Q I E R T I A V N Y T G L V N T T T A I
gi|156875 300 CAGATCGAGCGCACCATTGCCGTCAACTACACTGGCCTGGTCAACACCACGACGGCCATT
gi|156875 120 L D F W D K R K G G P G G I I C N I G S
gi|156875 360 CTGGACTTCTGGGACAAGCGCAAGGGCGGTCCCGGTGGTATCATCTGCAACATTGGATCC
gi|156875 140 V T G F N A I Y Q V P V Y S G T K A A V
gi|156875 420 GTCACTGGATTCAATGCCATCTACCAGGTGCCCGTCTACTCCGGCACCAAGGCCGCCGTG
gi|156875 160 V N F T S S L A K L A P I T G V T A Y T
gi|156875 480 GTCAACTTCACCAGCTCCCTGGCGAAACTGGCCCCCATTACCGGCGTGACGGCTTACACT
gi|156875 180 V N P G I T R T T L V H T F N S W L D V
gi|156875 540 GTGAACCCCGGCATCACCCGCACCACCCTGGTGCACACGTTCAACTCCTGGTTGGATGTT
gi|156875 200 E P Q V A E K L L A H P T Q P S L A C A
gi|156875 600 GAGCCTCAGGTTGCCGAGAAGCTCCTGGCTCATCCCACCCAGCCCTCGTTGGCCTGCGCC
gi|156875 220 E N F V K A I E L N Q N G A I W K L D L
gi|156875 660 GAGAACTTCGTCAAGGCTATCGAGCTGAACCAGAACGGAGCCATCTGGAAACTGGACTTG
gi|156875 240 G T L E A I Q W T K H W D S G I 256
gi|156875 720 GGCACCCTGGAGGCCATCCAGTGGACCAAGCACTGGGACTCCGGCATC 768
""",
)
protein_record = protein_alignment.sequences[19]
nucleotide_record = nucleotide_records[protein_record.id]
self.assertEqual(nucleotide_record.id, protein_record.id)
alignments = aligner.align(protein_record, nucleotide_record)
self.assertEqual(len(alignments), 1)
alignment = next(alignments)
codon_alignments.append(alignment)
self.assertTrue(
np.array_equal(alignment.coordinates, np.array([[0, 256], [0, 768]]))
)
self.assertEqual(
str(alignment),
"""\
gi|156873 0 M S F T L T N K N V I F V A G L G G I G
gi|156873 0 ATGTCGTTTACTTTGACCAACAAGAACGTGATTTTCGTGGCCGGTCTGGGAGGCATTGGT
gi|156873 20 L D T S K E L L K R D L K N L V I L D R
gi|156873 60 CTGGACACCAGCAAGGAGCTGCTCAAGCGCGATCTGAAGAACCTGGTGATCCTCGACCGC
gi|156873 40 I E N P A A I A E L K A I N P K V T V T
gi|156873 120 ATTGAGAACCCGGCTGCCATTGCCGAGCTGAAGGCAATCAATCCAAAGGTGACCGTCACC
gi|156873 60 F Y P Y D V T V P I A E T T K L L K T I
gi|156873 180 TTCTACCCCTATGATGTGACCGTGCCCATTGCCGAGACCACCAAGCTGCTGAAGACCATC
gi|156873 80 F A Q L K T V D V L I N G A G I L D D H
gi|156873 240 TTCGCCCAGCTGAAGACCGTCGATGTCCTGATCAACGGAGCTGGTATCCTGGACGATCAC
gi|156873 100 Q I E R T I A V N Y T G L V N T T T A I
gi|156873 300 CAGATCGAGCGCACCATTGCCGTCAACTACACTGGCCTGGTCAACACCACGACGGCCATT
gi|156873 120 L D F W D K R K G G P G G I I C N I G S
gi|156873 360 CTGGACTTCTGGGACAAGCGCAAGGGCGGTCCCGGTGGTATCATCTGCAACATTGGATCC
gi|156873 140 V T G F N A I Y Q V P V Y S G T K A A V
gi|156873 420 GTCACTGGATTCAATGCCATCTACCAGGTGCCCGTCTACTCCGGCACCAAGGCCGCCGTG
gi|156873 160 V N F T S S L A K L A P I T G V T A Y T
gi|156873 480 GTCAACTTCACCAGCTCCCTGGCGAAACTGGCCCCCATTACCGGCGTGACGGCTTACACT
gi|156873 180 V N P G I T R T T L V H T F N S W L D V
gi|156873 540 GTGAACCCCGGCATCACCCGCACCACCCTGGTGCACACGTTCAACTCCTGGTTGGATGTT
gi|156873 200 E P Q V A E K L L A H P T Q P S L A C A
gi|156873 600 GAGCCTCAGGTTGCCGAGAAGCTCCTGGCTCATCCCACCCAGCCCTCGTTGGCCTGCGCC
gi|156873 220 E N F V K A I E L N Q N G A I W K L D L
gi|156873 660 GAGAACTTCGTCAAGGCTATCGAGCTGAACCAGAACGGAGCCATCTGGAAACTGGACTTG
gi|156873 240 G T L E A I Q W T K H W D S G I 256
gi|156873 720 GGCACCCTGGAGGCCATCCAGTGGACCAAGCACTGGGACTCCGGCATC 768
""",
)
protein_record = protein_alignment.sequences[20]
nucleotide_record = nucleotide_records[protein_record.id]
self.assertEqual(nucleotide_record.id, protein_record.id)
alignments = aligner.align(protein_record, nucleotide_record)
self.assertEqual(len(alignments), 1)
alignment = next(alignments)
codon_alignments.append(alignment)
self.assertTrue(
np.array_equal(alignment.coordinates, np.array([[0, 256], [0, 768]]))
)
self.assertEqual(
str(alignment),
"""\
gi|156871 0 M S F T L T N K N V I F V A G L G G I G
gi|156871 0 ATGTCGTTTACTTTGACCAACAAGAACGTGATTTTCGTGGCCGGTCTGGGAGGCATTGGT
gi|156871 20 L D T S K E L L K R D L K N L V I L D R
gi|156871 60 CTGGACACCAGCAAGGAGCTGCTCAAGCGCGATCTGAAGAACCTGGTGATCCTCGACCGC
gi|156871 40 I E N P A A I A E L K A I N P K V T V T
gi|156871 120 ATTGAGAACCCGGCTGCCATTGCCGAGCTGAAGGCAATCAATCCAAAGGTGACCGTCACC
gi|156871 60 F Y P Y D V T V P I A E T T K L L K T I
gi|156871 180 TTCTACCCCTATGATGTGACCGTGCCCATTGCCGAGACCACCAAGCTGCTGAAGACCATC
gi|156871 80 F A Q L K T V D V L I N G A G I L D D H
gi|156871 240 TTCGCCCAGCTGAAGACCGTCGATGTCCTGATCAACGGAGCTGGTATCCTGGACGATCAC
gi|156871 100 Q I E R T I A V N Y T G L V N T T T A I
gi|156871 300 CAGATCGAGCGCACCATTGCCGTCAACTACACTGGCCTGGTCAACACCACGACGGCCATT
gi|156871 120 L D F W D K R K G G P G G I I C N I G S
gi|156871 360 CTGGACTTCTGGGACAAGCGCAAGGGCGGTCCCGGTGGTATCATCTGCAACATTGGATCC
gi|156871 140 V T G F N A I Y Q V P V Y S G T K A A V
gi|156871 420 GTCACTGGATTCAATGCCATCTACCAGGTGCCCGTCTACTCCGGCACCAAGGCCGCCGTG
gi|156871 160 V N F T S S L A K L A P I T G V T A Y T
gi|156871 480 GTCAACTTCACCAGCTCCCTGGCGAAACTGGCCCCCATTACCGGCGTGACGGCTTACACT
gi|156871 180 V N P G I T R T T L V H T F N S W L D V
gi|156871 540 GTGAACCCCGGCATCACCCGCACCACCCTGGTGCACACGTTCAACTCCTGGTTGGATGTT
gi|156871 200 E P Q V A E K L L A H P T Q P S L A C A
gi|156871 600 GAGCCTCAGGTTGCCGAGAAGCTCCTGGCTCATCCCACCCAGCCCTCGTTGGCCTGCGCC
gi|156871 220 E N F V K A I E L N Q N G A I W K L D L
gi|156871 660 GAGAACTTCGTCAAGGCTATCGAGCTGAACCAGAACGGAGCCATCTGGAAACTGGACTTG
gi|156871 240 G T L E A I Q W T K H W D S G I 256
gi|156871 720 GGCACCCTGGAGGCCATCCAGTGGACCAAGCACTGGGACTCCGGCATC 768
""",
)
protein_record = protein_alignment.sequences[21]
nucleotide_record = nucleotide_records[protein_record.id]
self.assertEqual(nucleotide_record.id, protein_record.id)
alignments = aligner.align(protein_record, nucleotide_record)
self.assertEqual(len(alignments), 1)
alignment = next(alignments)
codon_alignments.append(alignment)
self.assertTrue(
np.array_equal(alignment.coordinates, np.array([[0, 256], [0, 768]]))
)
self.assertEqual(
str(alignment),
"""\
gi|156863 0 M S F T L T N K N V I F V A G L G G I G
gi|156863 0 ATGTCGTTTACTTTGACCAACAAGAACGTGATTTTCGTTGCCGGTCTGGGAGGCATTGGT
gi|156863 20 L D T S K E L L K R D L K N L V I L D R
gi|156863 60 CTGGACACCAGCAAGGAGCTGCTCAAGCGCGATCTGAAGAACCTGGTGATCCTCGACCGC
gi|156863 40 I E N P A A I A E L K A I N P K V T V T
gi|156863 120 ATTGAGAACCCGGCTGCCATTGCCGAGCTGAAGGCAATCAATCCAAAGGTGACCGTCACC
gi|156863 60 F Y P Y D V T V P I A E T T K L L K T I
gi|156863 180 TTCTACCCCTATGATGTGACCGTGCCCATTGCCGAGACCACCAAGCTGCTGAAGACCATC
gi|156863 80 F A Q L K T V D V L I N G A G I L D D H
gi|156863 240 TTCGCCCAGCTGAAGACCGTCGATGTCCTGATCAACGGAGCTGGTATCCTGGACGATCAC
gi|156863 100 Q I E R T I A V N Y T G L V N T T T A I
gi|156863 300 CAGATCGAGCGCACCATTGCCGTCAACTACACTGGCCTGGTCAACACCACGACGGCCATT
gi|156863 120 L D F W D K R K G G P G G I I C N I G S
gi|156863 360 CTGGACTTCTGGGACAAGCGCAAGGGCGGTCCCGGTGGTATCATCTGCAACATTGGATCC
gi|156863 140 V T G F N A I Y Q V P V Y S G T K A A V
gi|156863 420 GTCACTGGATTCAATGCCATCTACCAGGTGCCCGTCTACTCCGGCACCAAGGCCGCCGTG
gi|156863 160 V N F T S S L A K L A P I T G V T A Y T
gi|156863 480 GTCAACTTCACCAGCTCCCTGGCGAAACTGGCCCCCATTACCGGCGTGACCGCTTACACC
gi|156863 180 V N P G I T R T T L V H K F N S W L D V
gi|156863 540 GTGAACCCCGGCATCACCCGCACCACCCTGGTGCACAAGTTCAACTCCTGGTTGGATGTT
gi|156863 200 E P Q V A E K L L A H P T Q P S L A C A
gi|156863 600 GAGCCCCAGGTTGCTGAGAAGCTCCTGGCTCATCCCACCCAGCCATCGTTGGCCTGCGCC
gi|156863 220 E N F V K A I E L N Q N G A I W K L D L
gi|156863 660 GAGAACTTCGTCAAGGCTATCGAACTGAACCAGAACGGAGCCATCTGGAAACTGGACTTG
gi|156863 240 G T L E A I Q W T K H W D S G I 256
gi|156863 720 GGCACCCTGGAGGCCATCCAGTGGACCAAGCACTGGGACTCCGGCATC 768
""",
)
protein_record = protein_alignment.sequences[22]
nucleotide_record = nucleotide_records[protein_record.id]
self.assertEqual(nucleotide_record.id, protein_record.id)
alignments = aligner.align(protein_record, nucleotide_record)
self.assertEqual(len(alignments), 1)
alignment = next(alignments)
codon_alignments.append(alignment)
self.assertTrue(
np.array_equal(alignment.coordinates, np.array([[0, 256], [0, 768]]))
)
self.assertEqual(
str(alignment),
"""\
gi|156869 0 M S F T L T N K N V I F V A G L G G I G
gi|156869 0 ATGTCGTTTACTTTGACCAACAAGAACGTGATTTTCGTGGCCGGTCTGGGAGGCATTGGT
gi|156869 20 L D T S K E L L K R D L K N L V I L D R
gi|156869 60 CTGGACACCAGCAAGGAGCTGCTCAAGCGCGATCTGAAGAACCTGGTGATCCTCGACCGC
gi|156869 40 I E N P A A I A E L K A I N P K V T V T
gi|156869 120 ATTGAGAACCCGGCTGCCATTGCCGAGCTGAAGGCAATCAATCCAAAGGTGACCGTCACC
gi|156869 60 F Y P Y D V T V P I A E T T K L L K T I
gi|156869 180 TTCTACCCCTATGATGTGACCGTGCCCATTGCCGAGACCACCAAGCTGCTGAAGACCATC
gi|156869 80 F A Q L K T V D V L I N G A G I L D D H
gi|156869 240 TTCGCCCAGCTGAAGACCGTCGATGTCCTGATCAACGGAGCTGGTATCCTGGACGATCAC
gi|156869 100 Q I E R T I A V N Y T G L V N T T T A I
gi|156869 300 CAGATCGAGCGCACCATTGCCGTCAACTACACTGGCCTGGTCAACACCACGACGGCCATT
gi|156869 120 L D F W D K R K G G P G G I I C N I G S
gi|156869 360 CTGGACTTCTGGGACAAGCGCAAGGGCGGTCCCGGTGGTATCATCTGCAACATTGGATCC
gi|156869 140 V T G F N A I Y Q V P V Y S G T K A A V
gi|156869 420 GTCACTGGATTCAATGCCATCTACCAGGTGCCCGTCTACTCCGGCACCAAGGCCGCCGTG
gi|156869 160 V N F T S S L A K L A P I T G V T A Y T
gi|156869 480 GTCAACTTCACCAGCTCCCTGGCGAAACTGGCCCCCATTACCGGCGTGACCGCTTACACT
gi|156869 180 V N P G I T R T T L V H K F N S W L D V
gi|156869 540 GTGAACCCCGGCATCACCCGCACCACCCTGGTGCACAAGTTCAACTCCTGGTTGGATGTT
gi|156869 200 E P Q V A E K L L A H P T Q P S L A C A
gi|156869 600 GAGCCTCAGGTTGCTGAGAAGCTCCTGGCTCATCCCACCCAGCCCTCGTTGGCCTGCGCC
gi|156869 220 E N F V K A I E L N Q N G A I W K L D L
gi|156869 660 GAGAACTTCGTCAAGGCTATCGAACTGAACCAGAACGGAGCCATCTGGAAACTGGACTTG
gi|156869 240 G T L E A I Q W T K H W D S G I 256
gi|156869 720 GGCACCCTGGAGGCCATCCAGTGGACCAAGCACTGGGACTCCGGCATC 768
""",
)
protein_record = protein_alignment.sequences[23]
nucleotide_record = nucleotide_records[protein_record.id]
self.assertEqual(nucleotide_record.id, protein_record.id)
alignments = aligner.align(protein_record, nucleotide_record)
self.assertEqual(len(alignments), 1)
alignment = next(alignments)
codon_alignments.append(alignment)
self.assertTrue(
np.array_equal(alignment.coordinates, np.array([[0, 256], [0, 768]]))
)
self.assertEqual(
str(alignment),
"""\
gi|156867 0 M S F T L T N K N V I F V A G L G G I G
gi|156867 0 ATGTCGTTTACTTTGACCAACAAGAACGTGATTTTCGTGGCCGGTCTGGGAGGCATTGGT
gi|156867 20 L D T S K E L L K R D L K N L V I L D R
gi|156867 60 CTGGACACCAGCAAGGAGCTGCTCAAGCGCGATCTGAAGAACCTGGTGATCCTCGACCGC
gi|156867 40 I E N P A A I A E L K A I N P K V T V T
gi|156867 120 ATTGAGAACCCGGCTGCCATTGCCGAGCTGAAGGCAATCAATCCAAAGGTGACCGTCACC
gi|156867 60 F Y P Y D V T V P I A E T T K L L K T I
gi|156867 180 TTCTACCCCTATGATGTGACCGTGCCCATTGCCGAGACCACCAAGCTGCTGAAGACCATC
gi|156867 80 F A Q L K T V D V L I N G A G I L D D H
gi|156867 240 TTCGCCCAGCTGAAGACCGTCGATGTCCTGATCAACGGAGCTGGTATCCTGGACGATCAC
gi|156867 100 Q I E R T I A V N Y T G L V N T T T A I
gi|156867 300 CAGATCGAGCGCACCATTGCCGTCAACTACACTGGCCTGGTCAACACCACGACGGCCATT
gi|156867 120 L D F W D K R K G G P G G I I C N I G S
gi|156867 360 CTGGACTTCTGGGACAAGCGCAAGGGCGGTCCCGGTGGTATCATCTGCAACATTGGATCC
gi|156867 140 V T G F N A I Y Q V P V Y S G T K A A V
gi|156867 420 GTCACTGGATTCAATGCCATCTACCAGGTGCCCGTCTACTCCGGCACCAAGGCCGCCGTG
gi|156867 160 V N F T S S L A K L A P I T G V T A Y T
gi|156867 480 GTCAACTTCACCAGCTCCCTGGCGAAACTGGCCCCCATTACCGGCGTGACCGCTTACACC
gi|156867 180 V N P G I T R T T L V H K F N S W L D V
gi|156867 540 GTGAACCCCGGCATCACCCGCACCACCCTGGTGCACAAGTTCAACTCCTGGTTGGATGTT
gi|156867 200 E P Q V A E K L L A H P T Q P S L A C A
gi|156867 600 GAGCCCCAGGTTGCTGAGAAGCTCCTGGCTCATCCCACCCAGCCATCGTTGGCCTGCGCC
gi|156867 220 E N F V K A I E L N Q N G A I W K L D L
gi|156867 660 GAGAACTTCGTCAAGGCTATCGAGCTGAACCAGAACGGAGCCATCTGGAAACTGGACTTG
gi|156867 240 G T L E A I Q W T K H W D S G I 256
gi|156867 720 GGCACCCTGGAGGCCATCCAGTGGACCAAGCACTGGGACTCCGGCATC 768
""",
)
protein_record = protein_alignment.sequences[24]
nucleotide_record = nucleotide_records[protein_record.id]
self.assertEqual(nucleotide_record.id, protein_record.id)
alignments = aligner.align(protein_record, nucleotide_record)
self.assertEqual(len(alignments), 1)
alignment = next(alignments)
codon_alignments.append(alignment)
self.assertTrue(
np.array_equal(alignment.coordinates, np.array([[0, 256], [0, 768]]))
)
self.assertEqual(
str(alignment),
"""\
gi|156865 0 M S F T L T N K N V I F V A G L G G I G
gi|156865 0 ATGTCGTTTACTTTGACCAACAAGAACGTGATTTTCGTTGCCGGTCTGGGAGGCATTGGT
gi|156865 20 L D T S K E L L K R D L K N L V I L D R
gi|156865 60 CTGGACACCAGCAAGGAGCTGCTCAAGCGCGATCTGAAGAACCTGGTGATCCTCGACCGC
gi|156865 40 I E N P A A I A E L K A I N P K V T V T
gi|156865 120 ATTGAGAACCCGGCTGCCATTGCCGAGCTGAAGGCAATCAATCCAAAGGTGACCGTCACC
gi|156865 60 F Y P Y D V T V P I A E T T K L L K T I
gi|156865 180 TTCTACCCCTATGATGTGACCGTGCCCATTGCCGAGACCACCAAGCTGCTGAAGACCATC
gi|156865 80 F A Q L K T V D V L I N G A G I L D D H
gi|156865 240 TTCGCCCAGCTGAAGACCGTCGATGTCCTGATCAACGGAGCTGGTATCCTGGACGATCAC
gi|156865 100 Q I E R T I A V N Y T G L V N T T T A I
gi|156865 300 CAGATCGAGCGCACCATTGCCGTCAACTACACTGGCCTGGTCAACACCACGACGGCCATT
gi|156865 120 L D F W D K R K G G P G G I I C N I G S
gi|156865 360 CTGGACTTCTGGGACAAGCGCAAGGGCGGTCCCGGTGGTATCATCTGCAACATTGGATCC
gi|156865 140 V T G F N A I Y Q V P V Y S G T K A A V
gi|156865 420 GTCACTGGATTCAATGCCATCTACCAGGTGCCCGTCTACTCCGGCACCAAGGCCGCCGTG
gi|156865 160 V N F T S S L A K L A P I T G V T A Y T
gi|156865 480 GTCAACTTCACCAGCTCCCTGGCGAAACTGGCCCCCATTACCGGCGTGACCGCTTACACC
gi|156865 180 V N P G I T R T T L V H K F N S W L D V
gi|156865 540 GTGAACCCCGGCATCACCCGCACCACCCTGGTGCACAAGTTCAACTCCTGGTTGGATGTT
gi|156865 200 E P Q V A E K L L A H P T Q P S L A C A
gi|156865 600 GAGCCCCAGGTTGCTGAGAAGCTCCTGGCTCATCCCACCCAGCCATCGTTGGCCTGCGCC
gi|156865 220 E N F V K A I E L N Q N G A I W K L D L
gi|156865 660 GAGAACTTCGTCAAGGCTATCGAACTGAACCAGAACGGAGCCATCTGGAAACTGGACTTG
gi|156865 240 G T L E A I Q W T K H W D S G I 256
gi|156865 720 GGCACCCTGGAGGCCATCCAGTGGACCAAGCACTGGGACTCCGGCATC 768
""",
)
protein_record = protein_alignment.sequences[25]
nucleotide_record = nucleotide_records[protein_record.id]
self.assertEqual(nucleotide_record.id, protein_record.id)
alignments = aligner.align(protein_record, nucleotide_record)
self.assertEqual(len(alignments), 1)
alignment = next(alignments)
codon_alignments.append(alignment)
self.assertTrue(
np.array_equal(alignment.coordinates, np.array([[0, 256], [0, 768]]))
)
self.assertEqual(
str(alignment),
"""\
gi|156861 0 M S F T L T N K N V I F V A G L G G I G
gi|156861 0 ATGTCGTTTACTTTGACCAACAAGAACGTGATTTTCGTTGCCGGTCTGGGAGGCATTGGT
gi|156861 20 L D T S K E L L K R D L K N L V I L D R
gi|156861 60 CTGGACACCAGCAAGGAGCTGCTCAAGCGCGATCTGAAGAACCTGGTGATCCTCGACCGC
gi|156861 40 I E N P A A I A E L K A I N P K V T V T
gi|156861 120 ATTGAGAACCCGGCTGCCATTGCCGAGCTGAAGGCAATCAATCCAAAGGTGACCGTCACC
gi|156861 60 F Y P Y D V T V P I A E T T K L L K T I
gi|156861 180 TTCTACCCCTATGATGTGACCGTGCCCATTGCCGAGACCACCAAGTTGCTGAAGACCATC
gi|156861 80 F A Q L K T V D V L I N G A G I L D D H
gi|156861 240 TTCGCCCAGCTGAAGACCGTCGATGTCCTGATCAACGGAGCTGGTATCCTGGACGATCAC
gi|156861 100 Q I E R T I A V N Y T G L V N T T T A I
gi|156861 300 CAGATCGAGCGCACCATTGCCGTCAACTACACTGGCCTGGTCAACACCACGACGGCTATT
gi|156861 120 L D F W D K R K G G P G G I I C N I G S
gi|156861 360 CTGGACTTCTGGGACAAGCGCAAGGGTGGTCCCGGTGGTATCATCTGCAACATTGGATCC
gi|156861 140 V T G F N A I Y Q V P V Y S G T K A A V
gi|156861 420 GTCACTGGATTCAATGCCATATACCAGGTGCCCGTCTACTCCGGCACCAAGGCCGCCGTG
gi|156861 160 V N F T S S L A K L A P I T G V T A Y T
gi|156861 480 GTCAACTTCACCAGCTCCCTGGCGAAACTGGCACCCATCACCGGCGTGACCGCTTACACC
gi|156861 180 V N P G I T R T T L V H K F N S W L D V
gi|156861 540 GTGAACCCCGGCATCACCCGCACCACCCTGGTGCACAAGTTCAACTCCTGGTTGGATGTT
gi|156861 200 E P Q V A E K L L A H P T Q P S L A C A
gi|156861 600 GAGCCCCAGGTTGCTGAGAAGCTCCTGGCTCATCCCACCCAGCCATCGTTGGCCTGCGCC
gi|156861 220 E N F V K A I E L N Q N G A I W K L D L
gi|156861 660 GAGAACTTCGTCAAGGCTATCGAGCTGAACCAGAACGGAGCCATCTGGAAACTGGACTTG
gi|156861 240 G T L E A I Q W T K H W D S G I 256
gi|156861 720 GGCACCCTGGAGGCCATCCAGTGGACCAAGCACTGGGACTCCGGCATC 768
""",
)
protein_record = protein_alignment.sequences[26]
nucleotide_record = nucleotide_records[protein_record.id]
self.assertEqual(nucleotide_record.id, protein_record.id)
alignments = aligner.align(protein_record, nucleotide_record)
self.assertEqual(len(alignments), 1)
alignment = next(alignments)
codon_alignments.append(alignment)
self.assertTrue(
np.array_equal(alignment.coordinates, np.array([[0, 256], [0, 768]]))
)
self.assertEqual(
str(alignment),
"""\
gi|156859 0 M S F T L T N K N V I F V A G L G G I G
gi|156859 0 ATGTCGTTTACTTTGACCAACAAGAACGTGATTTTCGTTGCCGGTCTGGGAGGCATTGGT
gi|156859 20 L D T S K E L L K R D L K N L V I L D R
gi|156859 60 CTGGACACCAGCAAGGAGCTGCTCAAGCGCGATCTGAAGAACCTGGTGATCCTCGACCGC
gi|156859 40 I E N P A A I A E L K A I N P K V T V T
gi|156859 120 ATTGAGAACCCGGCTGCCATTGCCGAGCTGAAGGCAATCAATCCAAAGGTGACCGTCACC
gi|156859 60 F Y P Y D V T V P I A E T T K L L K T I
gi|156859 180 TTCTACCCCTATGATGTGACCGTGCCCATTGCCGAGACCACCAAGTTGCTGAAGACCATC
gi|156859 80 F A Q L K T V D V L I N G A G I L D D H
gi|156859 240 TTCGCCCAGCTGAAGACCGTCGATGTCCTGATCAACGGAGCTGGTATCCTGGACGATCAC
gi|156859 100 Q I E R T I A V N Y T G L V N T T T A I
gi|156859 300 CAGATCGAGCGCACCATTGCCGTCAACTACACTGGCCTGGTCAACACCACGACGGCCATT
gi|156859 120 L D F W D K R K G G P G G I I C N I G S
gi|156859 360 CTGGACTTCTGGGACAAGCGCAAGGGTGGTCCCGGTGGTATCATCTGCAACATTGGATCC
gi|156859 140 V T G F N A I Y Q V P V Y S G T K A A V
gi|156859 420 GTCACTGGATTCAATGCCATATACCAGGTGCCCGTCTACTCCGGCACCAAGGCCGCCGTG
gi|156859 160 V N F T S S L A K L A P I T G V T A Y T
gi|156859 480 GTCAACTTCACCAGCTCCCTGGCGAAACTGGCACCCATCACCGGCGTGACCGCTTACACC
gi|156859 180 V N P G I T R T T L V H K F N S W L D V
gi|156859 540 GTGAACCCCGGCATCACCCGCACCACCCTGGTGCACAAGTTCAACTCCTGGTTGGATGTT
gi|156859 200 E P Q V A E K L L A H P T Q P S L A C A
gi|156859 600 GAGCCCCAGGTTGCTGAGAAGCTCCTGGCTCATCCCACCCAGCCATCGTTGGCCTGCGCC
gi|156859 220 E N F V K A I E L N Q N G A I W K L D L
gi|156859 660 GAGAACTTCGTCAAGGCTATCGAGCTGAACCAGAACGGAGCCATCTGGAAACTGGACTTG
gi|156859 240 G T L E A I Q W T K H W D S G I 256
gi|156859 720 GGCACCCTGGAGGCCATCCAGTGGACCAAGCACTGGGACTCCGGCATC 768
""",
)
nucleotide_records.close() # Close indexed FASTA file
alignment = protein_alignment.mapall(codon_alignments)
unique_species = [
"Drosophila simulans",
"Drosophila yakuba",
"D.melanogaster",
]
species = []
for record in alignment.sequences:
description = record.description
for s in unique_species:
if s in description:
break
else:
raise Exception(f"Failed to find species for {description}")
species.append(s)
pvalue = mktest(alignment, species)
self.assertAlmostEqual(pvalue, 0.0020645725725430097)
if __name__ == "__main__":
runner = unittest.TextTestRunner(verbosity=2)
unittest.main(testRunner=runner)
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