mirror of
https://github.com/biopython/biopython.git
synced 2025-10-20 13:43:47 +08:00
update (#4820)
Co-authored-by: Michiel de Hoon <michiel.dehoon@riken.jp>
This commit is contained in:
mdehoon
GitHub
@ -7,7 +7,15 @@
|
||||
|
||||
import unittest
|
||||
|
||||
import numpy as np
|
||||
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
|
||||
@ -8375,33 +8383,26 @@ gi|6478867|gb|M37394.2|RATEGFR AGAGTACCTGCGGGTGGCACCGCCAAGCAGTGAGTTTAGTGGAG
|
||||
self.assertAlmostEqual(ds_cal, ds_corr, places=4)
|
||||
|
||||
|
||||
try:
|
||||
import numpy
|
||||
except ImportError:
|
||||
numpy = None
|
||||
|
||||
if numpy:
|
||||
|
||||
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),
|
||||
"""\
|
||||
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
|
||||
|
||||
@ -8441,20 +8442,20 @@ 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),
|
||||
"""\
|
||||
)
|
||||
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
|
||||
|
||||
@ -8494,20 +8495,20 @@ 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),
|
||||
"""\
|
||||
)
|
||||
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
|
||||
|
||||
@ -8547,20 +8548,20 @@ 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),
|
||||
"""\
|
||||
)
|
||||
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
|
||||
|
||||
@ -8600,20 +8601,20 @@ 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),
|
||||
"""\
|
||||
)
|
||||
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
|
||||
|
||||
@ -8653,20 +8654,20 @@ 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),
|
||||
"""\
|
||||
)
|
||||
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
|
||||
|
||||
@ -8706,20 +8707,20 @@ 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),
|
||||
"""\
|
||||
)
|
||||
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
|
||||
|
||||
@ -8759,20 +8760,20 @@ 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),
|
||||
"""\
|
||||
)
|
||||
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
|
||||
|
||||
@ -8812,20 +8813,20 @@ 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),
|
||||
"""\
|
||||
)
|
||||
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
|
||||
|
||||
@ -8865,20 +8866,20 @@ 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),
|
||||
"""\
|
||||
)
|
||||
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
|
||||
|
||||
@ -8918,20 +8919,20 @@ 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),
|
||||
"""\
|
||||
)
|
||||
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
|
||||
|
||||
@ -8971,20 +8972,20 @@ 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),
|
||||
"""\
|
||||
)
|
||||
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
|
||||
|
||||
@ -9024,20 +9025,20 @@ 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),
|
||||
"""\
|
||||
)
|
||||
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
|
||||
|
||||
@ -9077,20 +9078,20 @@ 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),
|
||||
"""\
|
||||
)
|
||||
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
|
||||
|
||||
@ -9130,20 +9131,20 @@ 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),
|
||||
"""\
|
||||
)
|
||||
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
|
||||
|
||||
@ -9183,20 +9184,20 @@ 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),
|
||||
"""\
|
||||
)
|
||||
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
|
||||
|
||||
@ -9236,20 +9237,20 @@ 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),
|
||||
"""\
|
||||
)
|
||||
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
|
||||
|
||||
@ -9289,20 +9290,20 @@ 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),
|
||||
"""\
|
||||
)
|
||||
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
|
||||
|
||||
@ -9342,20 +9343,20 @@ 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),
|
||||
"""\
|
||||
)
|
||||
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
|
||||
|
||||
@ -9395,20 +9396,20 @@ 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),
|
||||
"""\
|
||||
)
|
||||
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
|
||||
|
||||
@ -9448,20 +9449,20 @@ 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),
|
||||
"""\
|
||||
)
|
||||
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
|
||||
|
||||
@ -9501,20 +9502,20 @@ 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),
|
||||
"""\
|
||||
)
|
||||
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
|
||||
|
||||
@ -9554,20 +9555,20 @@ 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),
|
||||
"""\
|
||||
)
|
||||
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
|
||||
|
||||
@ -9607,20 +9608,20 @@ 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),
|
||||
"""\
|
||||
)
|
||||
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
|
||||
|
||||
@ -9660,20 +9661,20 @@ 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),
|
||||
"""\
|
||||
)
|
||||
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
|
||||
|
||||
@ -9713,20 +9714,20 @@ 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),
|
||||
"""\
|
||||
)
|
||||
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
|
||||
|
||||
@ -9766,20 +9767,20 @@ 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),
|
||||
"""\
|
||||
)
|
||||
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
|
||||
|
||||
@ -9819,25 +9820,25 @@ 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)
|
||||
)
|
||||
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__":
|
||||
|
||||
Reference in New Issue
Block a user