mirror of
https://github.com/biopython/biopython.git
synced 2025-10-20 21:53:47 +08:00
e838eb90e6
* create template * tests * tests * update * update * update * update * update * update * update * update * update * update * update * update * update * update * stockholm * update * update * update * update * update * update * update * update * update * update * update * update --------- Co-authored-by: Michiel de Hoon <mdehoon@tkx288.genome.gsc.riken.jp> Co-authored-by: Michiel Jan Laurens de Hoon <mdehoon@Michiels-MacBook-Air.local>
9356 lines
474 KiB
Python
9356 lines
474 KiB
Python
# Copyright 2022 by Michiel de Hoon. All rights reserved.
|
|
# 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.
|
|
"""Tests for Align.bed module."""
|
|
import os
|
|
import tempfile
|
|
import unittest
|
|
from io import StringIO
|
|
|
|
import numpy as np
|
|
|
|
from Bio import Align
|
|
from Bio import SeqIO
|
|
from Bio.Align import Alignment
|
|
from Bio.Seq import Seq
|
|
from Bio.SeqRecord import SeqRecord
|
|
|
|
|
|
class TestAlign_dna_rna(unittest.TestCase):
|
|
# The BED file dna_rna.bed was generated using this command:
|
|
# pslToBed dna_rna.psl dna_rna.bed
|
|
|
|
def setUp(self):
|
|
data = {}
|
|
records = SeqIO.parse("Blat/dna.fa", "fasta")
|
|
for record in records:
|
|
name, start_end = record.id.split(":")
|
|
assert name == "chr3"
|
|
start, end = start_end.split("-")
|
|
start = int(start)
|
|
end = int(end)
|
|
sequence = str(record.seq)
|
|
assert len(sequence) == end - start
|
|
data[start] = sequence
|
|
self.dna = Seq(data, length=198295559) # hg38 chr3
|
|
records = SeqIO.parse("Blat/rna.fa", "fasta")
|
|
self.rna = {record.id: record.seq for record in records}
|
|
|
|
def check_alignments(self, alignments):
|
|
alignment = next(alignments)
|
|
self.assertEqual(alignment.score, 1000)
|
|
self.assertEqual(alignment.shape, (2, 1711))
|
|
self.assertLess(alignment.coordinates[0, 0], alignment.coordinates[0, -1])
|
|
self.assertGreater(alignment.coordinates[1, 0], alignment.coordinates[1, -1])
|
|
self.assertEqual(len(alignment), 2)
|
|
self.assertIs(alignment.sequences[0], alignment.target)
|
|
self.assertIs(alignment.sequences[1], alignment.query)
|
|
self.assertEqual(alignment.target.id, "chr3")
|
|
self.assertEqual(alignment.query.id, "NR_046654.1")
|
|
self.assertTrue(
|
|
np.array_equal(
|
|
alignment.coordinates,
|
|
# fmt: off
|
|
np.array([[42530895, 42530958, 42532020,
|
|
42532095, 42532563, 42532606],
|
|
[ 181, 118, 118,
|
|
43, 43, 0]])
|
|
# fmt: on
|
|
)
|
|
)
|
|
alignment.target.seq = self.dna
|
|
alignment.query.seq = self.rna[alignment.query.id]
|
|
self.assertTrue(
|
|
np.array_equal(
|
|
alignment.substitutions,
|
|
# fmt: off
|
|
np.array([[36., 0., 0., 0., 0., 0., 0., 0.],
|
|
[ 0., 40., 0., 0., 0., 0., 0., 0.],
|
|
[ 0., 0., 57., 0., 0., 0., 0., 0.],
|
|
[ 0., 0., 0., 42., 0., 0., 0., 0.],
|
|
[ 2., 0., 0., 0., 0., 0., 0., 0.],
|
|
[ 0., 1., 0., 0., 0., 0., 0., 0.],
|
|
[ 0., 0., 3., 0., 0., 0., 0., 0.],
|
|
[ 0., 0., 0., 0., 0., 0., 0., 0.],
|
|
])
|
|
)
|
|
)
|
|
self.assertEqual(alignment.substitutions.alphabet, "ACGTacgt")
|
|
self.assertEqual(
|
|
str(alignment),
|
|
"""\
|
|
chr3 42530895 CGGAAGTACTTCTGGGGGTACATACTCATCGGCTGGGGTATGGTACCAGGGAGGGCTTCC
|
|
0 ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
|
|
NR_046654 181 CGGAAGTACTTCTGGGGGTACATACTCATCGGCTGGGGTATGGTACCAGGGAGGGCTTCC
|
|
|
|
chr3 42530955 AGGCTGGGGACAGAGGGGGCAAGGCCTGGAGAACTCCCTAGGGGGAGGGTGCCAACCCAG
|
|
60 |||---------------------------------------------------------
|
|
NR_046654 121 AGG---------------------------------------------------------
|
|
|
|
chr3 42531015 CTTGCAGTCCTACGTCTTGCTTAGCTGCAGGTCCTGCCTGCAAGGATATCAGCCAAGGGT
|
|
120 ------------------------------------------------------------
|
|
NR_046654 118 ------------------------------------------------------------
|
|
|
|
chr3 42531075 CAAGAAAGTCCTCAAAATGTCTGATCCCAGGACAAGTCCCTCAGGTTGCAGCTGCACCTA
|
|
180 ------------------------------------------------------------
|
|
NR_046654 118 ------------------------------------------------------------
|
|
|
|
chr3 42531135 GGGCTGACCTGTGGGACAGATTTTGTGAACATCTTTCCATTTCCCTTTAGTTCCCGAAAT
|
|
240 ------------------------------------------------------------
|
|
NR_046654 118 ------------------------------------------------------------
|
|
|
|
chr3 42531195 ACAcagggccactgctaatctataaagggcctctgtcacaattagaaagagaatgtccgt
|
|
300 ------------------------------------------------------------
|
|
NR_046654 118 ------------------------------------------------------------
|
|
|
|
chr3 42531255 ctaggtagacacagcccttcaggcatacagcttCACCCCCTCAGTGGAGCATCCCTCCGT
|
|
360 ------------------------------------------------------------
|
|
NR_046654 118 ------------------------------------------------------------
|
|
|
|
chr3 42531315 GGTGAACAACCTATGCAACCAAAGACAGCAGACTGACAACCCACCCTTTtctctctccct
|
|
420 ------------------------------------------------------------
|
|
NR_046654 118 ------------------------------------------------------------
|
|
|
|
chr3 42531375 ccctctccctgcttttctccaaaatctctccctcatgccctctacccctgcttcctgtgc
|
|
480 ------------------------------------------------------------
|
|
NR_046654 118 ------------------------------------------------------------
|
|
|
|
chr3 42531435 cctctctgctctttcactctccctGGGCCTGACAGGGGTACCCAGCACATTCACCATGGT
|
|
540 ------------------------------------------------------------
|
|
NR_046654 118 ------------------------------------------------------------
|
|
|
|
chr3 42531495 GTGGACCATCGCCAGGATCCATTTTGAGGATTATGGGTGAGCTGCTGCCCCACACACTCC
|
|
600 ------------------------------------------------------------
|
|
NR_046654 118 ------------------------------------------------------------
|
|
|
|
chr3 42531555 CCCGGCCGCCATCACTTGGGCAGGCCCCCTGGGTGGGATGATAATGCCATCTGGCCTTGG
|
|
660 ------------------------------------------------------------
|
|
NR_046654 118 ------------------------------------------------------------
|
|
|
|
chr3 42531615 TGAGTGGACAAAAACCACAGCTCTCGGGCCAGAGGGGAGGCTGGAGGAGGACCTGGGGAG
|
|
720 ------------------------------------------------------------
|
|
NR_046654 118 ------------------------------------------------------------
|
|
|
|
chr3 42531675 CAACAGACTCTGGGCCCGGGGTTGCTAAAGTGCTCAGGAGCAGAGCTGGGGACAACTGGG
|
|
780 ------------------------------------------------------------
|
|
NR_046654 118 ------------------------------------------------------------
|
|
|
|
chr3 42531735 GGAGGTGCTGCTGAGTCTCTCTCTGGCTGAGGACAATCCCTCTCATTCCTCCCCACGGTC
|
|
840 ------------------------------------------------------------
|
|
NR_046654 118 ------------------------------------------------------------
|
|
|
|
chr3 42531795 TGCTCAGGTGCTGGGACACCATCAACTCCTCACTGTGGTGGATCATAAAGGGCCCCATCC
|
|
900 ------------------------------------------------------------
|
|
NR_046654 118 ------------------------------------------------------------
|
|
|
|
chr3 42531855 TCACCTCCATCTTGGTAAGATaccctcccaccacctagagatggggaaacaggcccaaag
|
|
960 ------------------------------------------------------------
|
|
NR_046654 118 ------------------------------------------------------------
|
|
|
|
chr3 42531915 ggcaggcaacttagcccaaggtcacatgggaaattagtatctaggtcagaactgaaacgt
|
|
1020 ------------------------------------------------------------
|
|
NR_046654 118 ------------------------------------------------------------
|
|
|
|
chr3 42531975 agcttcctaatgcccaatgcaggatcatccccacccctgtcctaccagTTCTTCCTTGAG
|
|
1080 ---------------------------------------------...||||||||||||
|
|
NR_046654 118 ---------------------------------------------CAGTTCTTCCTTGAG
|
|
|
|
chr3 42532035 CGTAAGCGGATTGGGAGCACAGTCCTTAGGGATTTGAAGGAGGTAGAGTTCCCGGATGAC
|
|
1140 ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
|
|
NR_046654 103 CGTAAGCGGATTGGGAGCACAGTCCTTAGGGATTTGAAGGAGGTAGAGTTCCCGGATGAC
|
|
|
|
chr3 42532095 CTGCCCAAAGGGGAAATGCCAGAGGAGAGGTAAGATAGAGAGAGGGGCAGCAGGACCCTG
|
|
1200 ------------------------------------------------------------
|
|
NR_046654 43 ------------------------------------------------------------
|
|
|
|
chr3 42532155 GGAAAGAAGACAGGCCAGCAGTCAAGGGGCCTGAACACCTCAGCCTTCCCGCTCTGACTG
|
|
1260 ------------------------------------------------------------
|
|
NR_046654 43 ------------------------------------------------------------
|
|
|
|
chr3 42532215 CCCGAACTCGGGTCCCCACCCACTAGGTAAACTTCATCCTGTTTATTTGCATCATCCGAA
|
|
1320 ------------------------------------------------------------
|
|
NR_046654 43 ------------------------------------------------------------
|
|
|
|
chr3 42532275 TCCTGCTTCAGAAACTGCGGCCCCCAGATATCAGGAAGAGTGACAGCAGTCCATACTCGT
|
|
1380 ------------------------------------------------------------
|
|
NR_046654 43 ------------------------------------------------------------
|
|
|
|
chr3 42532335 GAGTGTGGGCCTAGTGCCTCAGCCCCCAGTACCTCCATCCCCAGTCCTCAAATCATCCCA
|
|
1440 ------------------------------------------------------------
|
|
NR_046654 43 ------------------------------------------------------------
|
|
|
|
chr3 42532395 CATCTCCTTGAAGTCCTCCCACCCCAAACATCCAGAGTCACCAAAGAGCCACATTGTTCT
|
|
1500 ------------------------------------------------------------
|
|
NR_046654 43 ------------------------------------------------------------
|
|
|
|
chr3 42532455 TTCCCACCTCCACCATGGCCTGGCTcagcccaccaccatcccctgctccagccccaccct
|
|
1560 ------------------------------------------------------------
|
|
NR_046654 43 ------------------------------------------------------------
|
|
|
|
chr3 42532515 caCCAGGCTGCACTCAGAGCCCTGCATGCTTCTCCTGCCCACACTCACCTAGCATCCTTC
|
|
1620 ------------------------------------------------||||||||||||
|
|
NR_046654 43 ------------------------------------------------CTAGCATCCTTC
|
|
|
|
chr3 42532575 CCAGGTATGCATCTGCTGCCAAGCCAGGgag 42532606
|
|
1680 ||||||||||||||||||||||||||||... 1711
|
|
NR_046654 31 CCAGGTATGCATCTGCTGCCAAGCCAGGGAG 0
|
|
""",
|
|
)
|
|
self.assertEqual(
|
|
format(alignment, "bed"),
|
|
"""\
|
|
chr3 42530895 42532606 NR_046654.1 1000 - 42530895 42532606 0 3 63,75,43, 0,1125,1668,
|
|
""",
|
|
)
|
|
counts = alignment.counts()
|
|
self.assertEqual(counts.left_insertions, 0)
|
|
self.assertEqual(counts.left_deletions, 0)
|
|
self.assertEqual(counts.right_insertions, 0)
|
|
self.assertEqual(counts.right_deletions, 0)
|
|
self.assertEqual(counts.internal_insertions, 0)
|
|
self.assertEqual(counts.internal_deletions, 1530)
|
|
self.assertEqual(counts.left_gaps, 0)
|
|
self.assertEqual(counts.right_gaps, 0)
|
|
self.assertEqual(counts.internal_gaps, 1530)
|
|
self.assertEqual(counts.insertions, 0)
|
|
self.assertEqual(counts.deletions, 1530)
|
|
self.assertEqual(counts.gaps, 1530)
|
|
self.assertEqual(counts.aligned, 181)
|
|
self.assertEqual(counts.identities, 175)
|
|
self.assertEqual(counts.mismatches, 6)
|
|
alignment = next(alignments)
|
|
self.assertEqual(alignment.score, 978)
|
|
self.assertEqual(alignment.shape, (2, 1711))
|
|
self.assertLess(alignment.coordinates[0, 0], alignment.coordinates[0, -1])
|
|
self.assertGreater(alignment.coordinates[1, 0], alignment.coordinates[1, -1])
|
|
self.assertEqual(len(alignment), 2)
|
|
self.assertIs(alignment.sequences[0], alignment.target)
|
|
self.assertIs(alignment.sequences[1], alignment.query)
|
|
self.assertEqual(alignment.target.id, "chr3")
|
|
self.assertEqual(alignment.query.id, "NR_046654.1_modified")
|
|
self.assertTrue(
|
|
np.array_equal(
|
|
alignment.coordinates,
|
|
# fmt: off
|
|
np.array([[42530895, 42530922, 42530958, 42532020, 42532037,
|
|
42532039, 42532095, 42532563, 42532606],
|
|
[ 179, 152, 116, 116, 99,
|
|
99, 43, 43, 0]])
|
|
# fmt: on
|
|
)
|
|
)
|
|
self.assertEqual(
|
|
str(alignment),
|
|
"""\
|
|
chr3 42530895 ????????????????????????????????????????????????????????????
|
|
0 ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
|
|
NR_046654 179 ????????????????????????????????????????????????????????????
|
|
|
|
chr3 42530955 ????????????????????????????????????????????????????????????
|
|
60 |||---------------------------------------------------------
|
|
NR_046654 119 ???---------------------------------------------------------
|
|
|
|
chr3 42531015 ????????????????????????????????????????????????????????????
|
|
120 ------------------------------------------------------------
|
|
NR_046654 116 ------------------------------------------------------------
|
|
|
|
chr3 42531075 ????????????????????????????????????????????????????????????
|
|
180 ------------------------------------------------------------
|
|
NR_046654 116 ------------------------------------------------------------
|
|
|
|
chr3 42531135 ????????????????????????????????????????????????????????????
|
|
240 ------------------------------------------------------------
|
|
NR_046654 116 ------------------------------------------------------------
|
|
|
|
chr3 42531195 ????????????????????????????????????????????????????????????
|
|
300 ------------------------------------------------------------
|
|
NR_046654 116 ------------------------------------------------------------
|
|
|
|
chr3 42531255 ????????????????????????????????????????????????????????????
|
|
360 ------------------------------------------------------------
|
|
NR_046654 116 ------------------------------------------------------------
|
|
|
|
chr3 42531315 ????????????????????????????????????????????????????????????
|
|
420 ------------------------------------------------------------
|
|
NR_046654 116 ------------------------------------------------------------
|
|
|
|
chr3 42531375 ????????????????????????????????????????????????????????????
|
|
480 ------------------------------------------------------------
|
|
NR_046654 116 ------------------------------------------------------------
|
|
|
|
chr3 42531435 ????????????????????????????????????????????????????????????
|
|
540 ------------------------------------------------------------
|
|
NR_046654 116 ------------------------------------------------------------
|
|
|
|
chr3 42531495 ????????????????????????????????????????????????????????????
|
|
600 ------------------------------------------------------------
|
|
NR_046654 116 ------------------------------------------------------------
|
|
|
|
chr3 42531555 ????????????????????????????????????????????????????????????
|
|
660 ------------------------------------------------------------
|
|
NR_046654 116 ------------------------------------------------------------
|
|
|
|
chr3 42531615 ????????????????????????????????????????????????????????????
|
|
720 ------------------------------------------------------------
|
|
NR_046654 116 ------------------------------------------------------------
|
|
|
|
chr3 42531675 ????????????????????????????????????????????????????????????
|
|
780 ------------------------------------------------------------
|
|
NR_046654 116 ------------------------------------------------------------
|
|
|
|
chr3 42531735 ????????????????????????????????????????????????????????????
|
|
840 ------------------------------------------------------------
|
|
NR_046654 116 ------------------------------------------------------------
|
|
|
|
chr3 42531795 ????????????????????????????????????????????????????????????
|
|
900 ------------------------------------------------------------
|
|
NR_046654 116 ------------------------------------------------------------
|
|
|
|
chr3 42531855 ????????????????????????????????????????????????????????????
|
|
960 ------------------------------------------------------------
|
|
NR_046654 116 ------------------------------------------------------------
|
|
|
|
chr3 42531915 ????????????????????????????????????????????????????????????
|
|
1020 ------------------------------------------------------------
|
|
NR_046654 116 ------------------------------------------------------------
|
|
|
|
chr3 42531975 ????????????????????????????????????????????????????????????
|
|
1080 ---------------------------------------------|||||||||||||||
|
|
NR_046654 116 ---------------------------------------------???????????????
|
|
|
|
chr3 42532035 ????????????????????????????????????????????????????????????
|
|
1140 ||--||||||||||||||||||||||||||||||||||||||||||||||||||||||||
|
|
NR_046654 101 ??--????????????????????????????????????????????????????????
|
|
|
|
chr3 42532095 ????????????????????????????????????????????????????????????
|
|
1200 ------------------------------------------------------------
|
|
NR_046654 43 ------------------------------------------------------------
|
|
|
|
chr3 42532155 ????????????????????????????????????????????????????????????
|
|
1260 ------------------------------------------------------------
|
|
NR_046654 43 ------------------------------------------------------------
|
|
|
|
chr3 42532215 ????????????????????????????????????????????????????????????
|
|
1320 ------------------------------------------------------------
|
|
NR_046654 43 ------------------------------------------------------------
|
|
|
|
chr3 42532275 ????????????????????????????????????????????????????????????
|
|
1380 ------------------------------------------------------------
|
|
NR_046654 43 ------------------------------------------------------------
|
|
|
|
chr3 42532335 ????????????????????????????????????????????????????????????
|
|
1440 ------------------------------------------------------------
|
|
NR_046654 43 ------------------------------------------------------------
|
|
|
|
chr3 42532395 ????????????????????????????????????????????????????????????
|
|
1500 ------------------------------------------------------------
|
|
NR_046654 43 ------------------------------------------------------------
|
|
|
|
chr3 42532455 ????????????????????????????????????????????????????????????
|
|
1560 ------------------------------------------------------------
|
|
NR_046654 43 ------------------------------------------------------------
|
|
|
|
chr3 42532515 ????????????????????????????????????????????????????????????
|
|
1620 ------------------------------------------------||||||||||||
|
|
NR_046654 43 ------------------------------------------------????????????
|
|
|
|
chr3 42532575 ??????????????????????????????? 42532606
|
|
1680 ||||||||||||||||||||||||||||||| 1711
|
|
NR_046654 31 ??????????????????????????????? 0
|
|
""",
|
|
)
|
|
self.assertEqual(
|
|
format(alignment, "bed"),
|
|
"""\
|
|
chr3 42530895 42532606 NR_046654.1_modified 978 - 42530895 42532606 0 5 27,36,17,56,43, 0,27,1125,1144,1668,
|
|
""",
|
|
)
|
|
counts = alignment.counts()
|
|
self.assertEqual(counts.left_insertions, 0)
|
|
self.assertEqual(counts.left_deletions, 0)
|
|
self.assertEqual(counts.right_insertions, 0)
|
|
self.assertEqual(counts.right_deletions, 0)
|
|
self.assertEqual(counts.internal_insertions, 0)
|
|
self.assertEqual(counts.internal_deletions, 1532)
|
|
self.assertEqual(counts.left_gaps, 0)
|
|
self.assertEqual(counts.right_gaps, 0)
|
|
self.assertEqual(counts.internal_gaps, 1532)
|
|
self.assertEqual(counts.insertions, 0)
|
|
self.assertEqual(counts.deletions, 1532)
|
|
self.assertEqual(counts.gaps, 1532)
|
|
self.assertEqual(counts.aligned, 179)
|
|
alignment = next(alignments)
|
|
self.assertEqual(alignment.score, 1000)
|
|
self.assertEqual(alignment.shape, (2, 5407))
|
|
self.assertLess(alignment.coordinates[0, 0], alignment.coordinates[0, -1])
|
|
self.assertLess(alignment.coordinates[1, 0], alignment.coordinates[1, -1])
|
|
self.assertEqual(len(alignment), 2)
|
|
self.assertIs(alignment.sequences[0], alignment.target)
|
|
self.assertIs(alignment.sequences[1], alignment.query)
|
|
self.assertEqual(alignment.target.id, "chr3")
|
|
self.assertEqual(alignment.query.id, "NR_111921.1")
|
|
self.assertTrue(
|
|
np.array_equal(
|
|
alignment.coordinates,
|
|
# fmt: off
|
|
np.array([[48663767, 48663813, 48665640,
|
|
48665722, 48669098, 48669174],
|
|
[ 0, 46, 46,
|
|
128, 128, 204]])
|
|
# fmt: on
|
|
)
|
|
)
|
|
alignment.target.seq = self.dna
|
|
alignment.query.seq = self.rna[alignment.query.id]
|
|
self.assertTrue(
|
|
np.array_equal(
|
|
alignment.substitutions,
|
|
# fmt: off
|
|
np.array([[53., 0., 0., 0., 0., 0., 0., 0.],
|
|
[ 0., 35., 0., 0., 0., 0., 0., 0.],
|
|
[ 0., 0., 50., 0., 0., 0., 0., 0.],
|
|
[ 0., 0., 0., 27., 0., 0., 0., 0.],
|
|
[ 9., 0., 0., 0., 0., 0., 0., 0.],
|
|
[ 0., 7., 0., 0., 0., 0., 0., 0.],
|
|
[ 0., 0., 16., 0., 0., 0., 0., 0.],
|
|
[ 0., 0., 0., 7., 0., 0., 0., 0.],
|
|
])
|
|
)
|
|
)
|
|
self.assertEqual(alignment.substitutions.alphabet, "ACGTacgt")
|
|
self.assertEqual(
|
|
str(alignment),
|
|
"""\
|
|
chr3 48663767 CACGAGAGGAGCGGAGGCGAGGGGTGAACGCGGAGCACTCCAATCGGTCAGTCATTGTTT
|
|
0 ||||||||||||||||||||||||||||||||||||||||||||||--------------
|
|
NR_111921 0 CACGAGAGGAGCGGAGGCGAGGGGTGAACGCGGAGCACTCCAATCG--------------
|
|
|
|
chr3 48663827 CTATTGGCACAATGGGAGGCCCCGCCCCTCACGGCGGACTCATCGCATGGGGGAGGGGGC
|
|
60 ------------------------------------------------------------
|
|
NR_111921 46 ------------------------------------------------------------
|
|
|
|
chr3 48663887 TCCGCGGGTTGCCGGCTAACCGTGAGAGAGTCCGGGAGGTACACTATACGGACCGGCCTC
|
|
120 ------------------------------------------------------------
|
|
NR_111921 46 ------------------------------------------------------------
|
|
|
|
chr3 48663947 CAAAGGCGGAATCGATAACGAGCTGCAGCGCCGGGTGCAGAGGACGCGGGCATCCCGAAG
|
|
180 ------------------------------------------------------------
|
|
NR_111921 46 ------------------------------------------------------------
|
|
|
|
chr3 48664007 CCCAGGAAGAGGTCAGGGCCGGGACCCCAGAACGCTCCACAGGGTGCGGCTCCCGCGATG
|
|
240 ------------------------------------------------------------
|
|
NR_111921 46 ------------------------------------------------------------
|
|
|
|
chr3 48664067 GGGTGGATCCTGGTTCTAACAGGCGAGGAACTCCTGGCCAAGGCCTCTGGCCCGCCCCGA
|
|
300 ------------------------------------------------------------
|
|
NR_111921 46 ------------------------------------------------------------
|
|
|
|
chr3 48664127 ACGGTCCCTATGACATCACCATCAACCAATCAGTCGGCGCATCCTTTCGCCCCTTGACTG
|
|
360 ------------------------------------------------------------
|
|
NR_111921 46 ------------------------------------------------------------
|
|
|
|
chr3 48664187 CTCCGCTTCCGGGAGGCGGGGCTTCTGCGGGTTCCACCTCCCGAGCGCCCCTTGTGGCTA
|
|
420 ------------------------------------------------------------
|
|
NR_111921 46 ------------------------------------------------------------
|
|
|
|
chr3 48664247 CCAAGGTCAGGCAACAGGTGTCCAGTTGTTCCCTCTCCTGTCTACGAATCTGAGGACCTC
|
|
480 ------------------------------------------------------------
|
|
NR_111921 46 ------------------------------------------------------------
|
|
|
|
chr3 48664307 CCCAGGATCAGAGCTCTGGGCCTGATACACGGCCGGGGTTCCTACGGGTTTGTGAGTGGG
|
|
540 ------------------------------------------------------------
|
|
NR_111921 46 ------------------------------------------------------------
|
|
|
|
chr3 48664367 GGTGGAAGATCTGCAGAGGCACTTAGGGCTGAACTCCTTTGAATGGGAGCCAATCGGTGC
|
|
600 ------------------------------------------------------------
|
|
NR_111921 46 ------------------------------------------------------------
|
|
|
|
chr3 48664427 AGGGGCTGGAGGAGCGAGTCCCCCAAAGTAGttttatttatctatttagagacaaggtct
|
|
660 ------------------------------------------------------------
|
|
NR_111921 46 ------------------------------------------------------------
|
|
|
|
chr3 48664487 cactctttcggagtgcagtggtgatcacagctcaccgtagcctcgaactccccaggcgat
|
|
720 ------------------------------------------------------------
|
|
NR_111921 46 ------------------------------------------------------------
|
|
|
|
chr3 48664547 tctctcacctcagcctcccgagtagctgggactacgggtacatgtcatcacacttggcta
|
|
780 ------------------------------------------------------------
|
|
NR_111921 46 ------------------------------------------------------------
|
|
|
|
chr3 48664607 atttttgcattttttatagagacagggtctcaccatgtaggccagattagtcttgaactc
|
|
840 ------------------------------------------------------------
|
|
NR_111921 46 ------------------------------------------------------------
|
|
|
|
chr3 48664667 ctgggctcaagcaatccgcccatcttggcctcccaaagtgctgggattataggtgtgagc
|
|
900 ------------------------------------------------------------
|
|
NR_111921 46 ------------------------------------------------------------
|
|
|
|
chr3 48664727 caccgcgcccggcAACCCAGAAGTGGTTTTGACAGCAccagcgctttctgtgtccacaat
|
|
960 ------------------------------------------------------------
|
|
NR_111921 46 ------------------------------------------------------------
|
|
|
|
chr3 48664787 ctagtgagtagagggcacaaaacctgacaccacggaggcagacaggcaggggctctgccg
|
|
1020 ------------------------------------------------------------
|
|
NR_111921 46 ------------------------------------------------------------
|
|
|
|
chr3 48664847 gggaagggtgttggagtcccaaaggaggcgtctgagtcaccttcgcaacctgggacgcct
|
|
1080 ------------------------------------------------------------
|
|
NR_111921 46 ------------------------------------------------------------
|
|
|
|
chr3 48664907 tcttgcataagatgcctgagcagtgccttgaatgaccaaggggagatccgcatctgcaaa
|
|
1140 ------------------------------------------------------------
|
|
NR_111921 46 ------------------------------------------------------------
|
|
|
|
chr3 48664967 ggaagggcagggagggatagggattgggggtgggcatcctaggtcttggagactgtgtgg
|
|
1200 ------------------------------------------------------------
|
|
NR_111921 46 ------------------------------------------------------------
|
|
|
|
chr3 48665027 gcaaatgtgcagagacataaagggactatggctgagggaaatcaagCCCTGCCCTCTCAC
|
|
1260 ------------------------------------------------------------
|
|
NR_111921 46 ------------------------------------------------------------
|
|
|
|
chr3 48665087 CAATAGGGCTGGCGCTGGTCCCAGCTAACACTCCTTTTGGAGAGCAAAGCTCCTCACTTC
|
|
1320 ------------------------------------------------------------
|
|
NR_111921 46 ------------------------------------------------------------
|
|
|
|
chr3 48665147 TGAGTAGTGAGATTGATTGCGGATCACTCTCCATGTTGCTGCCTGCTGTGTGTCATCCCA
|
|
1380 ------------------------------------------------------------
|
|
NR_111921 46 ------------------------------------------------------------
|
|
|
|
chr3 48665207 CTGTCATCCTCCCTTTGTGGCTGTTCTGTGGAGCCCCTCTCCCTCAATCTGCACTCACCT
|
|
1440 ------------------------------------------------------------
|
|
NR_111921 46 ------------------------------------------------------------
|
|
|
|
chr3 48665267 CTATGCCCCAGCCCCATTGGCAGCTCCTAATGCACTCCCGGTaaaaaaaaaaaaacaaaa
|
|
1500 ------------------------------------------------------------
|
|
NR_111921 46 ------------------------------------------------------------
|
|
|
|
chr3 48665327 aCCAGATGTTAGTGATAGTGGTGGTAGTTCTTCTCTCCACCTCCAAATCTTGCCCTTGCC
|
|
1560 ------------------------------------------------------------
|
|
NR_111921 46 ------------------------------------------------------------
|
|
|
|
chr3 48665387 TCCTAATAAGACCCCTATGTGGTTTAACCTCAttttttttttttttttttttttttgaga
|
|
1620 ------------------------------------------------------------
|
|
NR_111921 46 ------------------------------------------------------------
|
|
|
|
chr3 48665447 tggagtttcactctgtcacccaggctggagtgaagtggtgtgatGGGGCTTCACCATGTg
|
|
1680 ------------------------------------------------------------
|
|
NR_111921 46 ------------------------------------------------------------
|
|
|
|
chr3 48665507 atggggcttcaccatgttggccaggctggtatcaaactcctgacctctagtgatctgccc
|
|
1740 ------------------------------------------------------------
|
|
NR_111921 46 ------------------------------------------------------------
|
|
|
|
chr3 48665567 gcctcagcctcccaaagtgctgggattaccggcatgaggcaccgtgcccagccTATCCTC
|
|
1800 ------------------------------------------------------------
|
|
NR_111921 46 ------------------------------------------------------------
|
|
|
|
chr3 48665627 CTTCTCTTATCAGCTCCCAACTAGAGGTCCACCCAGGACCCAGAGACCTGGATTTGAGGC
|
|
1860 -------------|||||||||||||||||||||||||||||||||||||||||||||||
|
|
NR_111921 46 -------------CTCCCAACTAGAGGTCCACCCAGGACCCAGAGACCTGGATTTGAGGC
|
|
|
|
chr3 48665687 TGCTGGGCGGCAGATGGAGCGATCAGAAGACCAGGGTAAGGGTGTGGCAGATACTGCCAC
|
|
1920 |||||||||||||||||||||||||||||||||||-------------------------
|
|
NR_111921 93 TGCTGGGCGGCAGATGGAGCGATCAGAAGACCAGG-------------------------
|
|
|
|
chr3 48665747 TAACACTTCTCAGCCTTTCCTTCTCCTGCCTTTTCCACCCCACCCTGTGTTTGTCTACTC
|
|
1980 ------------------------------------------------------------
|
|
NR_111921 128 ------------------------------------------------------------
|
|
|
|
chr3 48665807 CCAGCCAGGTGTACCTTTCCAGGGGAAGACCTGGCCAACCTGTCCAGCTCAATTAtccag
|
|
2040 ------------------------------------------------------------
|
|
NR_111921 128 ------------------------------------------------------------
|
|
|
|
chr3 48665867 cagttctttgacctcactgagatctcgagtccattgttcatcacctcagctattgacctg
|
|
2100 ------------------------------------------------------------
|
|
NR_111921 128 ------------------------------------------------------------
|
|
|
|
chr3 48665927 tgtcattagccttatagagttcagtgccacggaaactccctgccctgttctttttctttt
|
|
2160 ------------------------------------------------------------
|
|
NR_111921 128 ------------------------------------------------------------
|
|
|
|
chr3 48665987 tctttttttttttttttttgagacagagccttgctctgtcgcccaggctggagtgcagtg
|
|
2220 ------------------------------------------------------------
|
|
NR_111921 128 ------------------------------------------------------------
|
|
|
|
chr3 48666047 gcgcgatctcggctcactgcaagctctgcctcccaggttcacaccattctcctgactcag
|
|
2280 ------------------------------------------------------------
|
|
NR_111921 128 ------------------------------------------------------------
|
|
|
|
chr3 48666107 cctcccgagtagctgggactacaggcgtccaccaccatgcccagctaatttttttttttg
|
|
2340 ------------------------------------------------------------
|
|
NR_111921 128 ------------------------------------------------------------
|
|
|
|
chr3 48666167 tatttttagtagagacggcgtttcaccgtgttagccaggctggtctcgatctcctgacct
|
|
2400 ------------------------------------------------------------
|
|
NR_111921 128 ------------------------------------------------------------
|
|
|
|
chr3 48666227 tgtgatgctcccgcctcggcctcccaaagtgctgggattacaggcatgagccattgtgcc
|
|
2460 ------------------------------------------------------------
|
|
NR_111921 128 ------------------------------------------------------------
|
|
|
|
chr3 48666287 cggcctgccctgttcttcttagacaaacttgctgggctaaaatctaaccccgttaaaata
|
|
2520 ------------------------------------------------------------
|
|
NR_111921 128 ------------------------------------------------------------
|
|
|
|
chr3 48666347 gactatttacgtattgtttgcctctagcgcagcagaacattgctggagaaaaacaaacaa
|
|
2580 ------------------------------------------------------------
|
|
NR_111921 128 ------------------------------------------------------------
|
|
|
|
chr3 48666407 ccgtgctaattggtctcattttatattcatgaccacaagcctcagtattatatcggaggg
|
|
2640 ------------------------------------------------------------
|
|
NR_111921 128 ------------------------------------------------------------
|
|
|
|
chr3 48666467 cctatccagtgcagtagggcaagaaaaataataagttatgaagattggaagggaaaaaaa
|
|
2700 ------------------------------------------------------------
|
|
NR_111921 128 ------------------------------------------------------------
|
|
|
|
chr3 48666527 actaattcacaagcagtaggattgtatatgtaaaaatttcaaaggaacctataggtaagt
|
|
2760 ------------------------------------------------------------
|
|
NR_111921 128 ------------------------------------------------------------
|
|
|
|
chr3 48666587 tgttagaatgagttcagcaaagttgttggacacaagatcaatatataaaaatcagttgca
|
|
2820 ------------------------------------------------------------
|
|
NR_111921 128 ------------------------------------------------------------
|
|
|
|
chr3 48666647 atttctatatgtcaccaacagttagaaaataaatttcttgcctgggcatgttggctcaag
|
|
2880 ------------------------------------------------------------
|
|
NR_111921 128 ------------------------------------------------------------
|
|
|
|
chr3 48666707 cctgtaatcccagcactttgggtggccaaggcgggcagatcacctgaggtcaggagtttg
|
|
2940 ------------------------------------------------------------
|
|
NR_111921 128 ------------------------------------------------------------
|
|
|
|
chr3 48666767 agaccagtttggccaacatggtgaaatcccgtctctactaaaaatacagaaattagccgg
|
|
3000 ------------------------------------------------------------
|
|
NR_111921 128 ------------------------------------------------------------
|
|
|
|
chr3 48666827 gcgtggtggtgggcacctgtagtcccagctactgaggaggctgaggcaggagaatcactt
|
|
3060 ------------------------------------------------------------
|
|
NR_111921 128 ------------------------------------------------------------
|
|
|
|
chr3 48666887 gaacctgggaggcagaggttgcagtgaacgagaaaaaaaaattttttttcttaaaaacaa
|
|
3120 ------------------------------------------------------------
|
|
NR_111921 128 ------------------------------------------------------------
|
|
|
|
chr3 48666947 tgatgtttacaatagcatcaagtaatatcaaatgctgaggaataaacctaatgaaagatg
|
|
3180 ------------------------------------------------------------
|
|
NR_111921 128 ------------------------------------------------------------
|
|
|
|
chr3 48667007 tgcaaagactacatacacacatacaaaaaaactataaaacattattgagggaaataaaga
|
|
3240 ------------------------------------------------------------
|
|
NR_111921 128 ------------------------------------------------------------
|
|
|
|
chr3 48667067 cataggcctggcattggtggctcatgcctgaaatctcagcactttggagggccaaggtgg
|
|
3300 ------------------------------------------------------------
|
|
NR_111921 128 ------------------------------------------------------------
|
|
|
|
chr3 48667127 gtggatcatttgaggtcaggagttagagatcagtccggccaacatggtgaaacctcatct
|
|
3360 ------------------------------------------------------------
|
|
NR_111921 128 ------------------------------------------------------------
|
|
|
|
chr3 48667187 ctactaaaaatacaaaaaaattagcttggccaggtgcagtggctcacacctgtaatccca
|
|
3420 ------------------------------------------------------------
|
|
NR_111921 128 ------------------------------------------------------------
|
|
|
|
chr3 48667247 gcactttgggaggctgaggcgggcggatcatgaggtcaggagatcgagaccatcctggct
|
|
3480 ------------------------------------------------------------
|
|
NR_111921 128 ------------------------------------------------------------
|
|
|
|
chr3 48667307 aacacggtgaaaccctgtctctactaaaaatacaaaaaaaaattagccgggcctgatggc
|
|
3540 ------------------------------------------------------------
|
|
NR_111921 128 ------------------------------------------------------------
|
|
|
|
chr3 48667367 gggcgcccgtagtcccagctactcgggaggctgaggtagcagaatggcgtgaacctggga
|
|
3600 ------------------------------------------------------------
|
|
NR_111921 128 ------------------------------------------------------------
|
|
|
|
chr3 48667427 ggtgcagcttgcagtgagcctaaattgcgccactgcactccagcctgggtaacagagcga
|
|
3660 ------------------------------------------------------------
|
|
NR_111921 128 ------------------------------------------------------------
|
|
|
|
chr3 48667487 gactccgtttcaaaaaaaaaaaaaaaaattagctgggcatgctgttgtgcacctgcaatc
|
|
3720 ------------------------------------------------------------
|
|
NR_111921 128 ------------------------------------------------------------
|
|
|
|
chr3 48667547 ccagctactctggaggatgaggcagaagtgcctgaacctgggacacagaggttgcagtga
|
|
3780 ------------------------------------------------------------
|
|
NR_111921 128 ------------------------------------------------------------
|
|
|
|
chr3 48667607 gccaagatcatgccattgcactccagcctggacaacacagccagacgctatctgaaaaaa
|
|
3840 ------------------------------------------------------------
|
|
NR_111921 128 ------------------------------------------------------------
|
|
|
|
chr3 48667667 aaaaaaaaaaaaaaagtaaaaaaaatgagaaataaagacataaataaagtgaaaaattgt
|
|
3900 ------------------------------------------------------------
|
|
NR_111921 128 ------------------------------------------------------------
|
|
|
|
chr3 48667727 tccaatattggaaaagtcaatattataaaggtgccaattttcccaaattgatatatggat
|
|
3960 ------------------------------------------------------------
|
|
NR_111921 128 ------------------------------------------------------------
|
|
|
|
chr3 48667787 tcgatgcaacttcagttaaaaatcccactaaattttggctgggtgcggtggctcacacct
|
|
4020 ------------------------------------------------------------
|
|
NR_111921 128 ------------------------------------------------------------
|
|
|
|
chr3 48667847 gtaatcccagcactttgggaggctgaggcgggcggatcacaaggtcaggagatcgagacc
|
|
4080 ------------------------------------------------------------
|
|
NR_111921 128 ------------------------------------------------------------
|
|
|
|
chr3 48667907 atcttggctaacatggtgaaaccgtctctactaaaaatacaaaagttagccgggtgtggt
|
|
4140 ------------------------------------------------------------
|
|
NR_111921 128 ------------------------------------------------------------
|
|
|
|
chr3 48667967 ggcgggcacctgtagtcccagctacttgggaggctgagacagaatggcgtgaacctgggg
|
|
4200 ------------------------------------------------------------
|
|
NR_111921 128 ------------------------------------------------------------
|
|
|
|
chr3 48668027 aggcggagcttgcagtgagccaagttgacgccactgcactccagcctgggcgacagagca
|
|
4260 ------------------------------------------------------------
|
|
NR_111921 128 ------------------------------------------------------------
|
|
|
|
chr3 48668087 agactctgtctcaaaaaaaaaaaaaaaaaaaTCCCACTAGATTTTGTGTGTGTGTAAACT
|
|
4320 ------------------------------------------------------------
|
|
NR_111921 128 ------------------------------------------------------------
|
|
|
|
chr3 48668147 GACAAACTAGATTTAGcagcctgagcaacacagcaaaaccccatctctacaaaaaataca
|
|
4380 ------------------------------------------------------------
|
|
NR_111921 128 ------------------------------------------------------------
|
|
|
|
chr3 48668207 aaaattttgcacatgcctgtatagtcccagctacttgggaggctgaagtgggaggatcat
|
|
4440 ------------------------------------------------------------
|
|
NR_111921 128 ------------------------------------------------------------
|
|
|
|
chr3 48668267 gtgagctctggggaggtcgaggctgtagtgagctatgatcacatgctgcactctagcctg
|
|
4500 ------------------------------------------------------------
|
|
NR_111921 128 ------------------------------------------------------------
|
|
|
|
chr3 48668327 ggcaacagagcaagagaccctgtatctaaaaaaagaatgaaaattaaaaaataaaaaGAa
|
|
4560 ------------------------------------------------------------
|
|
NR_111921 128 ------------------------------------------------------------
|
|
|
|
chr3 48668387 accaagattgtgtggtactggtacgaggataggaagactaaaggaacgaaatccagagac
|
|
4620 ------------------------------------------------------------
|
|
NR_111921 128 ------------------------------------------------------------
|
|
|
|
chr3 48668447 aggcctgaagatgtgtggaaacttgaattttgacaagggtgGTTCTTCAGAGCTAACATG
|
|
4680 ------------------------------------------------------------
|
|
NR_111921 128 ------------------------------------------------------------
|
|
|
|
chr3 48668507 AAGAAAGGGTTGTTTTCTTTTTTTTGTTTCCCcaggagcaactctattaactgaaagaat
|
|
4740 ------------------------------------------------------------
|
|
NR_111921 128 ------------------------------------------------------------
|
|
|
|
chr3 48668567 aggcttttcaataaatgatgctgggtcagttggatatccatatagaaaaaattaaatgag
|
|
4800 ------------------------------------------------------------
|
|
NR_111921 128 ------------------------------------------------------------
|
|
|
|
chr3 48668627 atctctatttcacactgcttgcataatcaattccatataaatttgacatctgaaaatata
|
|
4860 ------------------------------------------------------------
|
|
NR_111921 128 ------------------------------------------------------------
|
|
|
|
chr3 48668687 cagtttctagaaaacagtatTAAGACCttgttttgttttttgttgttgttgttttttgtt
|
|
4920 ------------------------------------------------------------
|
|
NR_111921 128 ------------------------------------------------------------
|
|
|
|
chr3 48668747 ttgttttttgttttttgagacagagtctcgctctgtcgccaggctggaatacagtggtgc
|
|
4980 ------------------------------------------------------------
|
|
NR_111921 128 ------------------------------------------------------------
|
|
|
|
chr3 48668807 aaccttggctcactgcaacctctgactccctagttcaagcaattctcctgcctcagcctc
|
|
5040 ------------------------------------------------------------
|
|
NR_111921 128 ------------------------------------------------------------
|
|
|
|
chr3 48668867 ccgagtagctgcgattacaggcacatgccaccacgcccagctaatttttgtatttttagt
|
|
5100 ------------------------------------------------------------
|
|
NR_111921 128 ------------------------------------------------------------
|
|
|
|
chr3 48668927 agagatgggggtttcaccatgttggccaggatggtctcgatctcctgaccctgtaatccg
|
|
5160 ------------------------------------------------------------
|
|
NR_111921 128 ------------------------------------------------------------
|
|
|
|
chr3 48668987 cccacctcggcctcccaaagtgctgggattacaggcgtgagccactgcacctggccAAGA
|
|
5220 ------------------------------------------------------------
|
|
NR_111921 128 ------------------------------------------------------------
|
|
|
|
chr3 48669047 GAAGATCTTAAAGGTGACTTTAAGCAAACttttttttttttttttttacagagacgggag
|
|
5280 ---------------------------------------------------.........
|
|
NR_111921 128 ---------------------------------------------------AGACGGGAG
|
|
|
|
chr3 48669107 ctggagtgcagtggctgttcacaagcgtgaAAGCAAAGATTAAAAAATTTGTTTTTATAT
|
|
5340 ..............................||||||||||||||||||||||||||||||
|
|
NR_111921 137 CTGGAGTGCAGTGGCTGTTCACAAGCGTGAAAGCAAAGATTAAAAAATTTGTTTTTATAT
|
|
|
|
chr3 48669167 TAAAAAA 48669174
|
|
5400 ||||||| 5407
|
|
NR_111921 197 TAAAAAA 204
|
|
""",
|
|
)
|
|
self.assertEqual(
|
|
format(alignment, "bed"),
|
|
"""\
|
|
chr3 48663767 48669174 NR_111921.1 1000 + 48663767 48669174 0 3 46,82,76, 0,1873,5331,
|
|
""",
|
|
)
|
|
counts = alignment.counts()
|
|
self.assertEqual(counts.left_insertions, 0)
|
|
self.assertEqual(counts.left_deletions, 0)
|
|
self.assertEqual(counts.right_insertions, 0)
|
|
self.assertEqual(counts.right_deletions, 0)
|
|
self.assertEqual(counts.internal_insertions, 0)
|
|
self.assertEqual(counts.internal_deletions, 5203)
|
|
self.assertEqual(counts.left_gaps, 0)
|
|
self.assertEqual(counts.right_gaps, 0)
|
|
self.assertEqual(counts.internal_gaps, 5203)
|
|
self.assertEqual(counts.insertions, 0)
|
|
self.assertEqual(counts.deletions, 5203)
|
|
self.assertEqual(counts.gaps, 5203)
|
|
self.assertEqual(counts.aligned, 204)
|
|
self.assertEqual(counts.identities, 165)
|
|
self.assertEqual(counts.mismatches, 39)
|
|
alignment = next(alignments)
|
|
self.assertEqual(alignment.score, 972)
|
|
self.assertEqual(alignment.shape, (2, 5407))
|
|
self.assertLess(alignment.coordinates[0, 0], alignment.coordinates[0, -1])
|
|
self.assertLess(alignment.coordinates[1, 0], alignment.coordinates[1, -1])
|
|
self.assertEqual(len(alignment), 2)
|
|
self.assertIs(alignment.sequences[0], alignment.target)
|
|
self.assertIs(alignment.sequences[1], alignment.query)
|
|
self.assertEqual(alignment.target.id, "chr3")
|
|
self.assertEqual(alignment.query.id, "NR_111921.1_modified")
|
|
self.assertTrue(
|
|
np.array_equal(
|
|
alignment.coordinates,
|
|
# fmt: off
|
|
np.array([[48663767, 48663795, 48663796, 48663813, 48665640,
|
|
48665716, 48665722, 48669098, 48669174],
|
|
[ 0, 28, 28, 45, 45,
|
|
121, 127, 127, 203]])
|
|
# fmt: on
|
|
)
|
|
)
|
|
# The modified RNAs have gaps in their sequence. As this information is
|
|
# not stored in a BED file, we cannot calculate the substitution matrix.
|
|
self.assertEqual(
|
|
str(alignment),
|
|
"""\
|
|
chr3 48663767 ????????????????????????????????????????????????????????????
|
|
0 ||||||||||||||||||||||||||||-|||||||||||||||||--------------
|
|
NR_111921 0 ????????????????????????????-?????????????????--------------
|
|
|
|
chr3 48663827 ????????????????????????????????????????????????????????????
|
|
60 ------------------------------------------------------------
|
|
NR_111921 45 ------------------------------------------------------------
|
|
|
|
chr3 48663887 ????????????????????????????????????????????????????????????
|
|
120 ------------------------------------------------------------
|
|
NR_111921 45 ------------------------------------------------------------
|
|
|
|
chr3 48663947 ????????????????????????????????????????????????????????????
|
|
180 ------------------------------------------------------------
|
|
NR_111921 45 ------------------------------------------------------------
|
|
|
|
chr3 48664007 ????????????????????????????????????????????????????????????
|
|
240 ------------------------------------------------------------
|
|
NR_111921 45 ------------------------------------------------------------
|
|
|
|
chr3 48664067 ????????????????????????????????????????????????????????????
|
|
300 ------------------------------------------------------------
|
|
NR_111921 45 ------------------------------------------------------------
|
|
|
|
chr3 48664127 ????????????????????????????????????????????????????????????
|
|
360 ------------------------------------------------------------
|
|
NR_111921 45 ------------------------------------------------------------
|
|
|
|
chr3 48664187 ????????????????????????????????????????????????????????????
|
|
420 ------------------------------------------------------------
|
|
NR_111921 45 ------------------------------------------------------------
|
|
|
|
chr3 48664247 ????????????????????????????????????????????????????????????
|
|
480 ------------------------------------------------------------
|
|
NR_111921 45 ------------------------------------------------------------
|
|
|
|
chr3 48664307 ????????????????????????????????????????????????????????????
|
|
540 ------------------------------------------------------------
|
|
NR_111921 45 ------------------------------------------------------------
|
|
|
|
chr3 48664367 ????????????????????????????????????????????????????????????
|
|
600 ------------------------------------------------------------
|
|
NR_111921 45 ------------------------------------------------------------
|
|
|
|
chr3 48664427 ????????????????????????????????????????????????????????????
|
|
660 ------------------------------------------------------------
|
|
NR_111921 45 ------------------------------------------------------------
|
|
|
|
chr3 48664487 ????????????????????????????????????????????????????????????
|
|
720 ------------------------------------------------------------
|
|
NR_111921 45 ------------------------------------------------------------
|
|
|
|
chr3 48664547 ????????????????????????????????????????????????????????????
|
|
780 ------------------------------------------------------------
|
|
NR_111921 45 ------------------------------------------------------------
|
|
|
|
chr3 48664607 ????????????????????????????????????????????????????????????
|
|
840 ------------------------------------------------------------
|
|
NR_111921 45 ------------------------------------------------------------
|
|
|
|
chr3 48664667 ????????????????????????????????????????????????????????????
|
|
900 ------------------------------------------------------------
|
|
NR_111921 45 ------------------------------------------------------------
|
|
|
|
chr3 48664727 ????????????????????????????????????????????????????????????
|
|
960 ------------------------------------------------------------
|
|
NR_111921 45 ------------------------------------------------------------
|
|
|
|
chr3 48664787 ????????????????????????????????????????????????????????????
|
|
1020 ------------------------------------------------------------
|
|
NR_111921 45 ------------------------------------------------------------
|
|
|
|
chr3 48664847 ????????????????????????????????????????????????????????????
|
|
1080 ------------------------------------------------------------
|
|
NR_111921 45 ------------------------------------------------------------
|
|
|
|
chr3 48664907 ????????????????????????????????????????????????????????????
|
|
1140 ------------------------------------------------------------
|
|
NR_111921 45 ------------------------------------------------------------
|
|
|
|
chr3 48664967 ????????????????????????????????????????????????????????????
|
|
1200 ------------------------------------------------------------
|
|
NR_111921 45 ------------------------------------------------------------
|
|
|
|
chr3 48665027 ????????????????????????????????????????????????????????????
|
|
1260 ------------------------------------------------------------
|
|
NR_111921 45 ------------------------------------------------------------
|
|
|
|
chr3 48665087 ????????????????????????????????????????????????????????????
|
|
1320 ------------------------------------------------------------
|
|
NR_111921 45 ------------------------------------------------------------
|
|
|
|
chr3 48665147 ????????????????????????????????????????????????????????????
|
|
1380 ------------------------------------------------------------
|
|
NR_111921 45 ------------------------------------------------------------
|
|
|
|
chr3 48665207 ????????????????????????????????????????????????????????????
|
|
1440 ------------------------------------------------------------
|
|
NR_111921 45 ------------------------------------------------------------
|
|
|
|
chr3 48665267 ????????????????????????????????????????????????????????????
|
|
1500 ------------------------------------------------------------
|
|
NR_111921 45 ------------------------------------------------------------
|
|
|
|
chr3 48665327 ????????????????????????????????????????????????????????????
|
|
1560 ------------------------------------------------------------
|
|
NR_111921 45 ------------------------------------------------------------
|
|
|
|
chr3 48665387 ????????????????????????????????????????????????????????????
|
|
1620 ------------------------------------------------------------
|
|
NR_111921 45 ------------------------------------------------------------
|
|
|
|
chr3 48665447 ????????????????????????????????????????????????????????????
|
|
1680 ------------------------------------------------------------
|
|
NR_111921 45 ------------------------------------------------------------
|
|
|
|
chr3 48665507 ????????????????????????????????????????????????????????????
|
|
1740 ------------------------------------------------------------
|
|
NR_111921 45 ------------------------------------------------------------
|
|
|
|
chr3 48665567 ????????????????????????????????????????????????????????????
|
|
1800 ------------------------------------------------------------
|
|
NR_111921 45 ------------------------------------------------------------
|
|
|
|
chr3 48665627 ????????????????????????????????????????????????????????????
|
|
1860 -------------|||||||||||||||||||||||||||||||||||||||||||||||
|
|
NR_111921 45 -------------???????????????????????????????????????????????
|
|
|
|
chr3 48665687 ????????????????????????????????????????????????????????????
|
|
1920 |||||||||||||||||||||||||||||||||||-------------------------
|
|
NR_111921 92 ???????????????????????????????????-------------------------
|
|
|
|
chr3 48665747 ????????????????????????????????????????????????????????????
|
|
1980 ------------------------------------------------------------
|
|
NR_111921 127 ------------------------------------------------------------
|
|
|
|
chr3 48665807 ????????????????????????????????????????????????????????????
|
|
2040 ------------------------------------------------------------
|
|
NR_111921 127 ------------------------------------------------------------
|
|
|
|
chr3 48665867 ????????????????????????????????????????????????????????????
|
|
2100 ------------------------------------------------------------
|
|
NR_111921 127 ------------------------------------------------------------
|
|
|
|
chr3 48665927 ????????????????????????????????????????????????????????????
|
|
2160 ------------------------------------------------------------
|
|
NR_111921 127 ------------------------------------------------------------
|
|
|
|
chr3 48665987 ????????????????????????????????????????????????????????????
|
|
2220 ------------------------------------------------------------
|
|
NR_111921 127 ------------------------------------------------------------
|
|
|
|
chr3 48666047 ????????????????????????????????????????????????????????????
|
|
2280 ------------------------------------------------------------
|
|
NR_111921 127 ------------------------------------------------------------
|
|
|
|
chr3 48666107 ????????????????????????????????????????????????????????????
|
|
2340 ------------------------------------------------------------
|
|
NR_111921 127 ------------------------------------------------------------
|
|
|
|
chr3 48666167 ????????????????????????????????????????????????????????????
|
|
2400 ------------------------------------------------------------
|
|
NR_111921 127 ------------------------------------------------------------
|
|
|
|
chr3 48666227 ????????????????????????????????????????????????????????????
|
|
2460 ------------------------------------------------------------
|
|
NR_111921 127 ------------------------------------------------------------
|
|
|
|
chr3 48666287 ????????????????????????????????????????????????????????????
|
|
2520 ------------------------------------------------------------
|
|
NR_111921 127 ------------------------------------------------------------
|
|
|
|
chr3 48666347 ????????????????????????????????????????????????????????????
|
|
2580 ------------------------------------------------------------
|
|
NR_111921 127 ------------------------------------------------------------
|
|
|
|
chr3 48666407 ????????????????????????????????????????????????????????????
|
|
2640 ------------------------------------------------------------
|
|
NR_111921 127 ------------------------------------------------------------
|
|
|
|
chr3 48666467 ????????????????????????????????????????????????????????????
|
|
2700 ------------------------------------------------------------
|
|
NR_111921 127 ------------------------------------------------------------
|
|
|
|
chr3 48666527 ????????????????????????????????????????????????????????????
|
|
2760 ------------------------------------------------------------
|
|
NR_111921 127 ------------------------------------------------------------
|
|
|
|
chr3 48666587 ????????????????????????????????????????????????????????????
|
|
2820 ------------------------------------------------------------
|
|
NR_111921 127 ------------------------------------------------------------
|
|
|
|
chr3 48666647 ????????????????????????????????????????????????????????????
|
|
2880 ------------------------------------------------------------
|
|
NR_111921 127 ------------------------------------------------------------
|
|
|
|
chr3 48666707 ????????????????????????????????????????????????????????????
|
|
2940 ------------------------------------------------------------
|
|
NR_111921 127 ------------------------------------------------------------
|
|
|
|
chr3 48666767 ????????????????????????????????????????????????????????????
|
|
3000 ------------------------------------------------------------
|
|
NR_111921 127 ------------------------------------------------------------
|
|
|
|
chr3 48666827 ????????????????????????????????????????????????????????????
|
|
3060 ------------------------------------------------------------
|
|
NR_111921 127 ------------------------------------------------------------
|
|
|
|
chr3 48666887 ????????????????????????????????????????????????????????????
|
|
3120 ------------------------------------------------------------
|
|
NR_111921 127 ------------------------------------------------------------
|
|
|
|
chr3 48666947 ????????????????????????????????????????????????????????????
|
|
3180 ------------------------------------------------------------
|
|
NR_111921 127 ------------------------------------------------------------
|
|
|
|
chr3 48667007 ????????????????????????????????????????????????????????????
|
|
3240 ------------------------------------------------------------
|
|
NR_111921 127 ------------------------------------------------------------
|
|
|
|
chr3 48667067 ????????????????????????????????????????????????????????????
|
|
3300 ------------------------------------------------------------
|
|
NR_111921 127 ------------------------------------------------------------
|
|
|
|
chr3 48667127 ????????????????????????????????????????????????????????????
|
|
3360 ------------------------------------------------------------
|
|
NR_111921 127 ------------------------------------------------------------
|
|
|
|
chr3 48667187 ????????????????????????????????????????????????????????????
|
|
3420 ------------------------------------------------------------
|
|
NR_111921 127 ------------------------------------------------------------
|
|
|
|
chr3 48667247 ????????????????????????????????????????????????????????????
|
|
3480 ------------------------------------------------------------
|
|
NR_111921 127 ------------------------------------------------------------
|
|
|
|
chr3 48667307 ????????????????????????????????????????????????????????????
|
|
3540 ------------------------------------------------------------
|
|
NR_111921 127 ------------------------------------------------------------
|
|
|
|
chr3 48667367 ????????????????????????????????????????????????????????????
|
|
3600 ------------------------------------------------------------
|
|
NR_111921 127 ------------------------------------------------------------
|
|
|
|
chr3 48667427 ????????????????????????????????????????????????????????????
|
|
3660 ------------------------------------------------------------
|
|
NR_111921 127 ------------------------------------------------------------
|
|
|
|
chr3 48667487 ????????????????????????????????????????????????????????????
|
|
3720 ------------------------------------------------------------
|
|
NR_111921 127 ------------------------------------------------------------
|
|
|
|
chr3 48667547 ????????????????????????????????????????????????????????????
|
|
3780 ------------------------------------------------------------
|
|
NR_111921 127 ------------------------------------------------------------
|
|
|
|
chr3 48667607 ????????????????????????????????????????????????????????????
|
|
3840 ------------------------------------------------------------
|
|
NR_111921 127 ------------------------------------------------------------
|
|
|
|
chr3 48667667 ????????????????????????????????????????????????????????????
|
|
3900 ------------------------------------------------------------
|
|
NR_111921 127 ------------------------------------------------------------
|
|
|
|
chr3 48667727 ????????????????????????????????????????????????????????????
|
|
3960 ------------------------------------------------------------
|
|
NR_111921 127 ------------------------------------------------------------
|
|
|
|
chr3 48667787 ????????????????????????????????????????????????????????????
|
|
4020 ------------------------------------------------------------
|
|
NR_111921 127 ------------------------------------------------------------
|
|
|
|
chr3 48667847 ????????????????????????????????????????????????????????????
|
|
4080 ------------------------------------------------------------
|
|
NR_111921 127 ------------------------------------------------------------
|
|
|
|
chr3 48667907 ????????????????????????????????????????????????????????????
|
|
4140 ------------------------------------------------------------
|
|
NR_111921 127 ------------------------------------------------------------
|
|
|
|
chr3 48667967 ????????????????????????????????????????????????????????????
|
|
4200 ------------------------------------------------------------
|
|
NR_111921 127 ------------------------------------------------------------
|
|
|
|
chr3 48668027 ????????????????????????????????????????????????????????????
|
|
4260 ------------------------------------------------------------
|
|
NR_111921 127 ------------------------------------------------------------
|
|
|
|
chr3 48668087 ????????????????????????????????????????????????????????????
|
|
4320 ------------------------------------------------------------
|
|
NR_111921 127 ------------------------------------------------------------
|
|
|
|
chr3 48668147 ????????????????????????????????????????????????????????????
|
|
4380 ------------------------------------------------------------
|
|
NR_111921 127 ------------------------------------------------------------
|
|
|
|
chr3 48668207 ????????????????????????????????????????????????????????????
|
|
4440 ------------------------------------------------------------
|
|
NR_111921 127 ------------------------------------------------------------
|
|
|
|
chr3 48668267 ????????????????????????????????????????????????????????????
|
|
4500 ------------------------------------------------------------
|
|
NR_111921 127 ------------------------------------------------------------
|
|
|
|
chr3 48668327 ????????????????????????????????????????????????????????????
|
|
4560 ------------------------------------------------------------
|
|
NR_111921 127 ------------------------------------------------------------
|
|
|
|
chr3 48668387 ????????????????????????????????????????????????????????????
|
|
4620 ------------------------------------------------------------
|
|
NR_111921 127 ------------------------------------------------------------
|
|
|
|
chr3 48668447 ????????????????????????????????????????????????????????????
|
|
4680 ------------------------------------------------------------
|
|
NR_111921 127 ------------------------------------------------------------
|
|
|
|
chr3 48668507 ????????????????????????????????????????????????????????????
|
|
4740 ------------------------------------------------------------
|
|
NR_111921 127 ------------------------------------------------------------
|
|
|
|
chr3 48668567 ????????????????????????????????????????????????????????????
|
|
4800 ------------------------------------------------------------
|
|
NR_111921 127 ------------------------------------------------------------
|
|
|
|
chr3 48668627 ????????????????????????????????????????????????????????????
|
|
4860 ------------------------------------------------------------
|
|
NR_111921 127 ------------------------------------------------------------
|
|
|
|
chr3 48668687 ????????????????????????????????????????????????????????????
|
|
4920 ------------------------------------------------------------
|
|
NR_111921 127 ------------------------------------------------------------
|
|
|
|
chr3 48668747 ????????????????????????????????????????????????????????????
|
|
4980 ------------------------------------------------------------
|
|
NR_111921 127 ------------------------------------------------------------
|
|
|
|
chr3 48668807 ????????????????????????????????????????????????????????????
|
|
5040 ------------------------------------------------------------
|
|
NR_111921 127 ------------------------------------------------------------
|
|
|
|
chr3 48668867 ????????????????????????????????????????????????????????????
|
|
5100 ------------------------------------------------------------
|
|
NR_111921 127 ------------------------------------------------------------
|
|
|
|
chr3 48668927 ????????????????????????????????????????????????????????????
|
|
5160 ------------------------------------------------------------
|
|
NR_111921 127 ------------------------------------------------------------
|
|
|
|
chr3 48668987 ????????????????????????????????????????????????????????????
|
|
5220 ------------------------------------------------------------
|
|
NR_111921 127 ------------------------------------------------------------
|
|
|
|
chr3 48669047 ????????????????????????????????????????????????????????????
|
|
5280 ---------------------------------------------------|||||||||
|
|
NR_111921 127 ---------------------------------------------------?????????
|
|
|
|
chr3 48669107 ????????????????????????????????????????????????????????????
|
|
5340 ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
|
|
NR_111921 136 ????????????????????????????????????????????????????????????
|
|
|
|
chr3 48669167 ??????? 48669174
|
|
5400 ||||||| 5407
|
|
NR_111921 196 ??????? 203
|
|
""",
|
|
)
|
|
self.assertEqual(
|
|
format(alignment, "bed"),
|
|
"""\
|
|
chr3 48663767 48669174 NR_111921.1_modified 972 + 48663767 48669174 0 5 28,17,76,6,76, 0,29,1873,1949,5331,
|
|
""",
|
|
)
|
|
counts = alignment.counts()
|
|
self.assertEqual(counts.left_insertions, 0)
|
|
self.assertEqual(counts.left_deletions, 0)
|
|
self.assertEqual(counts.right_insertions, 0)
|
|
self.assertEqual(counts.right_deletions, 0)
|
|
self.assertEqual(counts.internal_insertions, 0)
|
|
self.assertEqual(counts.internal_deletions, 5204)
|
|
self.assertEqual(counts.left_gaps, 0)
|
|
self.assertEqual(counts.right_gaps, 0)
|
|
self.assertEqual(counts.internal_gaps, 5204)
|
|
self.assertEqual(counts.insertions, 0)
|
|
self.assertEqual(counts.deletions, 5204)
|
|
self.assertEqual(counts.gaps, 5204)
|
|
self.assertEqual(counts.aligned, 203)
|
|
self.assertRaises(StopIteration, next, alignments)
|
|
|
|
def test_reading(self):
|
|
"""Test parsing dna_rna.bed."""
|
|
path = "Blat/dna_rna.bed"
|
|
alignments = Align.parse(path, "bed")
|
|
self.check_alignments(alignments)
|
|
alignments = iter(alignments)
|
|
self.check_alignments(alignments)
|
|
with Align.parse(path, "bed") as alignments:
|
|
self.check_alignments(alignments)
|
|
with self.assertRaises(AttributeError):
|
|
alignments._stream
|
|
with Align.parse(path, "bed") as alignments:
|
|
pass
|
|
with self.assertRaises(AttributeError):
|
|
alignments._stream
|
|
|
|
def test_writing(self):
|
|
"""Test writing the alignments in dna_rna.bed."""
|
|
path = "Blat/dna_rna.bed"
|
|
with open(path) as stream:
|
|
original_data = stream.read()
|
|
alignments = Align.parse(path, "bed")
|
|
stream = StringIO()
|
|
n = Align.write(alignments, stream, "bed")
|
|
self.assertEqual(n, 4)
|
|
stream.seek(0)
|
|
written_data = stream.read()
|
|
stream.close()
|
|
self.assertEqual(original_data, written_data)
|
|
|
|
|
|
class TestAlign_dna(unittest.TestCase):
|
|
def test_reading_psl_34_001(self):
|
|
"""Test parsing psl_34_001.bed."""
|
|
path = "Blat/psl_34_001.bed"
|
|
alignments = Align.parse(path, "bed")
|
|
alignment = next(alignments)
|
|
self.assertEqual(alignment.score, 1000)
|
|
self.assertEqual(alignment.shape, (2, 16))
|
|
self.assertLess(alignment.coordinates[0, 0], alignment.coordinates[0, -1])
|
|
self.assertLess(alignment.coordinates[1, 0], alignment.coordinates[1, -1])
|
|
self.assertEqual(len(alignment), 2)
|
|
self.assertIs(alignment.sequences[0], alignment.target)
|
|
self.assertIs(alignment.sequences[1], alignment.query)
|
|
self.assertEqual(alignment.target.id, "chr4")
|
|
self.assertEqual(alignment.query.id, "hg19_dna")
|
|
self.assertTrue(
|
|
np.array_equal(
|
|
alignment.coordinates,
|
|
# fmt: off
|
|
np.array([[61646095, 61646111],
|
|
[ 0, 16]]),
|
|
# fmt: on
|
|
)
|
|
)
|
|
self.assertEqual(
|
|
str(alignment),
|
|
"""\
|
|
chr4 61646095 ???????????????? 61646111
|
|
0 |||||||||||||||| 16
|
|
hg19_dna 0 ???????????????? 16
|
|
""",
|
|
)
|
|
self.assertEqual(
|
|
format(alignment, "bed"),
|
|
"""\
|
|
chr4 61646095 61646111 hg19_dna 1000 + 61646095 61646111 0 1 16, 0,
|
|
""",
|
|
)
|
|
counts = alignment.counts()
|
|
self.assertEqual(counts.left_insertions, 0)
|
|
self.assertEqual(counts.left_deletions, 0)
|
|
self.assertEqual(counts.right_insertions, 0)
|
|
self.assertEqual(counts.right_deletions, 0)
|
|
self.assertEqual(counts.internal_insertions, 0)
|
|
self.assertEqual(counts.internal_deletions, 0)
|
|
self.assertEqual(counts.left_gaps, 0)
|
|
self.assertEqual(counts.right_gaps, 0)
|
|
self.assertEqual(counts.internal_gaps, 0)
|
|
self.assertEqual(counts.insertions, 0)
|
|
self.assertEqual(counts.deletions, 0)
|
|
self.assertEqual(counts.gaps, 0)
|
|
self.assertEqual(counts.aligned, 16)
|
|
alignment = next(alignments)
|
|
self.assertEqual(alignment.score, 1000)
|
|
self.assertEqual(alignment.shape, (2, 33))
|
|
self.assertLess(alignment.coordinates[0, 0], alignment.coordinates[0, -1])
|
|
self.assertLess(alignment.coordinates[1, 0], alignment.coordinates[1, -1])
|
|
self.assertEqual(len(alignment), 2)
|
|
self.assertIs(alignment.sequences[0], alignment.target)
|
|
self.assertIs(alignment.sequences[1], alignment.query)
|
|
self.assertEqual(alignment.target.id, "chr1")
|
|
self.assertEqual(alignment.query.id, "hg19_dna")
|
|
self.assertTrue(
|
|
np.array_equal(
|
|
alignment.coordinates,
|
|
# fmt: off
|
|
np.array([[10271783, 10271816],
|
|
[ 0, 33]]),
|
|
# fmt: on
|
|
)
|
|
)
|
|
self.assertEqual(
|
|
str(alignment),
|
|
"""\
|
|
chr1 10271783 ????????????????????????????????? 10271816
|
|
0 ||||||||||||||||||||||||||||||||| 33
|
|
hg19_dna 0 ????????????????????????????????? 33
|
|
""",
|
|
)
|
|
self.assertEqual(
|
|
format(alignment, "bed"),
|
|
"""\
|
|
chr1 10271783 10271816 hg19_dna 1000 + 10271783 10271816 0 1 33, 0,
|
|
""",
|
|
)
|
|
counts = alignment.counts()
|
|
self.assertEqual(counts.left_insertions, 0)
|
|
self.assertEqual(counts.left_deletions, 0)
|
|
self.assertEqual(counts.right_insertions, 0)
|
|
self.assertEqual(counts.right_deletions, 0)
|
|
self.assertEqual(counts.internal_insertions, 0)
|
|
self.assertEqual(counts.internal_deletions, 0)
|
|
self.assertEqual(counts.left_gaps, 0)
|
|
self.assertEqual(counts.right_gaps, 0)
|
|
self.assertEqual(counts.internal_gaps, 0)
|
|
self.assertEqual(counts.insertions, 0)
|
|
self.assertEqual(counts.deletions, 0)
|
|
self.assertEqual(counts.gaps, 0)
|
|
self.assertEqual(counts.aligned, 33)
|
|
alignment = next(alignments)
|
|
self.assertEqual(alignment.score, 1000)
|
|
self.assertEqual(alignment.shape, (2, 17))
|
|
self.assertLess(alignment.coordinates[0, 0], alignment.coordinates[0, -1])
|
|
self.assertGreater(alignment.coordinates[1, 0], alignment.coordinates[1, -1])
|
|
self.assertEqual(len(alignment), 2)
|
|
self.assertIs(alignment.sequences[0], alignment.target)
|
|
self.assertIs(alignment.sequences[1], alignment.query)
|
|
self.assertEqual(alignment.target.id, "chr2")
|
|
self.assertEqual(alignment.query.id, "hg19_dna")
|
|
self.assertTrue(
|
|
np.array_equal(
|
|
alignment.coordinates,
|
|
# fmt: off
|
|
np.array([[53575980, 53575997],
|
|
[ 17, 0]]),
|
|
# fmt: on
|
|
)
|
|
)
|
|
self.assertEqual(
|
|
str(alignment),
|
|
"""\
|
|
chr2 53575980 ????????????????? 53575997
|
|
0 ||||||||||||||||| 17
|
|
hg19_dna 17 ????????????????? 0
|
|
""",
|
|
)
|
|
self.assertEqual(
|
|
format(alignment, "bed"),
|
|
"""\
|
|
chr2 53575980 53575997 hg19_dna 1000 - 53575980 53575997 0 1 17, 0,
|
|
""",
|
|
)
|
|
counts = alignment.counts()
|
|
self.assertEqual(counts.left_insertions, 0)
|
|
self.assertEqual(counts.left_deletions, 0)
|
|
self.assertEqual(counts.right_insertions, 0)
|
|
self.assertEqual(counts.right_deletions, 0)
|
|
self.assertEqual(counts.internal_insertions, 0)
|
|
self.assertEqual(counts.internal_deletions, 0)
|
|
self.assertEqual(counts.left_gaps, 0)
|
|
self.assertEqual(counts.right_gaps, 0)
|
|
self.assertEqual(counts.internal_gaps, 0)
|
|
self.assertEqual(counts.insertions, 0)
|
|
self.assertEqual(counts.deletions, 0)
|
|
self.assertEqual(counts.gaps, 0)
|
|
self.assertEqual(counts.aligned, 17)
|
|
alignment = next(alignments)
|
|
self.assertEqual(alignment.score, 854)
|
|
self.assertEqual(alignment.shape, (2, 41))
|
|
self.assertLess(alignment.coordinates[0, 0], alignment.coordinates[0, -1])
|
|
self.assertLess(alignment.coordinates[1, 0], alignment.coordinates[1, -1])
|
|
self.assertEqual(len(alignment), 2)
|
|
self.assertIs(alignment.sequences[0], alignment.target)
|
|
self.assertIs(alignment.sequences[1], alignment.query)
|
|
self.assertEqual(alignment.target.id, "chr9")
|
|
self.assertEqual(alignment.query.id, "hg19_dna")
|
|
self.assertTrue(
|
|
np.array_equal(
|
|
alignment.coordinates,
|
|
# fmt: off
|
|
np.array([[85737865, 85737906],
|
|
[ 0, 41]]),
|
|
# fmt: on
|
|
)
|
|
)
|
|
self.assertEqual(
|
|
str(alignment),
|
|
"""\
|
|
chr9 85737865 ????????????????????????????????????????? 85737906
|
|
0 ||||||||||||||||||||||||||||||||||||||||| 41
|
|
hg19_dna 0 ????????????????????????????????????????? 41
|
|
""",
|
|
)
|
|
self.assertEqual(
|
|
format(alignment, "bed"),
|
|
"""\
|
|
chr9 85737865 85737906 hg19_dna 854 + 85737865 85737906 0 1 41, 0,
|
|
""",
|
|
)
|
|
counts = alignment.counts()
|
|
self.assertEqual(counts.left_insertions, 0)
|
|
self.assertEqual(counts.left_deletions, 0)
|
|
self.assertEqual(counts.right_insertions, 0)
|
|
self.assertEqual(counts.right_deletions, 0)
|
|
self.assertEqual(counts.internal_insertions, 0)
|
|
self.assertEqual(counts.internal_deletions, 0)
|
|
self.assertEqual(counts.left_gaps, 0)
|
|
self.assertEqual(counts.right_gaps, 0)
|
|
self.assertEqual(counts.internal_gaps, 0)
|
|
self.assertEqual(counts.insertions, 0)
|
|
self.assertEqual(counts.deletions, 0)
|
|
self.assertEqual(counts.gaps, 0)
|
|
self.assertEqual(counts.aligned, 41)
|
|
alignment = next(alignments)
|
|
self.assertEqual(alignment.score, 1000)
|
|
self.assertEqual(alignment.shape, (2, 41))
|
|
self.assertLess(alignment.coordinates[0, 0], alignment.coordinates[0, -1])
|
|
self.assertLess(alignment.coordinates[1, 0], alignment.coordinates[1, -1])
|
|
self.assertEqual(len(alignment), 2)
|
|
self.assertIs(alignment.sequences[0], alignment.target)
|
|
self.assertIs(alignment.sequences[1], alignment.query)
|
|
self.assertEqual(alignment.target.id, "chr8")
|
|
self.assertEqual(alignment.query.id, "hg19_dna")
|
|
self.assertTrue(
|
|
np.array_equal(
|
|
alignment.coordinates,
|
|
# fmt: off
|
|
np.array([[95160479, 95160520],
|
|
[ 0, 41]]),
|
|
# fmt: on
|
|
)
|
|
)
|
|
self.assertEqual(
|
|
str(alignment),
|
|
"""\
|
|
chr8 95160479 ????????????????????????????????????????? 95160520
|
|
0 ||||||||||||||||||||||||||||||||||||||||| 41
|
|
hg19_dna 0 ????????????????????????????????????????? 41
|
|
""",
|
|
)
|
|
self.assertEqual(
|
|
format(alignment, "bed"),
|
|
"""\
|
|
chr8 95160479 95160520 hg19_dna 1000 + 95160479 95160520 0 1 41, 0,
|
|
""",
|
|
)
|
|
counts = alignment.counts()
|
|
self.assertEqual(counts.left_insertions, 0)
|
|
self.assertEqual(counts.left_deletions, 0)
|
|
self.assertEqual(counts.right_insertions, 0)
|
|
self.assertEqual(counts.right_deletions, 0)
|
|
self.assertEqual(counts.internal_insertions, 0)
|
|
self.assertEqual(counts.internal_deletions, 0)
|
|
self.assertEqual(counts.left_gaps, 0)
|
|
self.assertEqual(counts.right_gaps, 0)
|
|
self.assertEqual(counts.internal_gaps, 0)
|
|
self.assertEqual(counts.insertions, 0)
|
|
self.assertEqual(counts.deletions, 0)
|
|
self.assertEqual(counts.gaps, 0)
|
|
self.assertEqual(counts.aligned, 41)
|
|
alignment = next(alignments)
|
|
self.assertEqual(alignment.score, 834)
|
|
self.assertEqual(alignment.shape, (2, 36))
|
|
self.assertLess(alignment.coordinates[0, 0], alignment.coordinates[0, -1])
|
|
self.assertLess(alignment.coordinates[1, 0], alignment.coordinates[1, -1])
|
|
self.assertEqual(len(alignment), 2)
|
|
self.assertIs(alignment.sequences[0], alignment.target)
|
|
self.assertIs(alignment.sequences[1], alignment.query)
|
|
self.assertEqual(alignment.target.id, "chr22")
|
|
self.assertEqual(alignment.query.id, "hg19_dna")
|
|
self.assertTrue(
|
|
np.array_equal(
|
|
alignment.coordinates,
|
|
# fmt: off
|
|
np.array([[42144400, 42144436],
|
|
[ 0, 36]]),
|
|
# fmt: on
|
|
)
|
|
)
|
|
self.assertEqual(
|
|
str(alignment),
|
|
"""\
|
|
chr22 42144400 ???????????????????????????????????? 42144436
|
|
0 |||||||||||||||||||||||||||||||||||| 36
|
|
hg19_dna 0 ???????????????????????????????????? 36
|
|
""",
|
|
)
|
|
self.assertEqual(
|
|
format(alignment, "bed"),
|
|
"""\
|
|
chr22 42144400 42144436 hg19_dna 834 + 42144400 42144436 0 1 36, 0,
|
|
""",
|
|
)
|
|
counts = alignment.counts()
|
|
self.assertEqual(counts.left_insertions, 0)
|
|
self.assertEqual(counts.left_deletions, 0)
|
|
self.assertEqual(counts.right_insertions, 0)
|
|
self.assertEqual(counts.right_deletions, 0)
|
|
self.assertEqual(counts.internal_insertions, 0)
|
|
self.assertEqual(counts.internal_deletions, 0)
|
|
self.assertEqual(counts.left_gaps, 0)
|
|
self.assertEqual(counts.right_gaps, 0)
|
|
self.assertEqual(counts.internal_gaps, 0)
|
|
self.assertEqual(counts.insertions, 0)
|
|
self.assertEqual(counts.deletions, 0)
|
|
self.assertEqual(counts.gaps, 0)
|
|
self.assertEqual(counts.aligned, 36)
|
|
alignment = next(alignments)
|
|
self.assertEqual(alignment.score, 682)
|
|
self.assertEqual(alignment.shape, (2, 44))
|
|
self.assertLess(alignment.coordinates[0, 0], alignment.coordinates[0, -1])
|
|
self.assertLess(alignment.coordinates[1, 0], alignment.coordinates[1, -1])
|
|
self.assertEqual(len(alignment), 2)
|
|
self.assertIs(alignment.sequences[0], alignment.target)
|
|
self.assertIs(alignment.sequences[1], alignment.query)
|
|
self.assertEqual(alignment.target.id, "chr2")
|
|
self.assertEqual(alignment.query.id, "hg19_dna")
|
|
self.assertTrue(
|
|
np.array_equal(
|
|
alignment.coordinates,
|
|
# fmt: off
|
|
np.array([[183925984, 183925990, 183926028],
|
|
[ 0, 6, 44]]),
|
|
# fmt: on
|
|
)
|
|
)
|
|
self.assertEqual(
|
|
str(alignment),
|
|
"""\
|
|
chr2 183925984 ???????????????????????????????????????????? 183926028
|
|
0 |||||||||||||||||||||||||||||||||||||||||||| 44
|
|
hg19_dna 0 ???????????????????????????????????????????? 44
|
|
""",
|
|
)
|
|
self.assertEqual(
|
|
format(alignment, "bed"),
|
|
"""\
|
|
chr2 183925984 183926028 hg19_dna 682 + 183925984 183926028 0 2 6,38, 0,6,
|
|
""",
|
|
)
|
|
counts = alignment.counts()
|
|
self.assertEqual(counts.left_insertions, 0)
|
|
self.assertEqual(counts.left_deletions, 0)
|
|
self.assertEqual(counts.right_insertions, 0)
|
|
self.assertEqual(counts.right_deletions, 0)
|
|
self.assertEqual(counts.internal_insertions, 0)
|
|
self.assertEqual(counts.internal_deletions, 0)
|
|
self.assertEqual(counts.left_gaps, 0)
|
|
self.assertEqual(counts.right_gaps, 0)
|
|
self.assertEqual(counts.internal_gaps, 0)
|
|
self.assertEqual(counts.insertions, 0)
|
|
self.assertEqual(counts.deletions, 0)
|
|
self.assertEqual(counts.gaps, 0)
|
|
self.assertEqual(counts.aligned, 44)
|
|
alignment = next(alignments)
|
|
self.assertEqual(alignment.score, 890)
|
|
self.assertEqual(alignment.shape, (2, 170))
|
|
self.assertLess(alignment.coordinates[0, 0], alignment.coordinates[0, -1])
|
|
self.assertLess(alignment.coordinates[1, 0], alignment.coordinates[1, -1])
|
|
self.assertEqual(len(alignment), 2)
|
|
self.assertIs(alignment.sequences[0], alignment.target)
|
|
self.assertIs(alignment.sequences[1], alignment.query)
|
|
self.assertEqual(alignment.target.id, "chr19")
|
|
self.assertEqual(alignment.query.id, "hg19_dna")
|
|
self.assertTrue(
|
|
np.array_equal(
|
|
alignment.coordinates,
|
|
# fmt: off
|
|
np.array([[35483340, 35483365, 35483499, 35483510],
|
|
[ 0, 25, 25, 36]]),
|
|
# fmt: on
|
|
)
|
|
)
|
|
self.assertEqual(
|
|
str(alignment),
|
|
"""\
|
|
chr19 35483340 ????????????????????????????????????????????????????????????
|
|
0 |||||||||||||||||||||||||-----------------------------------
|
|
hg19_dna 0 ?????????????????????????-----------------------------------
|
|
|
|
chr19 35483400 ????????????????????????????????????????????????????????????
|
|
60 ------------------------------------------------------------
|
|
hg19_dna 25 ------------------------------------------------------------
|
|
|
|
chr19 35483460 ?????????????????????????????????????????????????? 35483510
|
|
120 ---------------------------------------||||||||||| 170
|
|
hg19_dna 25 ---------------------------------------??????????? 36
|
|
""",
|
|
)
|
|
self.assertEqual(
|
|
format(alignment, "bed"),
|
|
"""\
|
|
chr19 35483340 35483510 hg19_dna 890 + 35483340 35483510 0 2 25,11, 0,159,
|
|
""",
|
|
)
|
|
counts = alignment.counts()
|
|
self.assertEqual(counts.left_insertions, 0)
|
|
self.assertEqual(counts.left_deletions, 0)
|
|
self.assertEqual(counts.right_insertions, 0)
|
|
self.assertEqual(counts.right_deletions, 0)
|
|
self.assertEqual(counts.internal_insertions, 0)
|
|
self.assertEqual(counts.internal_deletions, 134)
|
|
self.assertEqual(counts.left_gaps, 0)
|
|
self.assertEqual(counts.right_gaps, 0)
|
|
self.assertEqual(counts.internal_gaps, 134)
|
|
self.assertEqual(counts.insertions, 0)
|
|
self.assertEqual(counts.deletions, 134)
|
|
self.assertEqual(counts.gaps, 134)
|
|
self.assertEqual(counts.aligned, 36)
|
|
alignment = next(alignments)
|
|
self.assertEqual(alignment.score, 1000)
|
|
self.assertEqual(alignment.shape, (2, 39))
|
|
self.assertLess(alignment.coordinates[0, 0], alignment.coordinates[0, -1])
|
|
self.assertLess(alignment.coordinates[1, 0], alignment.coordinates[1, -1])
|
|
self.assertEqual(len(alignment), 2)
|
|
self.assertIs(alignment.sequences[0], alignment.target)
|
|
self.assertIs(alignment.sequences[1], alignment.query)
|
|
self.assertEqual(alignment.target.id, "chr18")
|
|
self.assertEqual(alignment.query.id, "hg19_dna")
|
|
self.assertTrue(
|
|
np.array_equal(
|
|
alignment.coordinates,
|
|
# fmt: off
|
|
np.array([[23891310, 23891349],
|
|
[ 0, 39]]),
|
|
# fmt: on
|
|
)
|
|
)
|
|
self.assertEqual(
|
|
str(alignment),
|
|
"""\
|
|
chr18 23891310 ??????????????????????????????????????? 23891349
|
|
0 ||||||||||||||||||||||||||||||||||||||| 39
|
|
hg19_dna 0 ??????????????????????????????????????? 39
|
|
""",
|
|
)
|
|
self.assertEqual(
|
|
format(alignment, "bed"),
|
|
"""\
|
|
chr18 23891310 23891349 hg19_dna 1000 + 23891310 23891349 0 1 39, 0,
|
|
""",
|
|
)
|
|
counts = alignment.counts()
|
|
self.assertEqual(counts.left_insertions, 0)
|
|
self.assertEqual(counts.left_deletions, 0)
|
|
self.assertEqual(counts.right_insertions, 0)
|
|
self.assertEqual(counts.right_deletions, 0)
|
|
self.assertEqual(counts.internal_insertions, 0)
|
|
self.assertEqual(counts.internal_deletions, 0)
|
|
self.assertEqual(counts.left_gaps, 0)
|
|
self.assertEqual(counts.right_gaps, 0)
|
|
self.assertEqual(counts.internal_gaps, 0)
|
|
self.assertEqual(counts.insertions, 0)
|
|
self.assertEqual(counts.deletions, 0)
|
|
self.assertEqual(counts.gaps, 0)
|
|
self.assertEqual(counts.aligned, 39)
|
|
alignment = next(alignments)
|
|
self.assertEqual(alignment.score, 930)
|
|
self.assertEqual(alignment.shape, (2, 28))
|
|
self.assertLess(alignment.coordinates[0, 0], alignment.coordinates[0, -1])
|
|
self.assertLess(alignment.coordinates[1, 0], alignment.coordinates[1, -1])
|
|
self.assertEqual(len(alignment), 2)
|
|
self.assertIs(alignment.sequences[0], alignment.target)
|
|
self.assertIs(alignment.sequences[1], alignment.query)
|
|
self.assertEqual(alignment.target.id, "chr18")
|
|
self.assertEqual(alignment.query.id, "hg19_dna")
|
|
self.assertTrue(
|
|
np.array_equal(
|
|
alignment.coordinates,
|
|
# fmt: off
|
|
np.array([[43252217, 43252245],
|
|
[ 0, 28]]),
|
|
# fmt: on
|
|
)
|
|
)
|
|
self.assertEqual(
|
|
str(alignment),
|
|
"""\
|
|
chr18 43252217 ???????????????????????????? 43252245
|
|
0 |||||||||||||||||||||||||||| 28
|
|
hg19_dna 0 ???????????????????????????? 28
|
|
""",
|
|
)
|
|
self.assertEqual(
|
|
format(alignment, "bed"),
|
|
"""\
|
|
chr18 43252217 43252245 hg19_dna 930 + 43252217 43252245 0 1 28, 0,
|
|
""",
|
|
)
|
|
counts = alignment.counts()
|
|
self.assertEqual(counts.left_insertions, 0)
|
|
self.assertEqual(counts.left_deletions, 0)
|
|
self.assertEqual(counts.right_insertions, 0)
|
|
self.assertEqual(counts.right_deletions, 0)
|
|
self.assertEqual(counts.internal_insertions, 0)
|
|
self.assertEqual(counts.internal_deletions, 0)
|
|
self.assertEqual(counts.left_gaps, 0)
|
|
self.assertEqual(counts.right_gaps, 0)
|
|
self.assertEqual(counts.internal_gaps, 0)
|
|
self.assertEqual(counts.insertions, 0)
|
|
self.assertEqual(counts.deletions, 0)
|
|
self.assertEqual(counts.gaps, 0)
|
|
self.assertEqual(counts.aligned, 28)
|
|
alignment = next(alignments)
|
|
self.assertEqual(alignment.score, 912)
|
|
self.assertEqual(alignment.shape, (2, 51))
|
|
self.assertLess(alignment.coordinates[0, 0], alignment.coordinates[0, -1])
|
|
self.assertLess(alignment.coordinates[1, 0], alignment.coordinates[1, -1])
|
|
self.assertEqual(len(alignment), 2)
|
|
self.assertIs(alignment.sequences[0], alignment.target)
|
|
self.assertIs(alignment.sequences[1], alignment.query)
|
|
self.assertEqual(alignment.target.id, "chr13")
|
|
self.assertEqual(alignment.query.id, "hg19_dna")
|
|
self.assertTrue(
|
|
np.array_equal(
|
|
alignment.coordinates,
|
|
# fmt: off
|
|
np.array([[52759147, 52759154, 52759160, 52759198],
|
|
[ 0, 7, 7, 45]]),
|
|
# fmt: on
|
|
)
|
|
)
|
|
self.assertEqual(
|
|
str(alignment),
|
|
"""\
|
|
chr13 52759147 ??????????????????????????????????????????????????? 52759198
|
|
0 |||||||------|||||||||||||||||||||||||||||||||||||| 51
|
|
hg19_dna 0 ???????------?????????????????????????????????????? 45
|
|
""",
|
|
)
|
|
self.assertEqual(
|
|
format(alignment, "bed"),
|
|
"""\
|
|
chr13 52759147 52759198 hg19_dna 912 + 52759147 52759198 0 2 7,38, 0,13,
|
|
""",
|
|
)
|
|
counts = alignment.counts()
|
|
self.assertEqual(counts.left_insertions, 0)
|
|
self.assertEqual(counts.left_deletions, 0)
|
|
self.assertEqual(counts.right_insertions, 0)
|
|
self.assertEqual(counts.right_deletions, 0)
|
|
self.assertEqual(counts.internal_insertions, 0)
|
|
self.assertEqual(counts.internal_deletions, 6)
|
|
self.assertEqual(counts.left_gaps, 0)
|
|
self.assertEqual(counts.right_gaps, 0)
|
|
self.assertEqual(counts.internal_gaps, 6)
|
|
self.assertEqual(counts.insertions, 0)
|
|
self.assertEqual(counts.deletions, 6)
|
|
self.assertEqual(counts.gaps, 6)
|
|
self.assertEqual(counts.aligned, 45)
|
|
alignment = next(alignments)
|
|
self.assertEqual(alignment.score, 1000)
|
|
self.assertEqual(alignment.shape, (2, 50))
|
|
self.assertLess(alignment.coordinates[0, 0], alignment.coordinates[0, -1])
|
|
self.assertLess(alignment.coordinates[1, 0], alignment.coordinates[1, -1])
|
|
self.assertEqual(len(alignment), 2)
|
|
self.assertIs(alignment.sequences[0], alignment.target)
|
|
self.assertIs(alignment.sequences[1], alignment.query)
|
|
self.assertEqual(alignment.target.id, "chr1")
|
|
self.assertEqual(alignment.query.id, "hg19_dna")
|
|
self.assertTrue(
|
|
np.array_equal(
|
|
alignment.coordinates,
|
|
# fmt: off
|
|
np.array([[1207056, 1207106],
|
|
[ 0, 50]]),
|
|
# fmt: on
|
|
)
|
|
)
|
|
self.assertEqual(
|
|
str(alignment),
|
|
"""\
|
|
chr1 1207056 ?????????????????????????????????????????????????? 1207106
|
|
0 |||||||||||||||||||||||||||||||||||||||||||||||||| 50
|
|
hg19_dna 0 ?????????????????????????????????????????????????? 50
|
|
""",
|
|
)
|
|
self.assertEqual(
|
|
format(alignment, "bed"),
|
|
"""\
|
|
chr1 1207056 1207106 hg19_dna 1000 + 1207056 1207106 0 1 50, 0,
|
|
""",
|
|
)
|
|
counts = alignment.counts()
|
|
self.assertEqual(counts.left_insertions, 0)
|
|
self.assertEqual(counts.left_deletions, 0)
|
|
self.assertEqual(counts.right_insertions, 0)
|
|
self.assertEqual(counts.right_deletions, 0)
|
|
self.assertEqual(counts.internal_insertions, 0)
|
|
self.assertEqual(counts.internal_deletions, 0)
|
|
self.assertEqual(counts.left_gaps, 0)
|
|
self.assertEqual(counts.right_gaps, 0)
|
|
self.assertEqual(counts.internal_gaps, 0)
|
|
self.assertEqual(counts.insertions, 0)
|
|
self.assertEqual(counts.deletions, 0)
|
|
self.assertEqual(counts.gaps, 0)
|
|
self.assertEqual(counts.aligned, 50)
|
|
alignment = next(alignments)
|
|
self.assertEqual(alignment.score, 824)
|
|
self.assertEqual(alignment.shape, (2, 34))
|
|
self.assertLess(alignment.coordinates[0, 0], alignment.coordinates[0, -1])
|
|
self.assertLess(alignment.coordinates[1, 0], alignment.coordinates[1, -1])
|
|
self.assertEqual(len(alignment), 2)
|
|
self.assertIs(alignment.sequences[0], alignment.target)
|
|
self.assertIs(alignment.sequences[1], alignment.query)
|
|
self.assertEqual(alignment.target.id, "chr1")
|
|
self.assertEqual(alignment.query.id, "hg19_dna")
|
|
self.assertTrue(
|
|
np.array_equal(
|
|
alignment.coordinates,
|
|
# fmt: off
|
|
np.array([[61700837, 61700871],
|
|
[ 0, 34]]),
|
|
# fmt: on
|
|
)
|
|
)
|
|
self.assertEqual(
|
|
str(alignment),
|
|
"""\
|
|
chr1 61700837 ?????????????????????????????????? 61700871
|
|
0 |||||||||||||||||||||||||||||||||| 34
|
|
hg19_dna 0 ?????????????????????????????????? 34
|
|
""",
|
|
)
|
|
self.assertEqual(
|
|
format(alignment, "bed"),
|
|
"""\
|
|
chr1 61700837 61700871 hg19_dna 824 + 61700837 61700871 0 1 34, 0,
|
|
""",
|
|
)
|
|
counts = alignment.counts()
|
|
self.assertEqual(counts.left_insertions, 0)
|
|
self.assertEqual(counts.left_deletions, 0)
|
|
self.assertEqual(counts.right_insertions, 0)
|
|
self.assertEqual(counts.right_deletions, 0)
|
|
self.assertEqual(counts.internal_insertions, 0)
|
|
self.assertEqual(counts.internal_deletions, 0)
|
|
self.assertEqual(counts.left_gaps, 0)
|
|
self.assertEqual(counts.right_gaps, 0)
|
|
self.assertEqual(counts.internal_gaps, 0)
|
|
self.assertEqual(counts.insertions, 0)
|
|
self.assertEqual(counts.deletions, 0)
|
|
self.assertEqual(counts.gaps, 0)
|
|
self.assertEqual(counts.aligned, 34)
|
|
alignment = next(alignments)
|
|
self.assertEqual(alignment.score, 572)
|
|
self.assertEqual(alignment.shape, (2, 34))
|
|
self.assertLess(alignment.coordinates[0, 0], alignment.coordinates[0, -1])
|
|
self.assertGreater(alignment.coordinates[1, 0], alignment.coordinates[1, -1])
|
|
self.assertEqual(len(alignment), 2)
|
|
self.assertIs(alignment.sequences[0], alignment.target)
|
|
self.assertIs(alignment.sequences[1], alignment.query)
|
|
self.assertEqual(alignment.target.id, "chr4")
|
|
self.assertEqual(alignment.query.id, "hg19_dna")
|
|
self.assertTrue(
|
|
np.array_equal(
|
|
alignment.coordinates,
|
|
# fmt: off
|
|
np.array([[37558157, 37558167, 37558173, 37558191],
|
|
[ 28, 18, 18, 0]]),
|
|
# fmt: on
|
|
)
|
|
)
|
|
self.assertEqual(
|
|
str(alignment),
|
|
"""\
|
|
chr4 37558157 ?????????????????????????????????? 37558191
|
|
0 ||||||||||------|||||||||||||||||| 34
|
|
hg19_dna 28 ??????????------?????????????????? 0
|
|
""",
|
|
)
|
|
self.assertEqual(
|
|
format(alignment, "bed"),
|
|
"""\
|
|
chr4 37558157 37558191 hg19_dna 572 - 37558157 37558191 0 2 10,18, 0,16,
|
|
""",
|
|
)
|
|
counts = alignment.counts()
|
|
self.assertEqual(counts.left_insertions, 0)
|
|
self.assertEqual(counts.left_deletions, 0)
|
|
self.assertEqual(counts.right_insertions, 0)
|
|
self.assertEqual(counts.right_deletions, 0)
|
|
self.assertEqual(counts.internal_insertions, 0)
|
|
self.assertEqual(counts.internal_deletions, 6)
|
|
self.assertEqual(counts.left_gaps, 0)
|
|
self.assertEqual(counts.right_gaps, 0)
|
|
self.assertEqual(counts.internal_gaps, 6)
|
|
self.assertEqual(counts.insertions, 0)
|
|
self.assertEqual(counts.deletions, 6)
|
|
self.assertEqual(counts.gaps, 6)
|
|
self.assertEqual(counts.aligned, 28)
|
|
alignment = next(alignments)
|
|
self.assertEqual(alignment.score, 892)
|
|
self.assertEqual(alignment.shape, (2, 37))
|
|
self.assertLess(alignment.coordinates[0, 0], alignment.coordinates[0, -1])
|
|
self.assertGreater(alignment.coordinates[1, 0], alignment.coordinates[1, -1])
|
|
self.assertEqual(len(alignment), 2)
|
|
self.assertIs(alignment.sequences[0], alignment.target)
|
|
self.assertIs(alignment.sequences[1], alignment.query)
|
|
self.assertEqual(alignment.target.id, "chr22")
|
|
self.assertEqual(alignment.query.id, "hg19_dna")
|
|
self.assertTrue(
|
|
np.array_equal(
|
|
alignment.coordinates,
|
|
# fmt: off
|
|
np.array([[48997405, 48997442],
|
|
[ 37, 0]]),
|
|
# fmt: on
|
|
)
|
|
)
|
|
self.assertEqual(
|
|
str(alignment),
|
|
"""\
|
|
chr22 48997405 ????????????????????????????????????? 48997442
|
|
0 ||||||||||||||||||||||||||||||||||||| 37
|
|
hg19_dna 37 ????????????????????????????????????? 0
|
|
""",
|
|
)
|
|
self.assertEqual(
|
|
format(alignment, "bed"),
|
|
"""\
|
|
chr22 48997405 48997442 hg19_dna 892 - 48997405 48997442 0 1 37, 0,
|
|
""",
|
|
)
|
|
counts = alignment.counts()
|
|
self.assertEqual(counts.left_insertions, 0)
|
|
self.assertEqual(counts.left_deletions, 0)
|
|
self.assertEqual(counts.right_insertions, 0)
|
|
self.assertEqual(counts.right_deletions, 0)
|
|
self.assertEqual(counts.internal_insertions, 0)
|
|
self.assertEqual(counts.internal_deletions, 0)
|
|
self.assertEqual(counts.left_gaps, 0)
|
|
self.assertEqual(counts.right_gaps, 0)
|
|
self.assertEqual(counts.internal_gaps, 0)
|
|
self.assertEqual(counts.insertions, 0)
|
|
self.assertEqual(counts.deletions, 0)
|
|
self.assertEqual(counts.gaps, 0)
|
|
self.assertEqual(counts.aligned, 37)
|
|
alignment = next(alignments)
|
|
self.assertEqual(alignment.score, 946)
|
|
self.assertEqual(alignment.shape, (2, 36))
|
|
self.assertLess(alignment.coordinates[0, 0], alignment.coordinates[0, -1])
|
|
self.assertGreater(alignment.coordinates[1, 0], alignment.coordinates[1, -1])
|
|
self.assertEqual(len(alignment), 2)
|
|
self.assertIs(alignment.sequences[0], alignment.target)
|
|
self.assertIs(alignment.sequences[1], alignment.query)
|
|
self.assertEqual(alignment.target.id, "chr2")
|
|
self.assertEqual(alignment.query.id, "hg19_dna")
|
|
self.assertTrue(
|
|
np.array_equal(
|
|
alignment.coordinates,
|
|
# fmt: off
|
|
np.array([[120641740, 120641776],
|
|
[ 36, 0]]),
|
|
# fmt: on
|
|
)
|
|
)
|
|
self.assertEqual(
|
|
str(alignment),
|
|
"""\
|
|
chr2 120641740 ???????????????????????????????????? 120641776
|
|
0 |||||||||||||||||||||||||||||||||||| 36
|
|
hg19_dna 36 ???????????????????????????????????? 0
|
|
""",
|
|
)
|
|
self.assertEqual(
|
|
format(alignment, "bed"),
|
|
"""\
|
|
chr2 120641740 120641776 hg19_dna 946 - 120641740 120641776 0 1 36, 0,
|
|
""",
|
|
)
|
|
counts = alignment.counts()
|
|
self.assertEqual(counts.left_insertions, 0)
|
|
self.assertEqual(counts.left_deletions, 0)
|
|
self.assertEqual(counts.right_insertions, 0)
|
|
self.assertEqual(counts.right_deletions, 0)
|
|
self.assertEqual(counts.internal_insertions, 0)
|
|
self.assertEqual(counts.internal_deletions, 0)
|
|
self.assertEqual(counts.left_gaps, 0)
|
|
self.assertEqual(counts.right_gaps, 0)
|
|
self.assertEqual(counts.internal_gaps, 0)
|
|
self.assertEqual(counts.insertions, 0)
|
|
self.assertEqual(counts.deletions, 0)
|
|
self.assertEqual(counts.gaps, 0)
|
|
self.assertEqual(counts.aligned, 36)
|
|
alignment = next(alignments)
|
|
self.assertEqual(alignment.score, 1000)
|
|
self.assertEqual(alignment.shape, (2, 39))
|
|
self.assertLess(alignment.coordinates[0, 0], alignment.coordinates[0, -1])
|
|
self.assertGreater(alignment.coordinates[1, 0], alignment.coordinates[1, -1])
|
|
self.assertEqual(len(alignment), 2)
|
|
self.assertIs(alignment.sequences[0], alignment.target)
|
|
self.assertIs(alignment.sequences[1], alignment.query)
|
|
self.assertEqual(alignment.target.id, "chr19")
|
|
self.assertEqual(alignment.query.id, "hg19_dna")
|
|
self.assertTrue(
|
|
np.array_equal(
|
|
alignment.coordinates,
|
|
# fmt: off
|
|
np.array([[54017130, 54017169],
|
|
[ 39, 0]]),
|
|
# fmt: on
|
|
)
|
|
)
|
|
self.assertEqual(
|
|
str(alignment),
|
|
"""\
|
|
chr19 54017130 ??????????????????????????????????????? 54017169
|
|
0 ||||||||||||||||||||||||||||||||||||||| 39
|
|
hg19_dna 39 ??????????????????????????????????????? 0
|
|
""",
|
|
)
|
|
self.assertEqual(
|
|
format(alignment, "bed"),
|
|
"""\
|
|
chr19 54017130 54017169 hg19_dna 1000 - 54017130 54017169 0 1 39, 0,
|
|
""",
|
|
)
|
|
counts = alignment.counts()
|
|
self.assertEqual(counts.left_insertions, 0)
|
|
self.assertEqual(counts.left_deletions, 0)
|
|
self.assertEqual(counts.right_insertions, 0)
|
|
self.assertEqual(counts.right_deletions, 0)
|
|
self.assertEqual(counts.internal_insertions, 0)
|
|
self.assertEqual(counts.internal_deletions, 0)
|
|
self.assertEqual(counts.left_gaps, 0)
|
|
self.assertEqual(counts.right_gaps, 0)
|
|
self.assertEqual(counts.internal_gaps, 0)
|
|
self.assertEqual(counts.insertions, 0)
|
|
self.assertEqual(counts.deletions, 0)
|
|
self.assertEqual(counts.gaps, 0)
|
|
self.assertEqual(counts.aligned, 39)
|
|
alignment = next(alignments)
|
|
self.assertEqual(alignment.score, 848)
|
|
self.assertEqual(alignment.shape, (2, 39))
|
|
self.assertLess(alignment.coordinates[0, 0], alignment.coordinates[0, -1])
|
|
self.assertGreater(alignment.coordinates[1, 0], alignment.coordinates[1, -1])
|
|
self.assertEqual(len(alignment), 2)
|
|
self.assertIs(alignment.sequences[0], alignment.target)
|
|
self.assertIs(alignment.sequences[1], alignment.query)
|
|
self.assertEqual(alignment.target.id, "chr19")
|
|
self.assertEqual(alignment.query.id, "hg19_dna")
|
|
self.assertTrue(
|
|
np.array_equal(
|
|
alignment.coordinates,
|
|
# fmt: off
|
|
np.array([[553742, 553781],
|
|
[ 39, 0]]),
|
|
# fmt: on
|
|
)
|
|
)
|
|
self.assertEqual(
|
|
str(alignment),
|
|
"""\
|
|
chr19 553742 ??????????????????????????????????????? 553781
|
|
0 ||||||||||||||||||||||||||||||||||||||| 39
|
|
hg19_dna 39 ??????????????????????????????????????? 0
|
|
""",
|
|
)
|
|
self.assertEqual(
|
|
format(alignment, "bed"),
|
|
"""\
|
|
chr19 553742 553781 hg19_dna 848 - 553742 553781 0 1 39, 0,
|
|
""",
|
|
)
|
|
counts = alignment.counts()
|
|
self.assertEqual(counts.left_insertions, 0)
|
|
self.assertEqual(counts.left_deletions, 0)
|
|
self.assertEqual(counts.right_insertions, 0)
|
|
self.assertEqual(counts.right_deletions, 0)
|
|
self.assertEqual(counts.internal_insertions, 0)
|
|
self.assertEqual(counts.internal_deletions, 0)
|
|
self.assertEqual(counts.left_gaps, 0)
|
|
self.assertEqual(counts.right_gaps, 0)
|
|
self.assertEqual(counts.internal_gaps, 0)
|
|
self.assertEqual(counts.insertions, 0)
|
|
self.assertEqual(counts.deletions, 0)
|
|
self.assertEqual(counts.gaps, 0)
|
|
self.assertEqual(counts.aligned, 39)
|
|
alignment = next(alignments)
|
|
self.assertEqual(alignment.score, 834)
|
|
self.assertEqual(alignment.shape, (2, 36))
|
|
self.assertLess(alignment.coordinates[0, 0], alignment.coordinates[0, -1])
|
|
self.assertGreater(alignment.coordinates[1, 0], alignment.coordinates[1, -1])
|
|
self.assertEqual(len(alignment), 2)
|
|
self.assertIs(alignment.sequences[0], alignment.target)
|
|
self.assertIs(alignment.sequences[1], alignment.query)
|
|
self.assertEqual(alignment.target.id, "chr10")
|
|
self.assertEqual(alignment.query.id, "hg19_dna")
|
|
self.assertTrue(
|
|
np.array_equal(
|
|
alignment.coordinates,
|
|
# fmt: off
|
|
np.array([[99388555, 99388591],
|
|
[ 36, 0]]),
|
|
# fmt: on
|
|
)
|
|
)
|
|
self.assertEqual(
|
|
str(alignment),
|
|
"""\
|
|
chr10 99388555 ???????????????????????????????????? 99388591
|
|
0 |||||||||||||||||||||||||||||||||||| 36
|
|
hg19_dna 36 ???????????????????????????????????? 0
|
|
""",
|
|
)
|
|
self.assertEqual(
|
|
format(alignment, "bed"),
|
|
"""\
|
|
chr10 99388555 99388591 hg19_dna 834 - 99388555 99388591 0 1 36, 0,
|
|
""",
|
|
)
|
|
counts = alignment.counts()
|
|
self.assertEqual(counts.left_insertions, 0)
|
|
self.assertEqual(counts.left_deletions, 0)
|
|
self.assertEqual(counts.right_insertions, 0)
|
|
self.assertEqual(counts.right_deletions, 0)
|
|
self.assertEqual(counts.internal_insertions, 0)
|
|
self.assertEqual(counts.internal_deletions, 0)
|
|
self.assertEqual(counts.left_gaps, 0)
|
|
self.assertEqual(counts.right_gaps, 0)
|
|
self.assertEqual(counts.internal_gaps, 0)
|
|
self.assertEqual(counts.insertions, 0)
|
|
self.assertEqual(counts.deletions, 0)
|
|
self.assertEqual(counts.gaps, 0)
|
|
self.assertEqual(counts.aligned, 36)
|
|
alignment = next(alignments)
|
|
self.assertEqual(alignment.score, 920)
|
|
self.assertEqual(alignment.shape, (2, 25))
|
|
self.assertLess(alignment.coordinates[0, 0], alignment.coordinates[0, -1])
|
|
self.assertGreater(alignment.coordinates[1, 0], alignment.coordinates[1, -1])
|
|
self.assertEqual(len(alignment), 2)
|
|
self.assertIs(alignment.sequences[0], alignment.target)
|
|
self.assertIs(alignment.sequences[1], alignment.query)
|
|
self.assertEqual(alignment.target.id, "chr10")
|
|
self.assertEqual(alignment.query.id, "hg19_dna")
|
|
self.assertTrue(
|
|
np.array_equal(
|
|
alignment.coordinates,
|
|
# fmt: off
|
|
np.array([[112178171, 112178196],
|
|
[ 25, 0]]),
|
|
# fmt: on
|
|
)
|
|
)
|
|
self.assertEqual(
|
|
str(alignment),
|
|
"""\
|
|
chr10 112178171 ????????????????????????? 112178196
|
|
0 ||||||||||||||||||||||||| 25
|
|
hg19_dna 25 ????????????????????????? 0
|
|
""",
|
|
)
|
|
self.assertEqual(
|
|
format(alignment, "bed"),
|
|
"""\
|
|
chr10 112178171 112178196 hg19_dna 920 - 112178171 112178196 0 1 25, 0,
|
|
""",
|
|
)
|
|
counts = alignment.counts()
|
|
self.assertEqual(counts.left_insertions, 0)
|
|
self.assertEqual(counts.left_deletions, 0)
|
|
self.assertEqual(counts.right_insertions, 0)
|
|
self.assertEqual(counts.right_deletions, 0)
|
|
self.assertEqual(counts.internal_insertions, 0)
|
|
self.assertEqual(counts.internal_deletions, 0)
|
|
self.assertEqual(counts.left_gaps, 0)
|
|
self.assertEqual(counts.right_gaps, 0)
|
|
self.assertEqual(counts.internal_gaps, 0)
|
|
self.assertEqual(counts.insertions, 0)
|
|
self.assertEqual(counts.deletions, 0)
|
|
self.assertEqual(counts.gaps, 0)
|
|
self.assertEqual(counts.aligned, 25)
|
|
alignment = next(alignments)
|
|
self.assertEqual(alignment.score, 946)
|
|
self.assertEqual(alignment.shape, (2, 36))
|
|
self.assertLess(alignment.coordinates[0, 0], alignment.coordinates[0, -1])
|
|
self.assertGreater(alignment.coordinates[1, 0], alignment.coordinates[1, -1])
|
|
self.assertEqual(len(alignment), 2)
|
|
self.assertIs(alignment.sequences[0], alignment.target)
|
|
self.assertIs(alignment.sequences[1], alignment.query)
|
|
self.assertEqual(alignment.target.id, "chr1")
|
|
self.assertEqual(alignment.query.id, "hg19_dna")
|
|
self.assertTrue(
|
|
np.array_equal(
|
|
alignment.coordinates,
|
|
# fmt: off
|
|
np.array([[39368490, 39368526],
|
|
[ 36, 0]]),
|
|
# fmt: on
|
|
)
|
|
)
|
|
self.assertEqual(
|
|
str(alignment),
|
|
"""\
|
|
chr1 39368490 ???????????????????????????????????? 39368526
|
|
0 |||||||||||||||||||||||||||||||||||| 36
|
|
hg19_dna 36 ???????????????????????????????????? 0
|
|
""",
|
|
)
|
|
self.assertEqual(
|
|
format(alignment, "bed"),
|
|
"""\
|
|
chr1 39368490 39368526 hg19_dna 946 - 39368490 39368526 0 1 36, 0,
|
|
""",
|
|
)
|
|
counts = alignment.counts()
|
|
self.assertEqual(counts.left_insertions, 0)
|
|
self.assertEqual(counts.left_deletions, 0)
|
|
self.assertEqual(counts.right_insertions, 0)
|
|
self.assertEqual(counts.right_deletions, 0)
|
|
self.assertEqual(counts.internal_insertions, 0)
|
|
self.assertEqual(counts.internal_deletions, 0)
|
|
self.assertEqual(counts.left_gaps, 0)
|
|
self.assertEqual(counts.right_gaps, 0)
|
|
self.assertEqual(counts.internal_gaps, 0)
|
|
self.assertEqual(counts.insertions, 0)
|
|
self.assertEqual(counts.deletions, 0)
|
|
self.assertEqual(counts.gaps, 0)
|
|
self.assertEqual(counts.aligned, 36)
|
|
alignment = next(alignments)
|
|
self.assertEqual(alignment.score, 942)
|
|
self.assertEqual(alignment.shape, (2, 34))
|
|
self.assertLess(alignment.coordinates[0, 0], alignment.coordinates[0, -1])
|
|
self.assertGreater(alignment.coordinates[1, 0], alignment.coordinates[1, -1])
|
|
self.assertEqual(len(alignment), 2)
|
|
self.assertIs(alignment.sequences[0], alignment.target)
|
|
self.assertIs(alignment.sequences[1], alignment.query)
|
|
self.assertEqual(alignment.target.id, "chr1")
|
|
self.assertEqual(alignment.query.id, "hg19_dna")
|
|
self.assertTrue(
|
|
np.array_equal(
|
|
alignment.coordinates,
|
|
# fmt: off
|
|
np.array([[220325687, 220325721],
|
|
[ 34, 0]]),
|
|
# fmt: on
|
|
)
|
|
)
|
|
self.assertEqual(
|
|
str(alignment),
|
|
"""\
|
|
chr1 220325687 ?????????????????????????????????? 220325721
|
|
0 |||||||||||||||||||||||||||||||||| 34
|
|
hg19_dna 34 ?????????????????????????????????? 0
|
|
""",
|
|
)
|
|
self.assertEqual(
|
|
format(alignment, "bed"),
|
|
"""\
|
|
chr1 220325687 220325721 hg19_dna 942 - 220325687 220325721 0 1 34, 0,
|
|
""",
|
|
)
|
|
counts = alignment.counts()
|
|
self.assertEqual(counts.left_insertions, 0)
|
|
self.assertEqual(counts.left_deletions, 0)
|
|
self.assertEqual(counts.right_insertions, 0)
|
|
self.assertEqual(counts.right_deletions, 0)
|
|
self.assertEqual(counts.internal_insertions, 0)
|
|
self.assertEqual(counts.internal_deletions, 0)
|
|
self.assertEqual(counts.left_gaps, 0)
|
|
self.assertEqual(counts.right_gaps, 0)
|
|
self.assertEqual(counts.internal_gaps, 0)
|
|
self.assertEqual(counts.insertions, 0)
|
|
self.assertEqual(counts.deletions, 0)
|
|
self.assertEqual(counts.gaps, 0)
|
|
self.assertEqual(counts.aligned, 34)
|
|
self.assertRaises(StopIteration, next, alignments)
|
|
|
|
def test_writing_psl_34_001(self):
|
|
"""Test writing the alignments in psl_34_001.bed."""
|
|
path = "Blat/psl_34_001.bed"
|
|
with open(path) as stream:
|
|
original_data = stream.read()
|
|
alignments = Align.parse(path, "bed")
|
|
stream = StringIO()
|
|
n = Align.write(alignments, stream, "bed")
|
|
self.assertEqual(n, 22)
|
|
stream.seek(0)
|
|
written_data = stream.read()
|
|
stream.close()
|
|
self.assertEqual(original_data, written_data)
|
|
|
|
def test_reading_psl_34_003(self):
|
|
"""Test parsing psl_34_003.bed."""
|
|
path = "Blat/psl_34_003.bed"
|
|
alignments = Align.parse(path, "bed")
|
|
alignment = next(alignments)
|
|
self.assertEqual(alignment.score, 1000)
|
|
self.assertEqual(alignment.shape, (2, 16))
|
|
self.assertLess(alignment.coordinates[0, 0], alignment.coordinates[0, -1])
|
|
self.assertLess(alignment.coordinates[1, 0], alignment.coordinates[1, -1])
|
|
self.assertEqual(len(alignment), 2)
|
|
self.assertIs(alignment.sequences[0], alignment.target)
|
|
self.assertIs(alignment.sequences[1], alignment.query)
|
|
self.assertEqual(alignment.target.id, "chr4")
|
|
self.assertEqual(alignment.query.id, "hg18_dna")
|
|
self.assertTrue(
|
|
np.array_equal(
|
|
alignment.coordinates,
|
|
# fmt: off
|
|
np.array([[61646095, 61646111],
|
|
[ 0, 16]]),
|
|
# fmt: on
|
|
)
|
|
)
|
|
self.assertEqual(
|
|
str(alignment),
|
|
"""\
|
|
chr4 61646095 ???????????????? 61646111
|
|
0 |||||||||||||||| 16
|
|
hg18_dna 0 ???????????????? 16
|
|
""",
|
|
)
|
|
self.assertEqual(
|
|
format(alignment, "bed"),
|
|
"""\
|
|
chr4 61646095 61646111 hg18_dna 1000 + 61646095 61646111 0 1 16, 0,
|
|
""",
|
|
)
|
|
counts = alignment.counts()
|
|
self.assertEqual(counts.left_insertions, 0)
|
|
self.assertEqual(counts.left_deletions, 0)
|
|
self.assertEqual(counts.right_insertions, 0)
|
|
self.assertEqual(counts.right_deletions, 0)
|
|
self.assertEqual(counts.internal_insertions, 0)
|
|
self.assertEqual(counts.internal_deletions, 0)
|
|
self.assertEqual(counts.left_gaps, 0)
|
|
self.assertEqual(counts.right_gaps, 0)
|
|
self.assertEqual(counts.internal_gaps, 0)
|
|
self.assertEqual(counts.insertions, 0)
|
|
self.assertEqual(counts.deletions, 0)
|
|
self.assertEqual(counts.gaps, 0)
|
|
self.assertEqual(counts.aligned, 16)
|
|
alignment = next(alignments)
|
|
self.assertEqual(alignment.score, 1000)
|
|
self.assertEqual(alignment.shape, (2, 33))
|
|
self.assertLess(alignment.coordinates[0, 0], alignment.coordinates[0, -1])
|
|
self.assertLess(alignment.coordinates[1, 0], alignment.coordinates[1, -1])
|
|
self.assertEqual(len(alignment), 2)
|
|
self.assertIs(alignment.sequences[0], alignment.target)
|
|
self.assertIs(alignment.sequences[1], alignment.query)
|
|
self.assertEqual(alignment.target.id, "chr1")
|
|
self.assertEqual(alignment.query.id, "hg18_dna")
|
|
self.assertTrue(
|
|
np.array_equal(
|
|
alignment.coordinates,
|
|
# fmt: off
|
|
np.array([[10271783, 10271816],
|
|
[ 0, 33]]),
|
|
# fmt: on
|
|
)
|
|
)
|
|
self.assertEqual(
|
|
str(alignment),
|
|
"""\
|
|
chr1 10271783 ????????????????????????????????? 10271816
|
|
0 ||||||||||||||||||||||||||||||||| 33
|
|
hg18_dna 0 ????????????????????????????????? 33
|
|
""",
|
|
)
|
|
self.assertEqual(
|
|
format(alignment, "bed"),
|
|
"""\
|
|
chr1 10271783 10271816 hg18_dna 1000 + 10271783 10271816 0 1 33, 0,
|
|
""",
|
|
)
|
|
counts = alignment.counts()
|
|
self.assertEqual(counts.left_insertions, 0)
|
|
self.assertEqual(counts.left_deletions, 0)
|
|
self.assertEqual(counts.right_insertions, 0)
|
|
self.assertEqual(counts.right_deletions, 0)
|
|
self.assertEqual(counts.internal_insertions, 0)
|
|
self.assertEqual(counts.internal_deletions, 0)
|
|
self.assertEqual(counts.left_gaps, 0)
|
|
self.assertEqual(counts.right_gaps, 0)
|
|
self.assertEqual(counts.internal_gaps, 0)
|
|
self.assertEqual(counts.insertions, 0)
|
|
self.assertEqual(counts.deletions, 0)
|
|
self.assertEqual(counts.gaps, 0)
|
|
self.assertEqual(counts.aligned, 33)
|
|
alignment = next(alignments)
|
|
self.assertEqual(alignment.score, 1000)
|
|
self.assertEqual(alignment.shape, (2, 17))
|
|
self.assertLess(alignment.coordinates[0, 0], alignment.coordinates[0, -1])
|
|
self.assertGreater(alignment.coordinates[1, 0], alignment.coordinates[1, -1])
|
|
self.assertEqual(len(alignment), 2)
|
|
self.assertIs(alignment.sequences[0], alignment.target)
|
|
self.assertIs(alignment.sequences[1], alignment.query)
|
|
self.assertEqual(alignment.target.id, "chr2")
|
|
self.assertEqual(alignment.query.id, "hg18_dna")
|
|
self.assertTrue(
|
|
np.array_equal(
|
|
alignment.coordinates,
|
|
# fmt: off
|
|
np.array([[53575980, 53575997],
|
|
[ 17, 0]]),
|
|
# fmt: on
|
|
)
|
|
)
|
|
self.assertEqual(
|
|
str(alignment),
|
|
"""\
|
|
chr2 53575980 ????????????????? 53575997
|
|
0 ||||||||||||||||| 17
|
|
hg18_dna 17 ????????????????? 0
|
|
""",
|
|
)
|
|
self.assertEqual(
|
|
format(alignment, "bed"),
|
|
"""\
|
|
chr2 53575980 53575997 hg18_dna 1000 - 53575980 53575997 0 1 17, 0,
|
|
""",
|
|
)
|
|
counts = alignment.counts()
|
|
self.assertEqual(counts.left_insertions, 0)
|
|
self.assertEqual(counts.left_deletions, 0)
|
|
self.assertEqual(counts.right_insertions, 0)
|
|
self.assertEqual(counts.right_deletions, 0)
|
|
self.assertEqual(counts.internal_insertions, 0)
|
|
self.assertEqual(counts.internal_deletions, 0)
|
|
self.assertEqual(counts.left_gaps, 0)
|
|
self.assertEqual(counts.right_gaps, 0)
|
|
self.assertEqual(counts.internal_gaps, 0)
|
|
self.assertEqual(counts.insertions, 0)
|
|
self.assertEqual(counts.deletions, 0)
|
|
self.assertEqual(counts.gaps, 0)
|
|
self.assertEqual(counts.aligned, 17)
|
|
self.assertRaises(StopIteration, next, alignments)
|
|
|
|
def test_writing_psl_34_003(self):
|
|
"""Test writing the alignments in psl_34_003.bed."""
|
|
path = "Blat/psl_34_003.bed"
|
|
with open(path) as stream:
|
|
original_data = stream.read()
|
|
alignments = Align.parse(path, "bed")
|
|
stream = StringIO()
|
|
n = Align.write(alignments, stream, "bed")
|
|
self.assertEqual(n, 3)
|
|
stream.seek(0)
|
|
written_data = stream.read()
|
|
stream.close()
|
|
self.assertEqual(original_data, written_data)
|
|
|
|
def test_reading_psl_34_004(self):
|
|
"""Test parsing psl_34_004.bed."""
|
|
path = "Blat/psl_34_004.bed"
|
|
alignments = Align.parse(path, "bed")
|
|
alignment = next(alignments)
|
|
self.assertEqual(alignment.score, 854)
|
|
self.assertEqual(alignment.shape, (2, 41))
|
|
self.assertLess(alignment.coordinates[0, 0], alignment.coordinates[0, -1])
|
|
self.assertLess(alignment.coordinates[1, 0], alignment.coordinates[1, -1])
|
|
self.assertEqual(len(alignment), 2)
|
|
self.assertIs(alignment.sequences[0], alignment.target)
|
|
self.assertIs(alignment.sequences[1], alignment.query)
|
|
self.assertEqual(alignment.target.id, "chr9")
|
|
self.assertEqual(alignment.query.id, "hg19_dna")
|
|
self.assertTrue(
|
|
np.array_equal(
|
|
alignment.coordinates,
|
|
# fmt: off
|
|
np.array([[85737865, 85737906],
|
|
[ 0, 41]]),
|
|
# fmt: on
|
|
)
|
|
)
|
|
self.assertEqual(
|
|
str(alignment),
|
|
"""\
|
|
chr9 85737865 ????????????????????????????????????????? 85737906
|
|
0 ||||||||||||||||||||||||||||||||||||||||| 41
|
|
hg19_dna 0 ????????????????????????????????????????? 41
|
|
""",
|
|
)
|
|
self.assertEqual(
|
|
format(alignment, "bed"),
|
|
"""\
|
|
chr9 85737865 85737906 hg19_dna 854 + 85737865 85737906 0 1 41, 0,
|
|
""",
|
|
)
|
|
counts = alignment.counts()
|
|
self.assertEqual(counts.left_insertions, 0)
|
|
self.assertEqual(counts.left_deletions, 0)
|
|
self.assertEqual(counts.right_insertions, 0)
|
|
self.assertEqual(counts.right_deletions, 0)
|
|
self.assertEqual(counts.internal_insertions, 0)
|
|
self.assertEqual(counts.internal_deletions, 0)
|
|
self.assertEqual(counts.left_gaps, 0)
|
|
self.assertEqual(counts.right_gaps, 0)
|
|
self.assertEqual(counts.internal_gaps, 0)
|
|
self.assertEqual(counts.insertions, 0)
|
|
self.assertEqual(counts.deletions, 0)
|
|
self.assertEqual(counts.gaps, 0)
|
|
self.assertEqual(counts.aligned, 41)
|
|
alignment = next(alignments)
|
|
self.assertEqual(alignment.score, 1000)
|
|
self.assertEqual(alignment.shape, (2, 41))
|
|
self.assertLess(alignment.coordinates[0, 0], alignment.coordinates[0, -1])
|
|
self.assertLess(alignment.coordinates[1, 0], alignment.coordinates[1, -1])
|
|
self.assertEqual(len(alignment), 2)
|
|
self.assertIs(alignment.sequences[0], alignment.target)
|
|
self.assertIs(alignment.sequences[1], alignment.query)
|
|
self.assertEqual(alignment.target.id, "chr8")
|
|
self.assertEqual(alignment.query.id, "hg19_dna")
|
|
self.assertTrue(
|
|
np.array_equal(
|
|
alignment.coordinates,
|
|
# fmt: off
|
|
np.array([[95160479, 95160520],
|
|
[ 0, 41]]),
|
|
# fmt: on
|
|
)
|
|
)
|
|
self.assertEqual(
|
|
str(alignment),
|
|
"""\
|
|
chr8 95160479 ????????????????????????????????????????? 95160520
|
|
0 ||||||||||||||||||||||||||||||||||||||||| 41
|
|
hg19_dna 0 ????????????????????????????????????????? 41
|
|
""",
|
|
)
|
|
self.assertEqual(
|
|
format(alignment, "bed"),
|
|
"""\
|
|
chr8 95160479 95160520 hg19_dna 1000 + 95160479 95160520 0 1 41, 0,
|
|
""",
|
|
)
|
|
counts = alignment.counts()
|
|
self.assertEqual(counts.left_insertions, 0)
|
|
self.assertEqual(counts.left_deletions, 0)
|
|
self.assertEqual(counts.right_insertions, 0)
|
|
self.assertEqual(counts.right_deletions, 0)
|
|
self.assertEqual(counts.internal_insertions, 0)
|
|
self.assertEqual(counts.internal_deletions, 0)
|
|
self.assertEqual(counts.left_gaps, 0)
|
|
self.assertEqual(counts.right_gaps, 0)
|
|
self.assertEqual(counts.internal_gaps, 0)
|
|
self.assertEqual(counts.insertions, 0)
|
|
self.assertEqual(counts.deletions, 0)
|
|
self.assertEqual(counts.gaps, 0)
|
|
self.assertEqual(counts.aligned, 41)
|
|
alignment = next(alignments)
|
|
self.assertEqual(alignment.score, 834)
|
|
self.assertEqual(alignment.shape, (2, 36))
|
|
self.assertLess(alignment.coordinates[0, 0], alignment.coordinates[0, -1])
|
|
self.assertLess(alignment.coordinates[1, 0], alignment.coordinates[1, -1])
|
|
self.assertEqual(len(alignment), 2)
|
|
self.assertIs(alignment.sequences[0], alignment.target)
|
|
self.assertIs(alignment.sequences[1], alignment.query)
|
|
self.assertEqual(alignment.target.id, "chr22")
|
|
self.assertEqual(alignment.query.id, "hg19_dna")
|
|
self.assertTrue(
|
|
np.array_equal(
|
|
alignment.coordinates,
|
|
# fmt: off
|
|
np.array([[42144400, 42144436],
|
|
[ 0, 36]]),
|
|
# fmt: on
|
|
)
|
|
)
|
|
self.assertEqual(
|
|
str(alignment),
|
|
"""\
|
|
chr22 42144400 ???????????????????????????????????? 42144436
|
|
0 |||||||||||||||||||||||||||||||||||| 36
|
|
hg19_dna 0 ???????????????????????????????????? 36
|
|
""",
|
|
)
|
|
self.assertEqual(
|
|
format(alignment, "bed"),
|
|
"""\
|
|
chr22 42144400 42144436 hg19_dna 834 + 42144400 42144436 0 1 36, 0,
|
|
""",
|
|
)
|
|
counts = alignment.counts()
|
|
self.assertEqual(counts.left_insertions, 0)
|
|
self.assertEqual(counts.left_deletions, 0)
|
|
self.assertEqual(counts.right_insertions, 0)
|
|
self.assertEqual(counts.right_deletions, 0)
|
|
self.assertEqual(counts.internal_insertions, 0)
|
|
self.assertEqual(counts.internal_deletions, 0)
|
|
self.assertEqual(counts.left_gaps, 0)
|
|
self.assertEqual(counts.right_gaps, 0)
|
|
self.assertEqual(counts.internal_gaps, 0)
|
|
self.assertEqual(counts.insertions, 0)
|
|
self.assertEqual(counts.deletions, 0)
|
|
self.assertEqual(counts.gaps, 0)
|
|
self.assertEqual(counts.aligned, 36)
|
|
alignment = next(alignments)
|
|
self.assertEqual(alignment.score, 682)
|
|
self.assertEqual(alignment.shape, (2, 44))
|
|
self.assertLess(alignment.coordinates[0, 0], alignment.coordinates[0, -1])
|
|
self.assertLess(alignment.coordinates[1, 0], alignment.coordinates[1, -1])
|
|
self.assertEqual(len(alignment), 2)
|
|
self.assertIs(alignment.sequences[0], alignment.target)
|
|
self.assertIs(alignment.sequences[1], alignment.query)
|
|
self.assertEqual(alignment.target.id, "chr2")
|
|
self.assertEqual(alignment.query.id, "hg19_dna")
|
|
self.assertTrue(
|
|
np.array_equal(
|
|
alignment.coordinates,
|
|
# fmt: off
|
|
np.array([[183925984, 183925990, 183926028],
|
|
[ 0, 6, 44]]),
|
|
# fmt: on
|
|
)
|
|
)
|
|
self.assertEqual(
|
|
str(alignment),
|
|
"""\
|
|
chr2 183925984 ???????????????????????????????????????????? 183926028
|
|
0 |||||||||||||||||||||||||||||||||||||||||||| 44
|
|
hg19_dna 0 ???????????????????????????????????????????? 44
|
|
""",
|
|
)
|
|
self.assertEqual(
|
|
format(alignment, "bed"),
|
|
"""\
|
|
chr2 183925984 183926028 hg19_dna 682 + 183925984 183926028 0 2 6,38, 0,6,
|
|
""",
|
|
)
|
|
counts = alignment.counts()
|
|
self.assertEqual(counts.left_insertions, 0)
|
|
self.assertEqual(counts.left_deletions, 0)
|
|
self.assertEqual(counts.right_insertions, 0)
|
|
self.assertEqual(counts.right_deletions, 0)
|
|
self.assertEqual(counts.internal_insertions, 0)
|
|
self.assertEqual(counts.internal_deletions, 0)
|
|
self.assertEqual(counts.left_gaps, 0)
|
|
self.assertEqual(counts.right_gaps, 0)
|
|
self.assertEqual(counts.internal_gaps, 0)
|
|
self.assertEqual(counts.insertions, 0)
|
|
self.assertEqual(counts.deletions, 0)
|
|
self.assertEqual(counts.gaps, 0)
|
|
self.assertEqual(counts.aligned, 44)
|
|
alignment = next(alignments)
|
|
self.assertEqual(alignment.score, 890)
|
|
self.assertEqual(alignment.shape, (2, 170))
|
|
self.assertLess(alignment.coordinates[0, 0], alignment.coordinates[0, -1])
|
|
self.assertLess(alignment.coordinates[1, 0], alignment.coordinates[1, -1])
|
|
self.assertEqual(len(alignment), 2)
|
|
self.assertIs(alignment.sequences[0], alignment.target)
|
|
self.assertIs(alignment.sequences[1], alignment.query)
|
|
self.assertEqual(alignment.target.id, "chr19")
|
|
self.assertEqual(alignment.query.id, "hg19_dna")
|
|
self.assertTrue(
|
|
np.array_equal(
|
|
alignment.coordinates,
|
|
# fmt: off
|
|
np.array([[35483340, 35483365, 35483499, 35483510],
|
|
[ 0, 25, 25, 36]]),
|
|
# fmt: on
|
|
)
|
|
)
|
|
self.assertEqual(
|
|
str(alignment),
|
|
"""\
|
|
chr19 35483340 ????????????????????????????????????????????????????????????
|
|
0 |||||||||||||||||||||||||-----------------------------------
|
|
hg19_dna 0 ?????????????????????????-----------------------------------
|
|
|
|
chr19 35483400 ????????????????????????????????????????????????????????????
|
|
60 ------------------------------------------------------------
|
|
hg19_dna 25 ------------------------------------------------------------
|
|
|
|
chr19 35483460 ?????????????????????????????????????????????????? 35483510
|
|
120 ---------------------------------------||||||||||| 170
|
|
hg19_dna 25 ---------------------------------------??????????? 36
|
|
""",
|
|
)
|
|
self.assertEqual(
|
|
format(alignment, "bed"),
|
|
"""\
|
|
chr19 35483340 35483510 hg19_dna 890 + 35483340 35483510 0 2 25,11, 0,159,
|
|
""",
|
|
)
|
|
counts = alignment.counts()
|
|
self.assertEqual(counts.left_insertions, 0)
|
|
self.assertEqual(counts.left_deletions, 0)
|
|
self.assertEqual(counts.right_insertions, 0)
|
|
self.assertEqual(counts.right_deletions, 0)
|
|
self.assertEqual(counts.internal_insertions, 0)
|
|
self.assertEqual(counts.internal_deletions, 134)
|
|
self.assertEqual(counts.left_gaps, 0)
|
|
self.assertEqual(counts.right_gaps, 0)
|
|
self.assertEqual(counts.internal_gaps, 134)
|
|
self.assertEqual(counts.insertions, 0)
|
|
self.assertEqual(counts.deletions, 134)
|
|
self.assertEqual(counts.gaps, 134)
|
|
self.assertEqual(counts.aligned, 36)
|
|
alignment = next(alignments)
|
|
self.assertEqual(alignment.score, 1000)
|
|
self.assertEqual(alignment.shape, (2, 39))
|
|
self.assertLess(alignment.coordinates[0, 0], alignment.coordinates[0, -1])
|
|
self.assertLess(alignment.coordinates[1, 0], alignment.coordinates[1, -1])
|
|
self.assertEqual(len(alignment), 2)
|
|
self.assertIs(alignment.sequences[0], alignment.target)
|
|
self.assertIs(alignment.sequences[1], alignment.query)
|
|
self.assertEqual(alignment.target.id, "chr18")
|
|
self.assertEqual(alignment.query.id, "hg19_dna")
|
|
self.assertTrue(
|
|
np.array_equal(
|
|
alignment.coordinates,
|
|
# fmt: off
|
|
np.array([[23891310, 23891349],
|
|
[ 0, 39]]),
|
|
# fmt: on
|
|
)
|
|
)
|
|
self.assertEqual(
|
|
str(alignment),
|
|
"""\
|
|
chr18 23891310 ??????????????????????????????????????? 23891349
|
|
0 ||||||||||||||||||||||||||||||||||||||| 39
|
|
hg19_dna 0 ??????????????????????????????????????? 39
|
|
""",
|
|
)
|
|
self.assertEqual(
|
|
format(alignment, "bed"),
|
|
"""\
|
|
chr18 23891310 23891349 hg19_dna 1000 + 23891310 23891349 0 1 39, 0,
|
|
""",
|
|
)
|
|
counts = alignment.counts()
|
|
self.assertEqual(counts.left_insertions, 0)
|
|
self.assertEqual(counts.left_deletions, 0)
|
|
self.assertEqual(counts.right_insertions, 0)
|
|
self.assertEqual(counts.right_deletions, 0)
|
|
self.assertEqual(counts.internal_insertions, 0)
|
|
self.assertEqual(counts.internal_deletions, 0)
|
|
self.assertEqual(counts.left_gaps, 0)
|
|
self.assertEqual(counts.right_gaps, 0)
|
|
self.assertEqual(counts.internal_gaps, 0)
|
|
self.assertEqual(counts.insertions, 0)
|
|
self.assertEqual(counts.deletions, 0)
|
|
self.assertEqual(counts.gaps, 0)
|
|
self.assertEqual(counts.aligned, 39)
|
|
alignment = next(alignments)
|
|
self.assertEqual(alignment.score, 930)
|
|
self.assertEqual(alignment.shape, (2, 28))
|
|
self.assertLess(alignment.coordinates[0, 0], alignment.coordinates[0, -1])
|
|
self.assertLess(alignment.coordinates[1, 0], alignment.coordinates[1, -1])
|
|
self.assertEqual(len(alignment), 2)
|
|
self.assertIs(alignment.sequences[0], alignment.target)
|
|
self.assertIs(alignment.sequences[1], alignment.query)
|
|
self.assertEqual(alignment.target.id, "chr18")
|
|
self.assertEqual(alignment.query.id, "hg19_dna")
|
|
self.assertTrue(
|
|
np.array_equal(
|
|
alignment.coordinates,
|
|
# fmt: off
|
|
np.array([[43252217, 43252245],
|
|
[ 0, 28]]),
|
|
# fmt: on
|
|
)
|
|
)
|
|
self.assertEqual(
|
|
str(alignment),
|
|
"""\
|
|
chr18 43252217 ???????????????????????????? 43252245
|
|
0 |||||||||||||||||||||||||||| 28
|
|
hg19_dna 0 ???????????????????????????? 28
|
|
""",
|
|
)
|
|
self.assertEqual(
|
|
format(alignment, "bed"),
|
|
"""\
|
|
chr18 43252217 43252245 hg19_dna 930 + 43252217 43252245 0 1 28, 0,
|
|
""",
|
|
)
|
|
counts = alignment.counts()
|
|
self.assertEqual(counts.left_insertions, 0)
|
|
self.assertEqual(counts.left_deletions, 0)
|
|
self.assertEqual(counts.right_insertions, 0)
|
|
self.assertEqual(counts.right_deletions, 0)
|
|
self.assertEqual(counts.internal_insertions, 0)
|
|
self.assertEqual(counts.internal_deletions, 0)
|
|
self.assertEqual(counts.left_gaps, 0)
|
|
self.assertEqual(counts.right_gaps, 0)
|
|
self.assertEqual(counts.internal_gaps, 0)
|
|
self.assertEqual(counts.insertions, 0)
|
|
self.assertEqual(counts.deletions, 0)
|
|
self.assertEqual(counts.gaps, 0)
|
|
self.assertEqual(counts.aligned, 28)
|
|
alignment = next(alignments)
|
|
self.assertEqual(alignment.score, 912)
|
|
self.assertEqual(alignment.shape, (2, 51))
|
|
self.assertLess(alignment.coordinates[0, 0], alignment.coordinates[0, -1])
|
|
self.assertLess(alignment.coordinates[1, 0], alignment.coordinates[1, -1])
|
|
self.assertEqual(len(alignment), 2)
|
|
self.assertIs(alignment.sequences[0], alignment.target)
|
|
self.assertIs(alignment.sequences[1], alignment.query)
|
|
self.assertEqual(alignment.target.id, "chr13")
|
|
self.assertEqual(alignment.query.id, "hg19_dna")
|
|
self.assertTrue(
|
|
np.array_equal(
|
|
alignment.coordinates,
|
|
# fmt: off
|
|
np.array([[52759147, 52759154, 52759160, 52759198],
|
|
[ 0, 7, 7, 45]]),
|
|
# fmt: on
|
|
)
|
|
)
|
|
self.assertEqual(
|
|
str(alignment),
|
|
"""\
|
|
chr13 52759147 ??????????????????????????????????????????????????? 52759198
|
|
0 |||||||------|||||||||||||||||||||||||||||||||||||| 51
|
|
hg19_dna 0 ???????------?????????????????????????????????????? 45
|
|
""",
|
|
)
|
|
self.assertEqual(
|
|
format(alignment, "bed"),
|
|
"""\
|
|
chr13 52759147 52759198 hg19_dna 912 + 52759147 52759198 0 2 7,38, 0,13,
|
|
""",
|
|
)
|
|
counts = alignment.counts()
|
|
self.assertEqual(counts.left_insertions, 0)
|
|
self.assertEqual(counts.left_deletions, 0)
|
|
self.assertEqual(counts.right_insertions, 0)
|
|
self.assertEqual(counts.right_deletions, 0)
|
|
self.assertEqual(counts.internal_insertions, 0)
|
|
self.assertEqual(counts.internal_deletions, 6)
|
|
self.assertEqual(counts.left_gaps, 0)
|
|
self.assertEqual(counts.right_gaps, 0)
|
|
self.assertEqual(counts.internal_gaps, 6)
|
|
self.assertEqual(counts.insertions, 0)
|
|
self.assertEqual(counts.deletions, 6)
|
|
self.assertEqual(counts.gaps, 6)
|
|
self.assertEqual(counts.aligned, 45)
|
|
alignment = next(alignments)
|
|
self.assertEqual(alignment.score, 1000)
|
|
self.assertEqual(alignment.shape, (2, 50))
|
|
self.assertLess(alignment.coordinates[0, 0], alignment.coordinates[0, -1])
|
|
self.assertLess(alignment.coordinates[1, 0], alignment.coordinates[1, -1])
|
|
self.assertEqual(len(alignment), 2)
|
|
self.assertIs(alignment.sequences[0], alignment.target)
|
|
self.assertIs(alignment.sequences[1], alignment.query)
|
|
self.assertEqual(alignment.target.id, "chr1")
|
|
self.assertEqual(alignment.query.id, "hg19_dna")
|
|
self.assertTrue(
|
|
np.array_equal(
|
|
alignment.coordinates,
|
|
# fmt: off
|
|
np.array([[1207056, 1207106],
|
|
[ 0, 50]]),
|
|
# fmt: on
|
|
)
|
|
)
|
|
self.assertEqual(
|
|
str(alignment),
|
|
"""\
|
|
chr1 1207056 ?????????????????????????????????????????????????? 1207106
|
|
0 |||||||||||||||||||||||||||||||||||||||||||||||||| 50
|
|
hg19_dna 0 ?????????????????????????????????????????????????? 50
|
|
""",
|
|
)
|
|
self.assertEqual(
|
|
format(alignment, "bed"),
|
|
"""\
|
|
chr1 1207056 1207106 hg19_dna 1000 + 1207056 1207106 0 1 50, 0,
|
|
""",
|
|
)
|
|
counts = alignment.counts()
|
|
self.assertEqual(counts.left_insertions, 0)
|
|
self.assertEqual(counts.left_deletions, 0)
|
|
self.assertEqual(counts.right_insertions, 0)
|
|
self.assertEqual(counts.right_deletions, 0)
|
|
self.assertEqual(counts.internal_insertions, 0)
|
|
self.assertEqual(counts.internal_deletions, 0)
|
|
self.assertEqual(counts.left_gaps, 0)
|
|
self.assertEqual(counts.right_gaps, 0)
|
|
self.assertEqual(counts.internal_gaps, 0)
|
|
self.assertEqual(counts.insertions, 0)
|
|
self.assertEqual(counts.deletions, 0)
|
|
self.assertEqual(counts.gaps, 0)
|
|
self.assertEqual(counts.aligned, 50)
|
|
alignment = next(alignments)
|
|
self.assertEqual(alignment.score, 824)
|
|
self.assertEqual(alignment.shape, (2, 34))
|
|
self.assertLess(alignment.coordinates[0, 0], alignment.coordinates[0, -1])
|
|
self.assertLess(alignment.coordinates[1, 0], alignment.coordinates[1, -1])
|
|
self.assertEqual(len(alignment), 2)
|
|
self.assertIs(alignment.sequences[0], alignment.target)
|
|
self.assertIs(alignment.sequences[1], alignment.query)
|
|
self.assertEqual(alignment.target.id, "chr1")
|
|
self.assertEqual(alignment.query.id, "hg19_dna")
|
|
self.assertTrue(
|
|
np.array_equal(
|
|
alignment.coordinates,
|
|
# fmt: off
|
|
np.array([[61700837, 61700871],
|
|
[ 0, 34]]),
|
|
# fmt: on
|
|
)
|
|
)
|
|
self.assertEqual(
|
|
str(alignment),
|
|
"""\
|
|
chr1 61700837 ?????????????????????????????????? 61700871
|
|
0 |||||||||||||||||||||||||||||||||| 34
|
|
hg19_dna 0 ?????????????????????????????????? 34
|
|
""",
|
|
)
|
|
self.assertEqual(
|
|
format(alignment, "bed"),
|
|
"""\
|
|
chr1 61700837 61700871 hg19_dna 824 + 61700837 61700871 0 1 34, 0,
|
|
""",
|
|
)
|
|
counts = alignment.counts()
|
|
self.assertEqual(counts.left_insertions, 0)
|
|
self.assertEqual(counts.left_deletions, 0)
|
|
self.assertEqual(counts.right_insertions, 0)
|
|
self.assertEqual(counts.right_deletions, 0)
|
|
self.assertEqual(counts.internal_insertions, 0)
|
|
self.assertEqual(counts.internal_deletions, 0)
|
|
self.assertEqual(counts.left_gaps, 0)
|
|
self.assertEqual(counts.right_gaps, 0)
|
|
self.assertEqual(counts.internal_gaps, 0)
|
|
self.assertEqual(counts.insertions, 0)
|
|
self.assertEqual(counts.deletions, 0)
|
|
self.assertEqual(counts.gaps, 0)
|
|
self.assertEqual(counts.aligned, 34)
|
|
alignment = next(alignments)
|
|
self.assertEqual(alignment.score, 572)
|
|
self.assertEqual(alignment.shape, (2, 34))
|
|
self.assertLess(alignment.coordinates[0, 0], alignment.coordinates[0, -1])
|
|
self.assertGreater(alignment.coordinates[1, 0], alignment.coordinates[1, -1])
|
|
self.assertEqual(len(alignment), 2)
|
|
self.assertIs(alignment.sequences[0], alignment.target)
|
|
self.assertIs(alignment.sequences[1], alignment.query)
|
|
self.assertEqual(alignment.target.id, "chr4")
|
|
self.assertEqual(alignment.query.id, "hg19_dna")
|
|
self.assertTrue(
|
|
np.array_equal(
|
|
alignment.coordinates,
|
|
# fmt: off
|
|
np.array([[37558157, 37558167, 37558173, 37558191],
|
|
[ 28, 18, 18, 0]]),
|
|
# fmt: on
|
|
)
|
|
)
|
|
self.assertEqual(
|
|
str(alignment),
|
|
"""\
|
|
chr4 37558157 ?????????????????????????????????? 37558191
|
|
0 ||||||||||------|||||||||||||||||| 34
|
|
hg19_dna 28 ??????????------?????????????????? 0
|
|
""",
|
|
)
|
|
self.assertEqual(
|
|
format(alignment, "bed"),
|
|
"""\
|
|
chr4 37558157 37558191 hg19_dna 572 - 37558157 37558191 0 2 10,18, 0,16,
|
|
""",
|
|
)
|
|
counts = alignment.counts()
|
|
self.assertEqual(counts.left_insertions, 0)
|
|
self.assertEqual(counts.left_deletions, 0)
|
|
self.assertEqual(counts.right_insertions, 0)
|
|
self.assertEqual(counts.right_deletions, 0)
|
|
self.assertEqual(counts.internal_insertions, 0)
|
|
self.assertEqual(counts.internal_deletions, 6)
|
|
self.assertEqual(counts.left_gaps, 0)
|
|
self.assertEqual(counts.right_gaps, 0)
|
|
self.assertEqual(counts.internal_gaps, 6)
|
|
self.assertEqual(counts.insertions, 0)
|
|
self.assertEqual(counts.deletions, 6)
|
|
self.assertEqual(counts.gaps, 6)
|
|
self.assertEqual(counts.aligned, 28)
|
|
alignment = next(alignments)
|
|
self.assertEqual(alignment.score, 892)
|
|
self.assertEqual(alignment.shape, (2, 37))
|
|
self.assertLess(alignment.coordinates[0, 0], alignment.coordinates[0, -1])
|
|
self.assertGreater(alignment.coordinates[1, 0], alignment.coordinates[1, -1])
|
|
self.assertEqual(len(alignment), 2)
|
|
self.assertIs(alignment.sequences[0], alignment.target)
|
|
self.assertIs(alignment.sequences[1], alignment.query)
|
|
self.assertEqual(alignment.target.id, "chr22")
|
|
self.assertEqual(alignment.query.id, "hg19_dna")
|
|
self.assertTrue(
|
|
np.array_equal(
|
|
alignment.coordinates,
|
|
# fmt: off
|
|
np.array([[48997405, 48997442],
|
|
[ 37, 0]]),
|
|
# fmt: on
|
|
)
|
|
)
|
|
self.assertEqual(
|
|
str(alignment),
|
|
"""\
|
|
chr22 48997405 ????????????????????????????????????? 48997442
|
|
0 ||||||||||||||||||||||||||||||||||||| 37
|
|
hg19_dna 37 ????????????????????????????????????? 0
|
|
""",
|
|
)
|
|
self.assertEqual(
|
|
format(alignment, "bed"),
|
|
"""\
|
|
chr22 48997405 48997442 hg19_dna 892 - 48997405 48997442 0 1 37, 0,
|
|
""",
|
|
)
|
|
counts = alignment.counts()
|
|
self.assertEqual(counts.left_insertions, 0)
|
|
self.assertEqual(counts.left_deletions, 0)
|
|
self.assertEqual(counts.right_insertions, 0)
|
|
self.assertEqual(counts.right_deletions, 0)
|
|
self.assertEqual(counts.internal_insertions, 0)
|
|
self.assertEqual(counts.internal_deletions, 0)
|
|
self.assertEqual(counts.left_gaps, 0)
|
|
self.assertEqual(counts.right_gaps, 0)
|
|
self.assertEqual(counts.internal_gaps, 0)
|
|
self.assertEqual(counts.insertions, 0)
|
|
self.assertEqual(counts.deletions, 0)
|
|
self.assertEqual(counts.gaps, 0)
|
|
self.assertEqual(counts.aligned, 37)
|
|
alignment = next(alignments)
|
|
self.assertEqual(alignment.score, 946)
|
|
self.assertEqual(alignment.shape, (2, 36))
|
|
self.assertLess(alignment.coordinates[0, 0], alignment.coordinates[0, -1])
|
|
self.assertGreater(alignment.coordinates[1, 0], alignment.coordinates[1, -1])
|
|
self.assertEqual(len(alignment), 2)
|
|
self.assertIs(alignment.sequences[0], alignment.target)
|
|
self.assertIs(alignment.sequences[1], alignment.query)
|
|
self.assertEqual(alignment.target.id, "chr2")
|
|
self.assertEqual(alignment.query.id, "hg19_dna")
|
|
self.assertTrue(
|
|
np.array_equal(
|
|
alignment.coordinates,
|
|
# fmt: off
|
|
np.array([[120641740, 120641776],
|
|
[ 36, 0]]),
|
|
# fmt: on
|
|
)
|
|
)
|
|
self.assertEqual(
|
|
str(alignment),
|
|
"""\
|
|
chr2 120641740 ???????????????????????????????????? 120641776
|
|
0 |||||||||||||||||||||||||||||||||||| 36
|
|
hg19_dna 36 ???????????????????????????????????? 0
|
|
""",
|
|
)
|
|
self.assertEqual(
|
|
format(alignment, "bed"),
|
|
"""\
|
|
chr2 120641740 120641776 hg19_dna 946 - 120641740 120641776 0 1 36, 0,
|
|
""",
|
|
)
|
|
counts = alignment.counts()
|
|
self.assertEqual(counts.left_insertions, 0)
|
|
self.assertEqual(counts.left_deletions, 0)
|
|
self.assertEqual(counts.right_insertions, 0)
|
|
self.assertEqual(counts.right_deletions, 0)
|
|
self.assertEqual(counts.internal_insertions, 0)
|
|
self.assertEqual(counts.internal_deletions, 0)
|
|
self.assertEqual(counts.left_gaps, 0)
|
|
self.assertEqual(counts.right_gaps, 0)
|
|
self.assertEqual(counts.internal_gaps, 0)
|
|
self.assertEqual(counts.insertions, 0)
|
|
self.assertEqual(counts.deletions, 0)
|
|
self.assertEqual(counts.gaps, 0)
|
|
self.assertEqual(counts.aligned, 36)
|
|
alignment = next(alignments)
|
|
self.assertEqual(alignment.score, 1000)
|
|
self.assertEqual(alignment.shape, (2, 39))
|
|
self.assertLess(alignment.coordinates[0, 0], alignment.coordinates[0, -1])
|
|
self.assertGreater(alignment.coordinates[1, 0], alignment.coordinates[1, -1])
|
|
self.assertEqual(len(alignment), 2)
|
|
self.assertIs(alignment.sequences[0], alignment.target)
|
|
self.assertIs(alignment.sequences[1], alignment.query)
|
|
self.assertEqual(alignment.target.id, "chr19")
|
|
self.assertEqual(alignment.query.id, "hg19_dna")
|
|
self.assertTrue(
|
|
np.array_equal(
|
|
alignment.coordinates,
|
|
# fmt: off
|
|
np.array([[54017130, 54017169],
|
|
[ 39, 0]]),
|
|
# fmt: on
|
|
)
|
|
)
|
|
self.assertEqual(
|
|
str(alignment),
|
|
"""\
|
|
chr19 54017130 ??????????????????????????????????????? 54017169
|
|
0 ||||||||||||||||||||||||||||||||||||||| 39
|
|
hg19_dna 39 ??????????????????????????????????????? 0
|
|
""",
|
|
)
|
|
self.assertEqual(
|
|
format(alignment, "bed"),
|
|
"""\
|
|
chr19 54017130 54017169 hg19_dna 1000 - 54017130 54017169 0 1 39, 0,
|
|
""",
|
|
)
|
|
counts = alignment.counts()
|
|
self.assertEqual(counts.left_insertions, 0)
|
|
self.assertEqual(counts.left_deletions, 0)
|
|
self.assertEqual(counts.right_insertions, 0)
|
|
self.assertEqual(counts.right_deletions, 0)
|
|
self.assertEqual(counts.internal_insertions, 0)
|
|
self.assertEqual(counts.internal_deletions, 0)
|
|
self.assertEqual(counts.left_gaps, 0)
|
|
self.assertEqual(counts.right_gaps, 0)
|
|
self.assertEqual(counts.internal_gaps, 0)
|
|
self.assertEqual(counts.insertions, 0)
|
|
self.assertEqual(counts.deletions, 0)
|
|
self.assertEqual(counts.gaps, 0)
|
|
self.assertEqual(counts.aligned, 39)
|
|
alignment = next(alignments)
|
|
self.assertEqual(alignment.score, 848)
|
|
self.assertEqual(alignment.shape, (2, 39))
|
|
self.assertLess(alignment.coordinates[0, 0], alignment.coordinates[0, -1])
|
|
self.assertGreater(alignment.coordinates[1, 0], alignment.coordinates[1, -1])
|
|
self.assertEqual(len(alignment), 2)
|
|
self.assertIs(alignment.sequences[0], alignment.target)
|
|
self.assertIs(alignment.sequences[1], alignment.query)
|
|
self.assertEqual(alignment.target.id, "chr19")
|
|
self.assertEqual(alignment.query.id, "hg19_dna")
|
|
self.assertTrue(
|
|
np.array_equal(
|
|
alignment.coordinates,
|
|
# fmt: off
|
|
np.array([[553742, 553781],
|
|
[ 39, 0]]),
|
|
# fmt: on
|
|
)
|
|
)
|
|
self.assertEqual(
|
|
str(alignment),
|
|
"""\
|
|
chr19 553742 ??????????????????????????????????????? 553781
|
|
0 ||||||||||||||||||||||||||||||||||||||| 39
|
|
hg19_dna 39 ??????????????????????????????????????? 0
|
|
""",
|
|
)
|
|
self.assertEqual(
|
|
format(alignment, "bed"),
|
|
"""\
|
|
chr19 553742 553781 hg19_dna 848 - 553742 553781 0 1 39, 0,
|
|
""",
|
|
)
|
|
counts = alignment.counts()
|
|
self.assertEqual(counts.left_insertions, 0)
|
|
self.assertEqual(counts.left_deletions, 0)
|
|
self.assertEqual(counts.right_insertions, 0)
|
|
self.assertEqual(counts.right_deletions, 0)
|
|
self.assertEqual(counts.internal_insertions, 0)
|
|
self.assertEqual(counts.internal_deletions, 0)
|
|
self.assertEqual(counts.left_gaps, 0)
|
|
self.assertEqual(counts.right_gaps, 0)
|
|
self.assertEqual(counts.internal_gaps, 0)
|
|
self.assertEqual(counts.insertions, 0)
|
|
self.assertEqual(counts.deletions, 0)
|
|
self.assertEqual(counts.gaps, 0)
|
|
self.assertEqual(counts.aligned, 39)
|
|
alignment = next(alignments)
|
|
self.assertEqual(alignment.score, 834)
|
|
self.assertEqual(alignment.shape, (2, 36))
|
|
self.assertLess(alignment.coordinates[0, 0], alignment.coordinates[0, -1])
|
|
self.assertGreater(alignment.coordinates[1, 0], alignment.coordinates[1, -1])
|
|
self.assertEqual(len(alignment), 2)
|
|
self.assertIs(alignment.sequences[0], alignment.target)
|
|
self.assertIs(alignment.sequences[1], alignment.query)
|
|
self.assertEqual(alignment.target.id, "chr10")
|
|
self.assertEqual(alignment.query.id, "hg19_dna")
|
|
self.assertTrue(
|
|
np.array_equal(
|
|
alignment.coordinates,
|
|
# fmt: off
|
|
np.array([[99388555, 99388591],
|
|
[ 36, 0]]),
|
|
# fmt: on
|
|
)
|
|
)
|
|
self.assertEqual(
|
|
str(alignment),
|
|
"""\
|
|
chr10 99388555 ???????????????????????????????????? 99388591
|
|
0 |||||||||||||||||||||||||||||||||||| 36
|
|
hg19_dna 36 ???????????????????????????????????? 0
|
|
""",
|
|
)
|
|
self.assertEqual(
|
|
format(alignment, "bed"),
|
|
"""\
|
|
chr10 99388555 99388591 hg19_dna 834 - 99388555 99388591 0 1 36, 0,
|
|
""",
|
|
)
|
|
counts = alignment.counts()
|
|
self.assertEqual(counts.left_insertions, 0)
|
|
self.assertEqual(counts.left_deletions, 0)
|
|
self.assertEqual(counts.right_insertions, 0)
|
|
self.assertEqual(counts.right_deletions, 0)
|
|
self.assertEqual(counts.internal_insertions, 0)
|
|
self.assertEqual(counts.internal_deletions, 0)
|
|
self.assertEqual(counts.left_gaps, 0)
|
|
self.assertEqual(counts.right_gaps, 0)
|
|
self.assertEqual(counts.internal_gaps, 0)
|
|
self.assertEqual(counts.insertions, 0)
|
|
self.assertEqual(counts.deletions, 0)
|
|
self.assertEqual(counts.gaps, 0)
|
|
self.assertEqual(counts.aligned, 36)
|
|
alignment = next(alignments)
|
|
self.assertEqual(alignment.score, 920)
|
|
self.assertEqual(alignment.shape, (2, 25))
|
|
self.assertLess(alignment.coordinates[0, 0], alignment.coordinates[0, -1])
|
|
self.assertGreater(alignment.coordinates[1, 0], alignment.coordinates[1, -1])
|
|
self.assertEqual(len(alignment), 2)
|
|
self.assertIs(alignment.sequences[0], alignment.target)
|
|
self.assertIs(alignment.sequences[1], alignment.query)
|
|
self.assertEqual(alignment.target.id, "chr10")
|
|
self.assertEqual(alignment.query.id, "hg19_dna")
|
|
self.assertTrue(
|
|
np.array_equal(
|
|
alignment.coordinates,
|
|
# fmt: off
|
|
np.array([[112178171, 112178196],
|
|
[ 25, 0]]),
|
|
# fmt: on
|
|
)
|
|
)
|
|
self.assertEqual(
|
|
str(alignment),
|
|
"""\
|
|
chr10 112178171 ????????????????????????? 112178196
|
|
0 ||||||||||||||||||||||||| 25
|
|
hg19_dna 25 ????????????????????????? 0
|
|
""",
|
|
)
|
|
self.assertEqual(
|
|
format(alignment, "bed"),
|
|
"""\
|
|
chr10 112178171 112178196 hg19_dna 920 - 112178171 112178196 0 1 25, 0,
|
|
""",
|
|
)
|
|
counts = alignment.counts()
|
|
self.assertEqual(counts.left_insertions, 0)
|
|
self.assertEqual(counts.left_deletions, 0)
|
|
self.assertEqual(counts.right_insertions, 0)
|
|
self.assertEqual(counts.right_deletions, 0)
|
|
self.assertEqual(counts.internal_insertions, 0)
|
|
self.assertEqual(counts.internal_deletions, 0)
|
|
self.assertEqual(counts.left_gaps, 0)
|
|
self.assertEqual(counts.right_gaps, 0)
|
|
self.assertEqual(counts.internal_gaps, 0)
|
|
self.assertEqual(counts.insertions, 0)
|
|
self.assertEqual(counts.deletions, 0)
|
|
self.assertEqual(counts.gaps, 0)
|
|
self.assertEqual(counts.aligned, 25)
|
|
alignment = next(alignments)
|
|
self.assertEqual(alignment.score, 946)
|
|
self.assertEqual(alignment.shape, (2, 36))
|
|
self.assertLess(alignment.coordinates[0, 0], alignment.coordinates[0, -1])
|
|
self.assertGreater(alignment.coordinates[1, 0], alignment.coordinates[1, -1])
|
|
self.assertEqual(len(alignment), 2)
|
|
self.assertIs(alignment.sequences[0], alignment.target)
|
|
self.assertIs(alignment.sequences[1], alignment.query)
|
|
self.assertEqual(alignment.target.id, "chr1")
|
|
self.assertEqual(alignment.query.id, "hg19_dna")
|
|
self.assertTrue(
|
|
np.array_equal(
|
|
alignment.coordinates,
|
|
# fmt: off
|
|
np.array([[39368490, 39368526],
|
|
[ 36, 0]]),
|
|
# fmt: on
|
|
)
|
|
)
|
|
self.assertEqual(
|
|
str(alignment),
|
|
"""\
|
|
chr1 39368490 ???????????????????????????????????? 39368526
|
|
0 |||||||||||||||||||||||||||||||||||| 36
|
|
hg19_dna 36 ???????????????????????????????????? 0
|
|
""",
|
|
)
|
|
self.assertEqual(
|
|
format(alignment, "bed"),
|
|
"""\
|
|
chr1 39368490 39368526 hg19_dna 946 - 39368490 39368526 0 1 36, 0,
|
|
""",
|
|
)
|
|
counts = alignment.counts()
|
|
self.assertEqual(counts.left_insertions, 0)
|
|
self.assertEqual(counts.left_deletions, 0)
|
|
self.assertEqual(counts.right_insertions, 0)
|
|
self.assertEqual(counts.right_deletions, 0)
|
|
self.assertEqual(counts.internal_insertions, 0)
|
|
self.assertEqual(counts.internal_deletions, 0)
|
|
self.assertEqual(counts.left_gaps, 0)
|
|
self.assertEqual(counts.right_gaps, 0)
|
|
self.assertEqual(counts.internal_gaps, 0)
|
|
self.assertEqual(counts.insertions, 0)
|
|
self.assertEqual(counts.deletions, 0)
|
|
self.assertEqual(counts.gaps, 0)
|
|
self.assertEqual(counts.aligned, 36)
|
|
alignment = next(alignments)
|
|
self.assertEqual(alignment.score, 942)
|
|
self.assertEqual(alignment.shape, (2, 34))
|
|
self.assertLess(alignment.coordinates[0, 0], alignment.coordinates[0, -1])
|
|
self.assertGreater(alignment.coordinates[1, 0], alignment.coordinates[1, -1])
|
|
self.assertEqual(len(alignment), 2)
|
|
self.assertIs(alignment.sequences[0], alignment.target)
|
|
self.assertIs(alignment.sequences[1], alignment.query)
|
|
self.assertEqual(alignment.target.id, "chr1")
|
|
self.assertEqual(alignment.query.id, "hg19_dna")
|
|
self.assertTrue(
|
|
np.array_equal(
|
|
alignment.coordinates,
|
|
# fmt: off
|
|
np.array([[220325687, 220325721],
|
|
[ 34, 0]]),
|
|
# fmt: on
|
|
)
|
|
)
|
|
self.assertEqual(
|
|
str(alignment),
|
|
"""\
|
|
chr1 220325687 ?????????????????????????????????? 220325721
|
|
0 |||||||||||||||||||||||||||||||||| 34
|
|
hg19_dna 34 ?????????????????????????????????? 0
|
|
""",
|
|
)
|
|
self.assertEqual(
|
|
format(alignment, "bed"),
|
|
"""\
|
|
chr1 220325687 220325721 hg19_dna 942 - 220325687 220325721 0 1 34, 0,
|
|
""",
|
|
)
|
|
counts = alignment.counts()
|
|
self.assertEqual(counts.left_insertions, 0)
|
|
self.assertEqual(counts.left_deletions, 0)
|
|
self.assertEqual(counts.right_insertions, 0)
|
|
self.assertEqual(counts.right_deletions, 0)
|
|
self.assertEqual(counts.internal_insertions, 0)
|
|
self.assertEqual(counts.internal_deletions, 0)
|
|
self.assertEqual(counts.left_gaps, 0)
|
|
self.assertEqual(counts.right_gaps, 0)
|
|
self.assertEqual(counts.internal_gaps, 0)
|
|
self.assertEqual(counts.insertions, 0)
|
|
self.assertEqual(counts.deletions, 0)
|
|
self.assertEqual(counts.gaps, 0)
|
|
self.assertEqual(counts.aligned, 34)
|
|
self.assertRaises(StopIteration, next, alignments)
|
|
|
|
def test_writing_psl_34_004(self):
|
|
"""Test writing the alignments in psl_34_004.bed."""
|
|
path = "Blat/psl_34_004.bed"
|
|
with open(path) as stream:
|
|
original_data = stream.read()
|
|
alignments = Align.parse(path, "bed")
|
|
stream = StringIO()
|
|
n = Align.write(alignments, stream, "bed")
|
|
self.assertEqual(n, 19)
|
|
stream.seek(0)
|
|
written_data = stream.read()
|
|
stream.close()
|
|
self.assertEqual(original_data, written_data)
|
|
|
|
def test_reading_psl_34_005(self):
|
|
"""Test parsing psl_34_005.bed."""
|
|
path = "Blat/psl_34_005.bed"
|
|
alignments = Align.parse(path, "bed")
|
|
alignment = next(alignments)
|
|
self.assertEqual(alignment.score, 1000)
|
|
self.assertEqual(alignment.shape, (2, 16))
|
|
self.assertLess(alignment.coordinates[0, 0], alignment.coordinates[0, -1])
|
|
self.assertLess(alignment.coordinates[1, 0], alignment.coordinates[1, -1])
|
|
self.assertEqual(len(alignment), 2)
|
|
self.assertIs(alignment.sequences[0], alignment.target)
|
|
self.assertIs(alignment.sequences[1], alignment.query)
|
|
self.assertEqual(alignment.target.id, "chr4")
|
|
self.assertEqual(alignment.query.id, "hg19_dna")
|
|
self.assertTrue(
|
|
np.array_equal(
|
|
alignment.coordinates,
|
|
# fmt: off
|
|
np.array([[61646095, 61646111],
|
|
[ 0, 16]]),
|
|
# fmt: on
|
|
)
|
|
)
|
|
self.assertEqual(
|
|
str(alignment),
|
|
"""\
|
|
chr4 61646095 ???????????????? 61646111
|
|
0 |||||||||||||||| 16
|
|
hg19_dna 0 ???????????????? 16
|
|
""",
|
|
)
|
|
self.assertEqual(
|
|
format(alignment, "bed"),
|
|
"""\
|
|
chr4 61646095 61646111 hg19_dna 1000 + 61646095 61646111 0 1 16, 0,
|
|
""",
|
|
)
|
|
counts = alignment.counts()
|
|
self.assertEqual(counts.left_insertions, 0)
|
|
self.assertEqual(counts.left_deletions, 0)
|
|
self.assertEqual(counts.right_insertions, 0)
|
|
self.assertEqual(counts.right_deletions, 0)
|
|
self.assertEqual(counts.internal_insertions, 0)
|
|
self.assertEqual(counts.internal_deletions, 0)
|
|
self.assertEqual(counts.left_gaps, 0)
|
|
self.assertEqual(counts.right_gaps, 0)
|
|
self.assertEqual(counts.internal_gaps, 0)
|
|
self.assertEqual(counts.insertions, 0)
|
|
self.assertEqual(counts.deletions, 0)
|
|
self.assertEqual(counts.gaps, 0)
|
|
self.assertEqual(counts.aligned, 16)
|
|
alignment = next(alignments)
|
|
self.assertEqual(alignment.score, 1000)
|
|
self.assertEqual(alignment.shape, (2, 33))
|
|
self.assertLess(alignment.coordinates[0, 0], alignment.coordinates[0, -1])
|
|
self.assertLess(alignment.coordinates[1, 0], alignment.coordinates[1, -1])
|
|
self.assertEqual(len(alignment), 2)
|
|
self.assertIs(alignment.sequences[0], alignment.target)
|
|
self.assertIs(alignment.sequences[1], alignment.query)
|
|
self.assertEqual(alignment.target.id, "chr1")
|
|
self.assertEqual(alignment.query.id, "hg19_dna")
|
|
self.assertTrue(
|
|
np.array_equal(
|
|
alignment.coordinates,
|
|
# fmt: off
|
|
np.array([[10271783, 10271816],
|
|
[ 0, 33]]),
|
|
# fmt: on
|
|
)
|
|
)
|
|
self.assertEqual(
|
|
str(alignment),
|
|
"""\
|
|
chr1 10271783 ????????????????????????????????? 10271816
|
|
0 ||||||||||||||||||||||||||||||||| 33
|
|
hg19_dna 0 ????????????????????????????????? 33
|
|
""",
|
|
)
|
|
self.assertEqual(
|
|
format(alignment, "bed"),
|
|
"""\
|
|
chr1 10271783 10271816 hg19_dna 1000 + 10271783 10271816 0 1 33, 0,
|
|
""",
|
|
)
|
|
counts = alignment.counts()
|
|
self.assertEqual(counts.left_insertions, 0)
|
|
self.assertEqual(counts.left_deletions, 0)
|
|
self.assertEqual(counts.right_insertions, 0)
|
|
self.assertEqual(counts.right_deletions, 0)
|
|
self.assertEqual(counts.internal_insertions, 0)
|
|
self.assertEqual(counts.internal_deletions, 0)
|
|
self.assertEqual(counts.left_gaps, 0)
|
|
self.assertEqual(counts.right_gaps, 0)
|
|
self.assertEqual(counts.internal_gaps, 0)
|
|
self.assertEqual(counts.insertions, 0)
|
|
self.assertEqual(counts.deletions, 0)
|
|
self.assertEqual(counts.gaps, 0)
|
|
self.assertEqual(counts.aligned, 33)
|
|
alignment = next(alignments)
|
|
self.assertEqual(alignment.score, 1000)
|
|
self.assertEqual(alignment.shape, (2, 17))
|
|
self.assertLess(alignment.coordinates[0, 0], alignment.coordinates[0, -1])
|
|
self.assertGreater(alignment.coordinates[1, 0], alignment.coordinates[1, -1])
|
|
self.assertEqual(len(alignment), 2)
|
|
self.assertIs(alignment.sequences[0], alignment.target)
|
|
self.assertIs(alignment.sequences[1], alignment.query)
|
|
self.assertEqual(alignment.target.id, "chr2")
|
|
self.assertEqual(alignment.query.id, "hg19_dna")
|
|
self.assertTrue(
|
|
np.array_equal(
|
|
alignment.coordinates,
|
|
# fmt: off
|
|
np.array([[53575980, 53575997],
|
|
[ 17, 0]]),
|
|
# fmt: on
|
|
)
|
|
)
|
|
self.assertEqual(
|
|
str(alignment),
|
|
"""\
|
|
chr2 53575980 ????????????????? 53575997
|
|
0 ||||||||||||||||| 17
|
|
hg19_dna 17 ????????????????? 0
|
|
""",
|
|
)
|
|
self.assertEqual(
|
|
format(alignment, "bed"),
|
|
"""\
|
|
chr2 53575980 53575997 hg19_dna 1000 - 53575980 53575997 0 1 17, 0,
|
|
""",
|
|
)
|
|
counts = alignment.counts()
|
|
self.assertEqual(counts.left_insertions, 0)
|
|
self.assertEqual(counts.left_deletions, 0)
|
|
self.assertEqual(counts.right_insertions, 0)
|
|
self.assertEqual(counts.right_deletions, 0)
|
|
self.assertEqual(counts.internal_insertions, 0)
|
|
self.assertEqual(counts.internal_deletions, 0)
|
|
self.assertEqual(counts.left_gaps, 0)
|
|
self.assertEqual(counts.right_gaps, 0)
|
|
self.assertEqual(counts.internal_gaps, 0)
|
|
self.assertEqual(counts.insertions, 0)
|
|
self.assertEqual(counts.deletions, 0)
|
|
self.assertEqual(counts.gaps, 0)
|
|
self.assertEqual(counts.aligned, 17)
|
|
alignment = next(alignments)
|
|
self.assertEqual(alignment.score, 854)
|
|
self.assertEqual(alignment.shape, (2, 41))
|
|
self.assertLess(alignment.coordinates[0, 0], alignment.coordinates[0, -1])
|
|
self.assertLess(alignment.coordinates[1, 0], alignment.coordinates[1, -1])
|
|
self.assertEqual(len(alignment), 2)
|
|
self.assertIs(alignment.sequences[0], alignment.target)
|
|
self.assertIs(alignment.sequences[1], alignment.query)
|
|
self.assertEqual(alignment.target.id, "chr9")
|
|
self.assertEqual(alignment.query.id, "hg19_dna")
|
|
self.assertTrue(
|
|
np.array_equal(
|
|
alignment.coordinates,
|
|
# fmt: off
|
|
np.array([[85737865, 85737906],
|
|
[ 0, 41]]),
|
|
# fmt: on
|
|
)
|
|
)
|
|
self.assertEqual(
|
|
str(alignment),
|
|
"""\
|
|
chr9 85737865 ????????????????????????????????????????? 85737906
|
|
0 ||||||||||||||||||||||||||||||||||||||||| 41
|
|
hg19_dna 0 ????????????????????????????????????????? 41
|
|
""",
|
|
)
|
|
self.assertEqual(
|
|
format(alignment, "bed"),
|
|
"""\
|
|
chr9 85737865 85737906 hg19_dna 854 + 85737865 85737906 0 1 41, 0,
|
|
""",
|
|
)
|
|
counts = alignment.counts()
|
|
self.assertEqual(counts.left_insertions, 0)
|
|
self.assertEqual(counts.left_deletions, 0)
|
|
self.assertEqual(counts.right_insertions, 0)
|
|
self.assertEqual(counts.right_deletions, 0)
|
|
self.assertEqual(counts.internal_insertions, 0)
|
|
self.assertEqual(counts.internal_deletions, 0)
|
|
self.assertEqual(counts.left_gaps, 0)
|
|
self.assertEqual(counts.right_gaps, 0)
|
|
self.assertEqual(counts.internal_gaps, 0)
|
|
self.assertEqual(counts.insertions, 0)
|
|
self.assertEqual(counts.deletions, 0)
|
|
self.assertEqual(counts.gaps, 0)
|
|
self.assertEqual(counts.aligned, 41)
|
|
alignment = next(alignments)
|
|
self.assertEqual(alignment.score, 1000)
|
|
self.assertEqual(alignment.shape, (2, 41))
|
|
self.assertLess(alignment.coordinates[0, 0], alignment.coordinates[0, -1])
|
|
self.assertLess(alignment.coordinates[1, 0], alignment.coordinates[1, -1])
|
|
self.assertEqual(len(alignment), 2)
|
|
self.assertIs(alignment.sequences[0], alignment.target)
|
|
self.assertIs(alignment.sequences[1], alignment.query)
|
|
self.assertEqual(alignment.target.id, "chr8")
|
|
self.assertEqual(alignment.query.id, "hg19_dna")
|
|
self.assertTrue(
|
|
np.array_equal(
|
|
alignment.coordinates,
|
|
# fmt: off
|
|
np.array([[95160479, 95160520],
|
|
[ 0, 41]]),
|
|
# fmt: on
|
|
)
|
|
)
|
|
self.assertEqual(
|
|
str(alignment),
|
|
"""\
|
|
chr8 95160479 ????????????????????????????????????????? 95160520
|
|
0 ||||||||||||||||||||||||||||||||||||||||| 41
|
|
hg19_dna 0 ????????????????????????????????????????? 41
|
|
""",
|
|
)
|
|
self.assertEqual(
|
|
format(alignment, "bed"),
|
|
"""\
|
|
chr8 95160479 95160520 hg19_dna 1000 + 95160479 95160520 0 1 41, 0,
|
|
""",
|
|
)
|
|
counts = alignment.counts()
|
|
self.assertEqual(counts.left_insertions, 0)
|
|
self.assertEqual(counts.left_deletions, 0)
|
|
self.assertEqual(counts.right_insertions, 0)
|
|
self.assertEqual(counts.right_deletions, 0)
|
|
self.assertEqual(counts.internal_insertions, 0)
|
|
self.assertEqual(counts.internal_deletions, 0)
|
|
self.assertEqual(counts.left_gaps, 0)
|
|
self.assertEqual(counts.right_gaps, 0)
|
|
self.assertEqual(counts.internal_gaps, 0)
|
|
self.assertEqual(counts.insertions, 0)
|
|
self.assertEqual(counts.deletions, 0)
|
|
self.assertEqual(counts.gaps, 0)
|
|
self.assertEqual(counts.aligned, 41)
|
|
alignment = next(alignments)
|
|
self.assertEqual(alignment.score, 834)
|
|
self.assertEqual(alignment.shape, (2, 36))
|
|
self.assertLess(alignment.coordinates[0, 0], alignment.coordinates[0, -1])
|
|
self.assertLess(alignment.coordinates[1, 0], alignment.coordinates[1, -1])
|
|
self.assertEqual(len(alignment), 2)
|
|
self.assertIs(alignment.sequences[0], alignment.target)
|
|
self.assertIs(alignment.sequences[1], alignment.query)
|
|
self.assertEqual(alignment.target.id, "chr22")
|
|
self.assertEqual(alignment.query.id, "hg19_dna")
|
|
self.assertTrue(
|
|
np.array_equal(
|
|
alignment.coordinates,
|
|
# fmt: off
|
|
np.array([[42144400, 42144436],
|
|
[ 0, 36]]),
|
|
# fmt: on
|
|
)
|
|
)
|
|
self.assertEqual(
|
|
str(alignment),
|
|
"""\
|
|
chr22 42144400 ???????????????????????????????????? 42144436
|
|
0 |||||||||||||||||||||||||||||||||||| 36
|
|
hg19_dna 0 ???????????????????????????????????? 36
|
|
""",
|
|
)
|
|
self.assertEqual(
|
|
format(alignment, "bed"),
|
|
"""\
|
|
chr22 42144400 42144436 hg19_dna 834 + 42144400 42144436 0 1 36, 0,
|
|
""",
|
|
)
|
|
counts = alignment.counts()
|
|
self.assertEqual(counts.left_insertions, 0)
|
|
self.assertEqual(counts.left_deletions, 0)
|
|
self.assertEqual(counts.right_insertions, 0)
|
|
self.assertEqual(counts.right_deletions, 0)
|
|
self.assertEqual(counts.internal_insertions, 0)
|
|
self.assertEqual(counts.internal_deletions, 0)
|
|
self.assertEqual(counts.left_gaps, 0)
|
|
self.assertEqual(counts.right_gaps, 0)
|
|
self.assertEqual(counts.internal_gaps, 0)
|
|
self.assertEqual(counts.insertions, 0)
|
|
self.assertEqual(counts.deletions, 0)
|
|
self.assertEqual(counts.gaps, 0)
|
|
self.assertEqual(counts.aligned, 36)
|
|
alignment = next(alignments)
|
|
self.assertEqual(alignment.score, 682)
|
|
self.assertEqual(alignment.shape, (2, 44))
|
|
self.assertLess(alignment.coordinates[0, 0], alignment.coordinates[0, -1])
|
|
self.assertLess(alignment.coordinates[1, 0], alignment.coordinates[1, -1])
|
|
self.assertEqual(len(alignment), 2)
|
|
self.assertIs(alignment.sequences[0], alignment.target)
|
|
self.assertIs(alignment.sequences[1], alignment.query)
|
|
self.assertEqual(alignment.target.id, "chr2")
|
|
self.assertEqual(alignment.query.id, "hg19_dna")
|
|
self.assertTrue(
|
|
np.array_equal(
|
|
alignment.coordinates,
|
|
# fmt: off
|
|
np.array([[183925984, 183925990, 183926028],
|
|
[ 0, 6, 44]]),
|
|
# fmt: on
|
|
)
|
|
)
|
|
self.assertEqual(
|
|
str(alignment),
|
|
"""\
|
|
chr2 183925984 ???????????????????????????????????????????? 183926028
|
|
0 |||||||||||||||||||||||||||||||||||||||||||| 44
|
|
hg19_dna 0 ???????????????????????????????????????????? 44
|
|
""",
|
|
)
|
|
self.assertEqual(
|
|
format(alignment, "bed"),
|
|
"""\
|
|
chr2 183925984 183926028 hg19_dna 682 + 183925984 183926028 0 2 6,38, 0,6,
|
|
""",
|
|
)
|
|
counts = alignment.counts()
|
|
self.assertEqual(counts.left_insertions, 0)
|
|
self.assertEqual(counts.left_deletions, 0)
|
|
self.assertEqual(counts.right_insertions, 0)
|
|
self.assertEqual(counts.right_deletions, 0)
|
|
self.assertEqual(counts.internal_insertions, 0)
|
|
self.assertEqual(counts.internal_deletions, 0)
|
|
self.assertEqual(counts.left_gaps, 0)
|
|
self.assertEqual(counts.right_gaps, 0)
|
|
self.assertEqual(counts.internal_gaps, 0)
|
|
self.assertEqual(counts.insertions, 0)
|
|
self.assertEqual(counts.deletions, 0)
|
|
self.assertEqual(counts.gaps, 0)
|
|
self.assertEqual(counts.aligned, 44)
|
|
alignment = next(alignments)
|
|
self.assertEqual(alignment.score, 890)
|
|
self.assertEqual(alignment.shape, (2, 170))
|
|
self.assertLess(alignment.coordinates[0, 0], alignment.coordinates[0, -1])
|
|
self.assertLess(alignment.coordinates[1, 0], alignment.coordinates[1, -1])
|
|
self.assertEqual(len(alignment), 2)
|
|
self.assertIs(alignment.sequences[0], alignment.target)
|
|
self.assertIs(alignment.sequences[1], alignment.query)
|
|
self.assertEqual(alignment.target.id, "chr19")
|
|
self.assertEqual(alignment.query.id, "hg19_dna")
|
|
self.assertTrue(
|
|
np.array_equal(
|
|
alignment.coordinates,
|
|
# fmt: off
|
|
np.array([[35483340, 35483365, 35483499, 35483510],
|
|
[ 0, 25, 25, 36]]),
|
|
# fmt: on
|
|
)
|
|
)
|
|
self.assertEqual(
|
|
str(alignment),
|
|
"""\
|
|
chr19 35483340 ????????????????????????????????????????????????????????????
|
|
0 |||||||||||||||||||||||||-----------------------------------
|
|
hg19_dna 0 ?????????????????????????-----------------------------------
|
|
|
|
chr19 35483400 ????????????????????????????????????????????????????????????
|
|
60 ------------------------------------------------------------
|
|
hg19_dna 25 ------------------------------------------------------------
|
|
|
|
chr19 35483460 ?????????????????????????????????????????????????? 35483510
|
|
120 ---------------------------------------||||||||||| 170
|
|
hg19_dna 25 ---------------------------------------??????????? 36
|
|
""",
|
|
)
|
|
self.assertEqual(
|
|
format(alignment, "bed"),
|
|
"""\
|
|
chr19 35483340 35483510 hg19_dna 890 + 35483340 35483510 0 2 25,11, 0,159,
|
|
""",
|
|
)
|
|
counts = alignment.counts()
|
|
self.assertEqual(counts.left_insertions, 0)
|
|
self.assertEqual(counts.left_deletions, 0)
|
|
self.assertEqual(counts.right_insertions, 0)
|
|
self.assertEqual(counts.right_deletions, 0)
|
|
self.assertEqual(counts.internal_insertions, 0)
|
|
self.assertEqual(counts.internal_deletions, 134)
|
|
self.assertEqual(counts.left_gaps, 0)
|
|
self.assertEqual(counts.right_gaps, 0)
|
|
self.assertEqual(counts.internal_gaps, 134)
|
|
self.assertEqual(counts.insertions, 0)
|
|
self.assertEqual(counts.deletions, 134)
|
|
self.assertEqual(counts.gaps, 134)
|
|
self.assertEqual(counts.aligned, 36)
|
|
alignment = next(alignments)
|
|
self.assertEqual(alignment.score, 1000)
|
|
self.assertEqual(alignment.shape, (2, 39))
|
|
self.assertLess(alignment.coordinates[0, 0], alignment.coordinates[0, -1])
|
|
self.assertLess(alignment.coordinates[1, 0], alignment.coordinates[1, -1])
|
|
self.assertEqual(len(alignment), 2)
|
|
self.assertIs(alignment.sequences[0], alignment.target)
|
|
self.assertIs(alignment.sequences[1], alignment.query)
|
|
self.assertEqual(alignment.target.id, "chr18")
|
|
self.assertEqual(alignment.query.id, "hg19_dna")
|
|
self.assertTrue(
|
|
np.array_equal(
|
|
alignment.coordinates,
|
|
# fmt: off
|
|
np.array([[23891310, 23891349],
|
|
[ 0, 39]]),
|
|
# fmt: on
|
|
)
|
|
)
|
|
self.assertEqual(
|
|
str(alignment),
|
|
"""\
|
|
chr18 23891310 ??????????????????????????????????????? 23891349
|
|
0 ||||||||||||||||||||||||||||||||||||||| 39
|
|
hg19_dna 0 ??????????????????????????????????????? 39
|
|
""",
|
|
)
|
|
self.assertEqual(
|
|
format(alignment, "bed"),
|
|
"""\
|
|
chr18 23891310 23891349 hg19_dna 1000 + 23891310 23891349 0 1 39, 0,
|
|
""",
|
|
)
|
|
counts = alignment.counts()
|
|
self.assertEqual(counts.left_insertions, 0)
|
|
self.assertEqual(counts.left_deletions, 0)
|
|
self.assertEqual(counts.right_insertions, 0)
|
|
self.assertEqual(counts.right_deletions, 0)
|
|
self.assertEqual(counts.internal_insertions, 0)
|
|
self.assertEqual(counts.internal_deletions, 0)
|
|
self.assertEqual(counts.left_gaps, 0)
|
|
self.assertEqual(counts.right_gaps, 0)
|
|
self.assertEqual(counts.internal_gaps, 0)
|
|
self.assertEqual(counts.insertions, 0)
|
|
self.assertEqual(counts.deletions, 0)
|
|
self.assertEqual(counts.gaps, 0)
|
|
self.assertEqual(counts.aligned, 39)
|
|
alignment = next(alignments)
|
|
self.assertEqual(alignment.score, 930)
|
|
self.assertEqual(alignment.shape, (2, 28))
|
|
self.assertLess(alignment.coordinates[0, 0], alignment.coordinates[0, -1])
|
|
self.assertLess(alignment.coordinates[1, 0], alignment.coordinates[1, -1])
|
|
self.assertEqual(len(alignment), 2)
|
|
self.assertIs(alignment.sequences[0], alignment.target)
|
|
self.assertIs(alignment.sequences[1], alignment.query)
|
|
self.assertEqual(alignment.target.id, "chr18")
|
|
self.assertEqual(alignment.query.id, "hg19_dna")
|
|
self.assertTrue(
|
|
np.array_equal(
|
|
alignment.coordinates,
|
|
# fmt: off
|
|
np.array([[43252217, 43252245],
|
|
[ 0, 28]]),
|
|
# fmt: on
|
|
)
|
|
)
|
|
self.assertEqual(
|
|
str(alignment),
|
|
"""\
|
|
chr18 43252217 ???????????????????????????? 43252245
|
|
0 |||||||||||||||||||||||||||| 28
|
|
hg19_dna 0 ???????????????????????????? 28
|
|
""",
|
|
)
|
|
self.assertEqual(
|
|
format(alignment, "bed"),
|
|
"""\
|
|
chr18 43252217 43252245 hg19_dna 930 + 43252217 43252245 0 1 28, 0,
|
|
""",
|
|
)
|
|
counts = alignment.counts()
|
|
self.assertEqual(counts.left_insertions, 0)
|
|
self.assertEqual(counts.left_deletions, 0)
|
|
self.assertEqual(counts.right_insertions, 0)
|
|
self.assertEqual(counts.right_deletions, 0)
|
|
self.assertEqual(counts.internal_insertions, 0)
|
|
self.assertEqual(counts.internal_deletions, 0)
|
|
self.assertEqual(counts.left_gaps, 0)
|
|
self.assertEqual(counts.right_gaps, 0)
|
|
self.assertEqual(counts.internal_gaps, 0)
|
|
self.assertEqual(counts.insertions, 0)
|
|
self.assertEqual(counts.deletions, 0)
|
|
self.assertEqual(counts.gaps, 0)
|
|
self.assertEqual(counts.aligned, 28)
|
|
alignment = next(alignments)
|
|
self.assertEqual(alignment.score, 912)
|
|
self.assertEqual(alignment.shape, (2, 51))
|
|
self.assertLess(alignment.coordinates[0, 0], alignment.coordinates[0, -1])
|
|
self.assertLess(alignment.coordinates[1, 0], alignment.coordinates[1, -1])
|
|
self.assertEqual(len(alignment), 2)
|
|
self.assertIs(alignment.sequences[0], alignment.target)
|
|
self.assertIs(alignment.sequences[1], alignment.query)
|
|
self.assertEqual(alignment.target.id, "chr13")
|
|
self.assertEqual(alignment.query.id, "hg19_dna")
|
|
self.assertTrue(
|
|
np.array_equal(
|
|
alignment.coordinates,
|
|
# fmt: off
|
|
np.array([[52759147, 52759154, 52759160, 52759198],
|
|
[ 0, 7, 7, 45]]),
|
|
# fmt: on
|
|
)
|
|
)
|
|
self.assertEqual(
|
|
str(alignment),
|
|
"""\
|
|
chr13 52759147 ??????????????????????????????????????????????????? 52759198
|
|
0 |||||||------|||||||||||||||||||||||||||||||||||||| 51
|
|
hg19_dna 0 ???????------?????????????????????????????????????? 45
|
|
""",
|
|
)
|
|
self.assertEqual(
|
|
format(alignment, "bed"),
|
|
"""\
|
|
chr13 52759147 52759198 hg19_dna 912 + 52759147 52759198 0 2 7,38, 0,13,
|
|
""",
|
|
)
|
|
counts = alignment.counts()
|
|
self.assertEqual(counts.left_insertions, 0)
|
|
self.assertEqual(counts.left_deletions, 0)
|
|
self.assertEqual(counts.right_insertions, 0)
|
|
self.assertEqual(counts.right_deletions, 0)
|
|
self.assertEqual(counts.internal_insertions, 0)
|
|
self.assertEqual(counts.internal_deletions, 6)
|
|
self.assertEqual(counts.left_gaps, 0)
|
|
self.assertEqual(counts.right_gaps, 0)
|
|
self.assertEqual(counts.internal_gaps, 6)
|
|
self.assertEqual(counts.insertions, 0)
|
|
self.assertEqual(counts.deletions, 6)
|
|
self.assertEqual(counts.gaps, 6)
|
|
self.assertEqual(counts.aligned, 45)
|
|
alignment = next(alignments)
|
|
self.assertEqual(alignment.score, 1000)
|
|
self.assertEqual(alignment.shape, (2, 50))
|
|
self.assertLess(alignment.coordinates[0, 0], alignment.coordinates[0, -1])
|
|
self.assertLess(alignment.coordinates[1, 0], alignment.coordinates[1, -1])
|
|
self.assertEqual(len(alignment), 2)
|
|
self.assertIs(alignment.sequences[0], alignment.target)
|
|
self.assertIs(alignment.sequences[1], alignment.query)
|
|
self.assertEqual(alignment.target.id, "chr1")
|
|
self.assertEqual(alignment.query.id, "hg19_dna")
|
|
self.assertTrue(
|
|
np.array_equal(
|
|
alignment.coordinates,
|
|
# fmt: off
|
|
np.array([[1207056, 1207106],
|
|
[ 0, 50]]),
|
|
# fmt: on
|
|
)
|
|
)
|
|
self.assertEqual(
|
|
str(alignment),
|
|
"""\
|
|
chr1 1207056 ?????????????????????????????????????????????????? 1207106
|
|
0 |||||||||||||||||||||||||||||||||||||||||||||||||| 50
|
|
hg19_dna 0 ?????????????????????????????????????????????????? 50
|
|
""",
|
|
)
|
|
self.assertEqual(
|
|
format(alignment, "bed"),
|
|
"""\
|
|
chr1 1207056 1207106 hg19_dna 1000 + 1207056 1207106 0 1 50, 0,
|
|
""",
|
|
)
|
|
counts = alignment.counts()
|
|
self.assertEqual(counts.left_insertions, 0)
|
|
self.assertEqual(counts.left_deletions, 0)
|
|
self.assertEqual(counts.right_insertions, 0)
|
|
self.assertEqual(counts.right_deletions, 0)
|
|
self.assertEqual(counts.internal_insertions, 0)
|
|
self.assertEqual(counts.internal_deletions, 0)
|
|
self.assertEqual(counts.left_gaps, 0)
|
|
self.assertEqual(counts.right_gaps, 0)
|
|
self.assertEqual(counts.internal_gaps, 0)
|
|
self.assertEqual(counts.insertions, 0)
|
|
self.assertEqual(counts.deletions, 0)
|
|
self.assertEqual(counts.gaps, 0)
|
|
self.assertEqual(counts.aligned, 50)
|
|
alignment = next(alignments)
|
|
self.assertEqual(alignment.score, 824)
|
|
self.assertEqual(alignment.shape, (2, 34))
|
|
self.assertLess(alignment.coordinates[0, 0], alignment.coordinates[0, -1])
|
|
self.assertLess(alignment.coordinates[1, 0], alignment.coordinates[1, -1])
|
|
self.assertEqual(len(alignment), 2)
|
|
self.assertIs(alignment.sequences[0], alignment.target)
|
|
self.assertIs(alignment.sequences[1], alignment.query)
|
|
self.assertEqual(alignment.target.id, "chr1")
|
|
self.assertEqual(alignment.query.id, "hg19_dna")
|
|
self.assertTrue(
|
|
np.array_equal(
|
|
alignment.coordinates,
|
|
# fmt: off
|
|
np.array([[61700837, 61700871],
|
|
[ 0, 34]]),
|
|
# fmt: on
|
|
)
|
|
)
|
|
self.assertEqual(
|
|
str(alignment),
|
|
"""\
|
|
chr1 61700837 ?????????????????????????????????? 61700871
|
|
0 |||||||||||||||||||||||||||||||||| 34
|
|
hg19_dna 0 ?????????????????????????????????? 34
|
|
""",
|
|
)
|
|
self.assertEqual(
|
|
format(alignment, "bed"),
|
|
"""\
|
|
chr1 61700837 61700871 hg19_dna 824 + 61700837 61700871 0 1 34, 0,
|
|
""",
|
|
)
|
|
counts = alignment.counts()
|
|
self.assertEqual(counts.left_insertions, 0)
|
|
self.assertEqual(counts.left_deletions, 0)
|
|
self.assertEqual(counts.right_insertions, 0)
|
|
self.assertEqual(counts.right_deletions, 0)
|
|
self.assertEqual(counts.internal_insertions, 0)
|
|
self.assertEqual(counts.internal_deletions, 0)
|
|
self.assertEqual(counts.left_gaps, 0)
|
|
self.assertEqual(counts.right_gaps, 0)
|
|
self.assertEqual(counts.internal_gaps, 0)
|
|
self.assertEqual(counts.insertions, 0)
|
|
self.assertEqual(counts.deletions, 0)
|
|
self.assertEqual(counts.gaps, 0)
|
|
self.assertEqual(counts.aligned, 34)
|
|
alignment = next(alignments)
|
|
self.assertEqual(alignment.score, 572)
|
|
self.assertEqual(alignment.shape, (2, 34))
|
|
self.assertLess(alignment.coordinates[0, 0], alignment.coordinates[0, -1])
|
|
self.assertGreater(alignment.coordinates[1, 0], alignment.coordinates[1, -1])
|
|
self.assertEqual(len(alignment), 2)
|
|
self.assertIs(alignment.sequences[0], alignment.target)
|
|
self.assertIs(alignment.sequences[1], alignment.query)
|
|
self.assertEqual(alignment.target.id, "chr4")
|
|
self.assertEqual(alignment.query.id, "hg19_dna")
|
|
self.assertTrue(
|
|
np.array_equal(
|
|
alignment.coordinates,
|
|
# fmt: off
|
|
np.array([[37558157, 37558167, 37558173, 37558191],
|
|
[ 28, 18, 18, 0]]),
|
|
# fmt: on
|
|
)
|
|
)
|
|
self.assertEqual(
|
|
str(alignment),
|
|
"""\
|
|
chr4 37558157 ?????????????????????????????????? 37558191
|
|
0 ||||||||||------|||||||||||||||||| 34
|
|
hg19_dna 28 ??????????------?????????????????? 0
|
|
""",
|
|
)
|
|
self.assertEqual(
|
|
format(alignment, "bed"),
|
|
"""\
|
|
chr4 37558157 37558191 hg19_dna 572 - 37558157 37558191 0 2 10,18, 0,16,
|
|
""",
|
|
)
|
|
counts = alignment.counts()
|
|
self.assertEqual(counts.left_insertions, 0)
|
|
self.assertEqual(counts.left_deletions, 0)
|
|
self.assertEqual(counts.right_insertions, 0)
|
|
self.assertEqual(counts.right_deletions, 0)
|
|
self.assertEqual(counts.internal_insertions, 0)
|
|
self.assertEqual(counts.internal_deletions, 6)
|
|
self.assertEqual(counts.left_gaps, 0)
|
|
self.assertEqual(counts.right_gaps, 0)
|
|
self.assertEqual(counts.internal_gaps, 6)
|
|
self.assertEqual(counts.insertions, 0)
|
|
self.assertEqual(counts.deletions, 6)
|
|
self.assertEqual(counts.gaps, 6)
|
|
self.assertEqual(counts.aligned, 28)
|
|
alignment = next(alignments)
|
|
self.assertEqual(alignment.score, 892)
|
|
self.assertEqual(alignment.shape, (2, 37))
|
|
self.assertLess(alignment.coordinates[0, 0], alignment.coordinates[0, -1])
|
|
self.assertGreater(alignment.coordinates[1, 0], alignment.coordinates[1, -1])
|
|
self.assertEqual(len(alignment), 2)
|
|
self.assertIs(alignment.sequences[0], alignment.target)
|
|
self.assertIs(alignment.sequences[1], alignment.query)
|
|
self.assertEqual(alignment.target.id, "chr22")
|
|
self.assertEqual(alignment.query.id, "hg19_dna")
|
|
self.assertTrue(
|
|
np.array_equal(
|
|
alignment.coordinates,
|
|
# fmt: off
|
|
np.array([[48997405, 48997442],
|
|
[ 37, 0]]),
|
|
# fmt: on
|
|
)
|
|
)
|
|
self.assertEqual(
|
|
str(alignment),
|
|
"""\
|
|
chr22 48997405 ????????????????????????????????????? 48997442
|
|
0 ||||||||||||||||||||||||||||||||||||| 37
|
|
hg19_dna 37 ????????????????????????????????????? 0
|
|
""",
|
|
)
|
|
self.assertEqual(
|
|
format(alignment, "bed"),
|
|
"""\
|
|
chr22 48997405 48997442 hg19_dna 892 - 48997405 48997442 0 1 37, 0,
|
|
""",
|
|
)
|
|
counts = alignment.counts()
|
|
self.assertEqual(counts.left_insertions, 0)
|
|
self.assertEqual(counts.left_deletions, 0)
|
|
self.assertEqual(counts.right_insertions, 0)
|
|
self.assertEqual(counts.right_deletions, 0)
|
|
self.assertEqual(counts.internal_insertions, 0)
|
|
self.assertEqual(counts.internal_deletions, 0)
|
|
self.assertEqual(counts.left_gaps, 0)
|
|
self.assertEqual(counts.right_gaps, 0)
|
|
self.assertEqual(counts.internal_gaps, 0)
|
|
self.assertEqual(counts.insertions, 0)
|
|
self.assertEqual(counts.deletions, 0)
|
|
self.assertEqual(counts.gaps, 0)
|
|
self.assertEqual(counts.aligned, 37)
|
|
alignment = next(alignments)
|
|
self.assertEqual(alignment.score, 946)
|
|
self.assertEqual(alignment.shape, (2, 36))
|
|
self.assertLess(alignment.coordinates[0, 0], alignment.coordinates[0, -1])
|
|
self.assertGreater(alignment.coordinates[1, 0], alignment.coordinates[1, -1])
|
|
self.assertEqual(len(alignment), 2)
|
|
self.assertIs(alignment.sequences[0], alignment.target)
|
|
self.assertIs(alignment.sequences[1], alignment.query)
|
|
self.assertEqual(alignment.target.id, "chr2")
|
|
self.assertEqual(alignment.query.id, "hg19_dna")
|
|
self.assertTrue(
|
|
np.array_equal(
|
|
alignment.coordinates,
|
|
# fmt: off
|
|
np.array([[120641740, 120641776],
|
|
[ 36, 0]]),
|
|
# fmt: on
|
|
)
|
|
)
|
|
self.assertEqual(
|
|
str(alignment),
|
|
"""\
|
|
chr2 120641740 ???????????????????????????????????? 120641776
|
|
0 |||||||||||||||||||||||||||||||||||| 36
|
|
hg19_dna 36 ???????????????????????????????????? 0
|
|
""",
|
|
)
|
|
self.assertEqual(
|
|
format(alignment, "bed"),
|
|
"""\
|
|
chr2 120641740 120641776 hg19_dna 946 - 120641740 120641776 0 1 36, 0,
|
|
""",
|
|
)
|
|
counts = alignment.counts()
|
|
self.assertEqual(counts.left_insertions, 0)
|
|
self.assertEqual(counts.left_deletions, 0)
|
|
self.assertEqual(counts.right_insertions, 0)
|
|
self.assertEqual(counts.right_deletions, 0)
|
|
self.assertEqual(counts.internal_insertions, 0)
|
|
self.assertEqual(counts.internal_deletions, 0)
|
|
self.assertEqual(counts.left_gaps, 0)
|
|
self.assertEqual(counts.right_gaps, 0)
|
|
self.assertEqual(counts.internal_gaps, 0)
|
|
self.assertEqual(counts.insertions, 0)
|
|
self.assertEqual(counts.deletions, 0)
|
|
self.assertEqual(counts.gaps, 0)
|
|
self.assertEqual(counts.aligned, 36)
|
|
alignment = next(alignments)
|
|
self.assertEqual(alignment.score, 1000)
|
|
self.assertEqual(alignment.shape, (2, 39))
|
|
self.assertLess(alignment.coordinates[0, 0], alignment.coordinates[0, -1])
|
|
self.assertGreater(alignment.coordinates[1, 0], alignment.coordinates[1, -1])
|
|
self.assertEqual(len(alignment), 2)
|
|
self.assertIs(alignment.sequences[0], alignment.target)
|
|
self.assertIs(alignment.sequences[1], alignment.query)
|
|
self.assertEqual(alignment.target.id, "chr19")
|
|
self.assertEqual(alignment.query.id, "hg19_dna")
|
|
self.assertTrue(
|
|
np.array_equal(
|
|
alignment.coordinates,
|
|
# fmt: off
|
|
np.array([[54017130, 54017169],
|
|
[ 39, 0]]),
|
|
# fmt: on
|
|
)
|
|
)
|
|
self.assertEqual(
|
|
str(alignment),
|
|
"""\
|
|
chr19 54017130 ??????????????????????????????????????? 54017169
|
|
0 ||||||||||||||||||||||||||||||||||||||| 39
|
|
hg19_dna 39 ??????????????????????????????????????? 0
|
|
""",
|
|
)
|
|
self.assertEqual(
|
|
format(alignment, "bed"),
|
|
"""\
|
|
chr19 54017130 54017169 hg19_dna 1000 - 54017130 54017169 0 1 39, 0,
|
|
""",
|
|
)
|
|
counts = alignment.counts()
|
|
self.assertEqual(counts.left_insertions, 0)
|
|
self.assertEqual(counts.left_deletions, 0)
|
|
self.assertEqual(counts.right_insertions, 0)
|
|
self.assertEqual(counts.right_deletions, 0)
|
|
self.assertEqual(counts.internal_insertions, 0)
|
|
self.assertEqual(counts.internal_deletions, 0)
|
|
self.assertEqual(counts.left_gaps, 0)
|
|
self.assertEqual(counts.right_gaps, 0)
|
|
self.assertEqual(counts.internal_gaps, 0)
|
|
self.assertEqual(counts.insertions, 0)
|
|
self.assertEqual(counts.deletions, 0)
|
|
self.assertEqual(counts.gaps, 0)
|
|
self.assertEqual(counts.aligned, 39)
|
|
alignment = next(alignments)
|
|
self.assertEqual(alignment.score, 848)
|
|
self.assertEqual(alignment.shape, (2, 39))
|
|
self.assertLess(alignment.coordinates[0, 0], alignment.coordinates[0, -1])
|
|
self.assertGreater(alignment.coordinates[1, 0], alignment.coordinates[1, -1])
|
|
self.assertEqual(len(alignment), 2)
|
|
self.assertIs(alignment.sequences[0], alignment.target)
|
|
self.assertIs(alignment.sequences[1], alignment.query)
|
|
self.assertEqual(alignment.target.id, "chr19")
|
|
self.assertEqual(alignment.query.id, "hg19_dna")
|
|
self.assertTrue(
|
|
np.array_equal(
|
|
alignment.coordinates,
|
|
# fmt: off
|
|
np.array([[553742, 553781],
|
|
[ 39, 0]]),
|
|
# fmt: on
|
|
)
|
|
)
|
|
self.assertEqual(
|
|
str(alignment),
|
|
"""\
|
|
chr19 553742 ??????????????????????????????????????? 553781
|
|
0 ||||||||||||||||||||||||||||||||||||||| 39
|
|
hg19_dna 39 ??????????????????????????????????????? 0
|
|
""",
|
|
)
|
|
self.assertEqual(
|
|
format(alignment, "bed"),
|
|
"""\
|
|
chr19 553742 553781 hg19_dna 848 - 553742 553781 0 1 39, 0,
|
|
""",
|
|
)
|
|
counts = alignment.counts()
|
|
self.assertEqual(counts.left_insertions, 0)
|
|
self.assertEqual(counts.left_deletions, 0)
|
|
self.assertEqual(counts.right_insertions, 0)
|
|
self.assertEqual(counts.right_deletions, 0)
|
|
self.assertEqual(counts.internal_insertions, 0)
|
|
self.assertEqual(counts.internal_deletions, 0)
|
|
self.assertEqual(counts.left_gaps, 0)
|
|
self.assertEqual(counts.right_gaps, 0)
|
|
self.assertEqual(counts.internal_gaps, 0)
|
|
self.assertEqual(counts.insertions, 0)
|
|
self.assertEqual(counts.deletions, 0)
|
|
self.assertEqual(counts.gaps, 0)
|
|
self.assertEqual(counts.aligned, 39)
|
|
alignment = next(alignments)
|
|
self.assertEqual(alignment.score, 834)
|
|
self.assertEqual(alignment.shape, (2, 36))
|
|
self.assertLess(alignment.coordinates[0, 0], alignment.coordinates[0, -1])
|
|
self.assertGreater(alignment.coordinates[1, 0], alignment.coordinates[1, -1])
|
|
self.assertEqual(len(alignment), 2)
|
|
self.assertIs(alignment.sequences[0], alignment.target)
|
|
self.assertIs(alignment.sequences[1], alignment.query)
|
|
self.assertEqual(alignment.target.id, "chr10")
|
|
self.assertEqual(alignment.query.id, "hg19_dna")
|
|
self.assertTrue(
|
|
np.array_equal(
|
|
alignment.coordinates,
|
|
# fmt: off
|
|
np.array([[99388555, 99388591],
|
|
[ 36, 0]]),
|
|
# fmt: on
|
|
)
|
|
)
|
|
self.assertEqual(
|
|
str(alignment),
|
|
"""\
|
|
chr10 99388555 ???????????????????????????????????? 99388591
|
|
0 |||||||||||||||||||||||||||||||||||| 36
|
|
hg19_dna 36 ???????????????????????????????????? 0
|
|
""",
|
|
)
|
|
self.assertEqual(
|
|
format(alignment, "bed"),
|
|
"""\
|
|
chr10 99388555 99388591 hg19_dna 834 - 99388555 99388591 0 1 36, 0,
|
|
""",
|
|
)
|
|
counts = alignment.counts()
|
|
self.assertEqual(counts.left_insertions, 0)
|
|
self.assertEqual(counts.left_deletions, 0)
|
|
self.assertEqual(counts.right_insertions, 0)
|
|
self.assertEqual(counts.right_deletions, 0)
|
|
self.assertEqual(counts.internal_insertions, 0)
|
|
self.assertEqual(counts.internal_deletions, 0)
|
|
self.assertEqual(counts.left_gaps, 0)
|
|
self.assertEqual(counts.right_gaps, 0)
|
|
self.assertEqual(counts.internal_gaps, 0)
|
|
self.assertEqual(counts.insertions, 0)
|
|
self.assertEqual(counts.deletions, 0)
|
|
self.assertEqual(counts.gaps, 0)
|
|
self.assertEqual(counts.aligned, 36)
|
|
alignment = next(alignments)
|
|
self.assertEqual(alignment.score, 920)
|
|
self.assertEqual(alignment.shape, (2, 25))
|
|
self.assertLess(alignment.coordinates[0, 0], alignment.coordinates[0, -1])
|
|
self.assertGreater(alignment.coordinates[1, 0], alignment.coordinates[1, -1])
|
|
self.assertEqual(len(alignment), 2)
|
|
self.assertIs(alignment.sequences[0], alignment.target)
|
|
self.assertIs(alignment.sequences[1], alignment.query)
|
|
self.assertEqual(alignment.target.id, "chr10")
|
|
self.assertEqual(alignment.query.id, "hg19_dna")
|
|
self.assertTrue(
|
|
np.array_equal(
|
|
alignment.coordinates,
|
|
# fmt: off
|
|
np.array([[112178171, 112178196],
|
|
[ 25, 0]]),
|
|
# fmt: on
|
|
)
|
|
)
|
|
self.assertEqual(
|
|
str(alignment),
|
|
"""\
|
|
chr10 112178171 ????????????????????????? 112178196
|
|
0 ||||||||||||||||||||||||| 25
|
|
hg19_dna 25 ????????????????????????? 0
|
|
""",
|
|
)
|
|
self.assertEqual(
|
|
format(alignment, "bed"),
|
|
"""\
|
|
chr10 112178171 112178196 hg19_dna 920 - 112178171 112178196 0 1 25, 0,
|
|
""",
|
|
)
|
|
counts = alignment.counts()
|
|
self.assertEqual(counts.left_insertions, 0)
|
|
self.assertEqual(counts.left_deletions, 0)
|
|
self.assertEqual(counts.right_insertions, 0)
|
|
self.assertEqual(counts.right_deletions, 0)
|
|
self.assertEqual(counts.internal_insertions, 0)
|
|
self.assertEqual(counts.internal_deletions, 0)
|
|
self.assertEqual(counts.left_gaps, 0)
|
|
self.assertEqual(counts.right_gaps, 0)
|
|
self.assertEqual(counts.internal_gaps, 0)
|
|
self.assertEqual(counts.insertions, 0)
|
|
self.assertEqual(counts.deletions, 0)
|
|
self.assertEqual(counts.gaps, 0)
|
|
self.assertEqual(counts.aligned, 25)
|
|
alignment = next(alignments)
|
|
self.assertEqual(alignment.score, 946)
|
|
self.assertEqual(alignment.shape, (2, 36))
|
|
self.assertLess(alignment.coordinates[0, 0], alignment.coordinates[0, -1])
|
|
self.assertGreater(alignment.coordinates[1, 0], alignment.coordinates[1, -1])
|
|
self.assertEqual(len(alignment), 2)
|
|
self.assertIs(alignment.sequences[0], alignment.target)
|
|
self.assertIs(alignment.sequences[1], alignment.query)
|
|
self.assertEqual(alignment.target.id, "chr1")
|
|
self.assertEqual(alignment.query.id, "hg19_dna")
|
|
self.assertTrue(
|
|
np.array_equal(
|
|
alignment.coordinates,
|
|
# fmt: off
|
|
np.array([[39368490, 39368526],
|
|
[ 36, 0]]),
|
|
# fmt: on
|
|
)
|
|
)
|
|
self.assertEqual(
|
|
str(alignment),
|
|
"""\
|
|
chr1 39368490 ???????????????????????????????????? 39368526
|
|
0 |||||||||||||||||||||||||||||||||||| 36
|
|
hg19_dna 36 ???????????????????????????????????? 0
|
|
""",
|
|
)
|
|
self.assertEqual(
|
|
format(alignment, "bed"),
|
|
"""\
|
|
chr1 39368490 39368526 hg19_dna 946 - 39368490 39368526 0 1 36, 0,
|
|
""",
|
|
)
|
|
counts = alignment.counts()
|
|
self.assertEqual(counts.left_insertions, 0)
|
|
self.assertEqual(counts.left_deletions, 0)
|
|
self.assertEqual(counts.right_insertions, 0)
|
|
self.assertEqual(counts.right_deletions, 0)
|
|
self.assertEqual(counts.internal_insertions, 0)
|
|
self.assertEqual(counts.internal_deletions, 0)
|
|
self.assertEqual(counts.left_gaps, 0)
|
|
self.assertEqual(counts.right_gaps, 0)
|
|
self.assertEqual(counts.internal_gaps, 0)
|
|
self.assertEqual(counts.insertions, 0)
|
|
self.assertEqual(counts.deletions, 0)
|
|
self.assertEqual(counts.gaps, 0)
|
|
self.assertEqual(counts.aligned, 36)
|
|
alignment = next(alignments)
|
|
self.assertEqual(alignment.score, 942)
|
|
self.assertEqual(alignment.shape, (2, 34))
|
|
self.assertLess(alignment.coordinates[0, 0], alignment.coordinates[0, -1])
|
|
self.assertGreater(alignment.coordinates[1, 0], alignment.coordinates[1, -1])
|
|
self.assertEqual(len(alignment), 2)
|
|
self.assertIs(alignment.sequences[0], alignment.target)
|
|
self.assertIs(alignment.sequences[1], alignment.query)
|
|
self.assertEqual(alignment.target.id, "chr1")
|
|
self.assertEqual(alignment.query.id, "hg19_dna")
|
|
self.assertTrue(
|
|
np.array_equal(
|
|
alignment.coordinates,
|
|
# fmt: off
|
|
np.array([[220325687, 220325721],
|
|
[ 34, 0]]),
|
|
# fmt: on
|
|
)
|
|
)
|
|
self.assertEqual(
|
|
str(alignment),
|
|
"""\
|
|
chr1 220325687 ?????????????????????????????????? 220325721
|
|
0 |||||||||||||||||||||||||||||||||| 34
|
|
hg19_dna 34 ?????????????????????????????????? 0
|
|
""",
|
|
)
|
|
self.assertEqual(
|
|
format(alignment, "bed"),
|
|
"""\
|
|
chr1 220325687 220325721 hg19_dna 942 - 220325687 220325721 0 1 34, 0,
|
|
""",
|
|
)
|
|
counts = alignment.counts()
|
|
self.assertEqual(counts.left_insertions, 0)
|
|
self.assertEqual(counts.left_deletions, 0)
|
|
self.assertEqual(counts.right_insertions, 0)
|
|
self.assertEqual(counts.right_deletions, 0)
|
|
self.assertEqual(counts.internal_insertions, 0)
|
|
self.assertEqual(counts.internal_deletions, 0)
|
|
self.assertEqual(counts.left_gaps, 0)
|
|
self.assertEqual(counts.right_gaps, 0)
|
|
self.assertEqual(counts.internal_gaps, 0)
|
|
self.assertEqual(counts.insertions, 0)
|
|
self.assertEqual(counts.deletions, 0)
|
|
self.assertEqual(counts.gaps, 0)
|
|
self.assertEqual(counts.aligned, 34)
|
|
self.assertRaises(StopIteration, next, alignments)
|
|
|
|
def test_writing_psl_34_005(self):
|
|
"""Test writing the alignments in psl_34_005.bed."""
|
|
path = "Blat/psl_34_005.bed"
|
|
with open(path) as stream:
|
|
original_data = stream.read()
|
|
alignments = Align.parse(path, "bed")
|
|
stream = StringIO()
|
|
n = Align.write(alignments, stream, "bed")
|
|
self.assertEqual(n, 22)
|
|
stream.seek(0)
|
|
written_data = stream.read()
|
|
stream.close()
|
|
self.assertEqual(original_data, written_data)
|
|
|
|
|
|
class TestAlign_dnax_prot(unittest.TestCase):
|
|
def test_reading_psl_35_001(self):
|
|
"""Test parsing psl_35_001.bed."""
|
|
path = "Blat/psl_35_001.bed"
|
|
alignments = Align.parse(path, "bed")
|
|
alignment = next(alignments)
|
|
self.assertEqual(alignment.score, 1000)
|
|
self.assertLess(alignment.coordinates[0, 0], alignment.coordinates[0, -1])
|
|
self.assertLess(alignment.coordinates[1, 0], alignment.coordinates[1, -1])
|
|
self.assertEqual(len(alignment), 2)
|
|
self.assertIs(alignment.sequences[0], alignment.target)
|
|
self.assertIs(alignment.sequences[1], alignment.query)
|
|
self.assertEqual(alignment.target.id, "chr13")
|
|
self.assertEqual(alignment.query.id, "CAG33136.1")
|
|
self.assertTrue(
|
|
np.array_equal(
|
|
alignment.coordinates,
|
|
# fmt: off
|
|
np.array([[75566694, 75566850],
|
|
[ 0, 156]]),
|
|
# fmt: on
|
|
)
|
|
)
|
|
self.assertEqual(
|
|
str(alignment),
|
|
"""\
|
|
chr13 75566694 ????????????????????????????????????????????????????????????
|
|
0 ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
|
|
CAG33136. 0 ????????????????????????????????????????????????????????????
|
|
|
|
chr13 75566754 ????????????????????????????????????????????????????????????
|
|
60 ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
|
|
CAG33136. 60 ????????????????????????????????????????????????????????????
|
|
|
|
chr13 75566814 ???????????????????????????????????? 75566850
|
|
120 |||||||||||||||||||||||||||||||||||| 156
|
|
CAG33136. 120 ???????????????????????????????????? 156
|
|
""",
|
|
)
|
|
self.assertEqual(
|
|
format(alignment, "bed"),
|
|
"""\
|
|
chr13 75566694 75566850 CAG33136.1 1000 + 75566694 75566850 0 1 156, 0,
|
|
""",
|
|
)
|
|
counts = alignment.counts()
|
|
self.assertEqual(counts.left_insertions, 0)
|
|
self.assertEqual(counts.left_deletions, 0)
|
|
self.assertEqual(counts.right_insertions, 0)
|
|
self.assertEqual(counts.right_deletions, 0)
|
|
self.assertEqual(counts.internal_insertions, 0)
|
|
self.assertEqual(counts.internal_deletions, 0)
|
|
self.assertEqual(counts.left_gaps, 0)
|
|
self.assertEqual(counts.right_gaps, 0)
|
|
self.assertEqual(counts.internal_gaps, 0)
|
|
self.assertEqual(counts.insertions, 0)
|
|
self.assertEqual(counts.deletions, 0)
|
|
self.assertEqual(counts.gaps, 0)
|
|
self.assertEqual(counts.aligned, 156)
|
|
alignment = next(alignments)
|
|
self.assertEqual(alignment.score, 1000)
|
|
self.assertLess(alignment.coordinates[0, 0], alignment.coordinates[0, -1])
|
|
self.assertLess(alignment.coordinates[1, 0], alignment.coordinates[1, -1])
|
|
self.assertEqual(len(alignment), 2)
|
|
self.assertIs(alignment.sequences[0], alignment.target)
|
|
self.assertIs(alignment.sequences[1], alignment.query)
|
|
self.assertEqual(alignment.target.id, "chr13")
|
|
self.assertEqual(alignment.query.id, "CAG33136.1")
|
|
self.assertTrue(
|
|
np.array_equal(
|
|
alignment.coordinates,
|
|
# fmt: off
|
|
np.array([[75560749, 75560881],
|
|
[ 0, 132]]),
|
|
# fmt: on
|
|
)
|
|
)
|
|
self.assertEqual(
|
|
str(alignment),
|
|
"""\
|
|
chr13 75560749 ????????????????????????????????????????????????????????????
|
|
0 ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
|
|
CAG33136. 0 ????????????????????????????????????????????????????????????
|
|
|
|
chr13 75560809 ????????????????????????????????????????????????????????????
|
|
60 ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
|
|
CAG33136. 60 ????????????????????????????????????????????????????????????
|
|
|
|
chr13 75560869 ???????????? 75560881
|
|
120 |||||||||||| 132
|
|
CAG33136. 120 ???????????? 132
|
|
""",
|
|
)
|
|
self.assertEqual(
|
|
format(alignment, "bed"),
|
|
"""\
|
|
chr13 75560749 75560881 CAG33136.1 1000 + 75560749 75560881 0 1 132, 0,
|
|
""",
|
|
)
|
|
counts = alignment.counts()
|
|
self.assertEqual(counts.left_insertions, 0)
|
|
self.assertEqual(counts.left_deletions, 0)
|
|
self.assertEqual(counts.right_insertions, 0)
|
|
self.assertEqual(counts.right_deletions, 0)
|
|
self.assertEqual(counts.internal_insertions, 0)
|
|
self.assertEqual(counts.internal_deletions, 0)
|
|
self.assertEqual(counts.left_gaps, 0)
|
|
self.assertEqual(counts.right_gaps, 0)
|
|
self.assertEqual(counts.internal_gaps, 0)
|
|
self.assertEqual(counts.insertions, 0)
|
|
self.assertEqual(counts.deletions, 0)
|
|
self.assertEqual(counts.gaps, 0)
|
|
self.assertEqual(counts.aligned, 132)
|
|
alignment = next(alignments)
|
|
self.assertEqual(alignment.score, 986)
|
|
self.assertLess(alignment.coordinates[0, 0], alignment.coordinates[0, -1])
|
|
self.assertLess(alignment.coordinates[1, 0], alignment.coordinates[1, -1])
|
|
self.assertEqual(len(alignment), 2)
|
|
self.assertIs(alignment.sequences[0], alignment.target)
|
|
self.assertIs(alignment.sequences[1], alignment.query)
|
|
self.assertEqual(alignment.target.id, "chr13")
|
|
self.assertEqual(alignment.query.id, "CAG33136.1")
|
|
self.assertTrue(
|
|
np.array_equal(
|
|
alignment.coordinates,
|
|
# fmt: off
|
|
np.array([[75549820, 75549865, 75567225, 75567312],
|
|
[ 0, 45, 45, 132]]),
|
|
# fmt: on
|
|
)
|
|
)
|
|
self.assertEqual(
|
|
str(alignment),
|
|
"""\
|
|
chr13 75549820 ????????????????????????????????????????????????????????????
|
|
0 |||||||||||||||||||||||||||||||||||||||||||||---------------
|
|
CAG33136. 0 ?????????????????????????????????????????????---------------
|
|
|
|
chr13 75549880 ????????????????????????????????????????????????????????????
|
|
60 ------------------------------------------------------------
|
|
CAG33136. 45 ------------------------------------------------------------
|
|
|
|
chr13 75549940 ????????????????????????????????????????????????????????????
|
|
120 ------------------------------------------------------------
|
|
CAG33136. 45 ------------------------------------------------------------
|
|
|
|
chr13 75550000 ????????????????????????????????????????????????????????????
|
|
180 ------------------------------------------------------------
|
|
CAG33136. 45 ------------------------------------------------------------
|
|
|
|
chr13 75550060 ????????????????????????????????????????????????????????????
|
|
240 ------------------------------------------------------------
|
|
CAG33136. 45 ------------------------------------------------------------
|
|
|
|
chr13 75550120 ????????????????????????????????????????????????????????????
|
|
300 ------------------------------------------------------------
|
|
CAG33136. 45 ------------------------------------------------------------
|
|
|
|
chr13 75550180 ????????????????????????????????????????????????????????????
|
|
360 ------------------------------------------------------------
|
|
CAG33136. 45 ------------------------------------------------------------
|
|
|
|
chr13 75550240 ????????????????????????????????????????????????????????????
|
|
420 ------------------------------------------------------------
|
|
CAG33136. 45 ------------------------------------------------------------
|
|
|
|
chr13 75550300 ????????????????????????????????????????????????????????????
|
|
480 ------------------------------------------------------------
|
|
CAG33136. 45 ------------------------------------------------------------
|
|
|
|
chr13 75550360 ????????????????????????????????????????????????????????????
|
|
540 ------------------------------------------------------------
|
|
CAG33136. 45 ------------------------------------------------------------
|
|
|
|
chr13 75550420 ????????????????????????????????????????????????????????????
|
|
600 ------------------------------------------------------------
|
|
CAG33136. 45 ------------------------------------------------------------
|
|
|
|
chr13 75550480 ????????????????????????????????????????????????????????????
|
|
660 ------------------------------------------------------------
|
|
CAG33136. 45 ------------------------------------------------------------
|
|
|
|
chr13 75550540 ????????????????????????????????????????????????????????????
|
|
720 ------------------------------------------------------------
|
|
CAG33136. 45 ------------------------------------------------------------
|
|
|
|
chr13 75550600 ????????????????????????????????????????????????????????????
|
|
780 ------------------------------------------------------------
|
|
CAG33136. 45 ------------------------------------------------------------
|
|
|
|
chr13 75550660 ????????????????????????????????????????????????????????????
|
|
840 ------------------------------------------------------------
|
|
CAG33136. 45 ------------------------------------------------------------
|
|
|
|
chr13 75550720 ????????????????????????????????????????????????????????????
|
|
900 ------------------------------------------------------------
|
|
CAG33136. 45 ------------------------------------------------------------
|
|
|
|
chr13 75550780 ????????????????????????????????????????????????????????????
|
|
960 ------------------------------------------------------------
|
|
CAG33136. 45 ------------------------------------------------------------
|
|
|
|
chr13 75550840 ????????????????????????????????????????????????????????????
|
|
1020 ------------------------------------------------------------
|
|
CAG33136. 45 ------------------------------------------------------------
|
|
|
|
chr13 75550900 ????????????????????????????????????????????????????????????
|
|
1080 ------------------------------------------------------------
|
|
CAG33136. 45 ------------------------------------------------------------
|
|
|
|
chr13 75550960 ????????????????????????????????????????????????????????????
|
|
1140 ------------------------------------------------------------
|
|
CAG33136. 45 ------------------------------------------------------------
|
|
|
|
chr13 75551020 ????????????????????????????????????????????????????????????
|
|
1200 ------------------------------------------------------------
|
|
CAG33136. 45 ------------------------------------------------------------
|
|
|
|
chr13 75551080 ????????????????????????????????????????????????????????????
|
|
1260 ------------------------------------------------------------
|
|
CAG33136. 45 ------------------------------------------------------------
|
|
|
|
chr13 75551140 ????????????????????????????????????????????????????????????
|
|
1320 ------------------------------------------------------------
|
|
CAG33136. 45 ------------------------------------------------------------
|
|
|
|
chr13 75551200 ????????????????????????????????????????????????????????????
|
|
1380 ------------------------------------------------------------
|
|
CAG33136. 45 ------------------------------------------------------------
|
|
|
|
chr13 75551260 ????????????????????????????????????????????????????????????
|
|
1440 ------------------------------------------------------------
|
|
CAG33136. 45 ------------------------------------------------------------
|
|
|
|
chr13 75551320 ????????????????????????????????????????????????????????????
|
|
1500 ------------------------------------------------------------
|
|
CAG33136. 45 ------------------------------------------------------------
|
|
|
|
chr13 75551380 ????????????????????????????????????????????????????????????
|
|
1560 ------------------------------------------------------------
|
|
CAG33136. 45 ------------------------------------------------------------
|
|
|
|
chr13 75551440 ????????????????????????????????????????????????????????????
|
|
1620 ------------------------------------------------------------
|
|
CAG33136. 45 ------------------------------------------------------------
|
|
|
|
chr13 75551500 ????????????????????????????????????????????????????????????
|
|
1680 ------------------------------------------------------------
|
|
CAG33136. 45 ------------------------------------------------------------
|
|
|
|
chr13 75551560 ????????????????????????????????????????????????????????????
|
|
1740 ------------------------------------------------------------
|
|
CAG33136. 45 ------------------------------------------------------------
|
|
|
|
chr13 75551620 ????????????????????????????????????????????????????????????
|
|
1800 ------------------------------------------------------------
|
|
CAG33136. 45 ------------------------------------------------------------
|
|
|
|
chr13 75551680 ????????????????????????????????????????????????????????????
|
|
1860 ------------------------------------------------------------
|
|
CAG33136. 45 ------------------------------------------------------------
|
|
|
|
chr13 75551740 ????????????????????????????????????????????????????????????
|
|
1920 ------------------------------------------------------------
|
|
CAG33136. 45 ------------------------------------------------------------
|
|
|
|
chr13 75551800 ????????????????????????????????????????????????????????????
|
|
1980 ------------------------------------------------------------
|
|
CAG33136. 45 ------------------------------------------------------------
|
|
|
|
chr13 75551860 ????????????????????????????????????????????????????????????
|
|
2040 ------------------------------------------------------------
|
|
CAG33136. 45 ------------------------------------------------------------
|
|
|
|
chr13 75551920 ????????????????????????????????????????????????????????????
|
|
2100 ------------------------------------------------------------
|
|
CAG33136. 45 ------------------------------------------------------------
|
|
|
|
chr13 75551980 ????????????????????????????????????????????????????????????
|
|
2160 ------------------------------------------------------------
|
|
CAG33136. 45 ------------------------------------------------------------
|
|
|
|
chr13 75552040 ????????????????????????????????????????????????????????????
|
|
2220 ------------------------------------------------------------
|
|
CAG33136. 45 ------------------------------------------------------------
|
|
|
|
chr13 75552100 ????????????????????????????????????????????????????????????
|
|
2280 ------------------------------------------------------------
|
|
CAG33136. 45 ------------------------------------------------------------
|
|
|
|
chr13 75552160 ????????????????????????????????????????????????????????????
|
|
2340 ------------------------------------------------------------
|
|
CAG33136. 45 ------------------------------------------------------------
|
|
|
|
chr13 75552220 ????????????????????????????????????????????????????????????
|
|
2400 ------------------------------------------------------------
|
|
CAG33136. 45 ------------------------------------------------------------
|
|
|
|
chr13 75552280 ????????????????????????????????????????????????????????????
|
|
2460 ------------------------------------------------------------
|
|
CAG33136. 45 ------------------------------------------------------------
|
|
|
|
chr13 75552340 ????????????????????????????????????????????????????????????
|
|
2520 ------------------------------------------------------------
|
|
CAG33136. 45 ------------------------------------------------------------
|
|
|
|
chr13 75552400 ????????????????????????????????????????????????????????????
|
|
2580 ------------------------------------------------------------
|
|
CAG33136. 45 ------------------------------------------------------------
|
|
|
|
chr13 75552460 ????????????????????????????????????????????????????????????
|
|
2640 ------------------------------------------------------------
|
|
CAG33136. 45 ------------------------------------------------------------
|
|
|
|
chr13 75552520 ????????????????????????????????????????????????????????????
|
|
2700 ------------------------------------------------------------
|
|
CAG33136. 45 ------------------------------------------------------------
|
|
|
|
chr13 75552580 ????????????????????????????????????????????????????????????
|
|
2760 ------------------------------------------------------------
|
|
CAG33136. 45 ------------------------------------------------------------
|
|
|
|
chr13 75552640 ????????????????????????????????????????????????????????????
|
|
2820 ------------------------------------------------------------
|
|
CAG33136. 45 ------------------------------------------------------------
|
|
|
|
chr13 75552700 ????????????????????????????????????????????????????????????
|
|
2880 ------------------------------------------------------------
|
|
CAG33136. 45 ------------------------------------------------------------
|
|
|
|
chr13 75552760 ????????????????????????????????????????????????????????????
|
|
2940 ------------------------------------------------------------
|
|
CAG33136. 45 ------------------------------------------------------------
|
|
|
|
chr13 75552820 ????????????????????????????????????????????????????????????
|
|
3000 ------------------------------------------------------------
|
|
CAG33136. 45 ------------------------------------------------------------
|
|
|
|
chr13 75552880 ????????????????????????????????????????????????????????????
|
|
3060 ------------------------------------------------------------
|
|
CAG33136. 45 ------------------------------------------------------------
|
|
|
|
chr13 75552940 ????????????????????????????????????????????????????????????
|
|
3120 ------------------------------------------------------------
|
|
CAG33136. 45 ------------------------------------------------------------
|
|
|
|
chr13 75553000 ????????????????????????????????????????????????????????????
|
|
3180 ------------------------------------------------------------
|
|
CAG33136. 45 ------------------------------------------------------------
|
|
|
|
chr13 75553060 ????????????????????????????????????????????????????????????
|
|
3240 ------------------------------------------------------------
|
|
CAG33136. 45 ------------------------------------------------------------
|
|
|
|
chr13 75553120 ????????????????????????????????????????????????????????????
|
|
3300 ------------------------------------------------------------
|
|
CAG33136. 45 ------------------------------------------------------------
|
|
|
|
chr13 75553180 ????????????????????????????????????????????????????????????
|
|
3360 ------------------------------------------------------------
|
|
CAG33136. 45 ------------------------------------------------------------
|
|
|
|
chr13 75553240 ????????????????????????????????????????????????????????????
|
|
3420 ------------------------------------------------------------
|
|
CAG33136. 45 ------------------------------------------------------------
|
|
|
|
chr13 75553300 ????????????????????????????????????????????????????????????
|
|
3480 ------------------------------------------------------------
|
|
CAG33136. 45 ------------------------------------------------------------
|
|
|
|
chr13 75553360 ????????????????????????????????????????????????????????????
|
|
3540 ------------------------------------------------------------
|
|
CAG33136. 45 ------------------------------------------------------------
|
|
|
|
chr13 75553420 ????????????????????????????????????????????????????????????
|
|
3600 ------------------------------------------------------------
|
|
CAG33136. 45 ------------------------------------------------------------
|
|
|
|
chr13 75553480 ????????????????????????????????????????????????????????????
|
|
3660 ------------------------------------------------------------
|
|
CAG33136. 45 ------------------------------------------------------------
|
|
|
|
chr13 75553540 ????????????????????????????????????????????????????????????
|
|
3720 ------------------------------------------------------------
|
|
CAG33136. 45 ------------------------------------------------------------
|
|
|
|
chr13 75553600 ????????????????????????????????????????????????????????????
|
|
3780 ------------------------------------------------------------
|
|
CAG33136. 45 ------------------------------------------------------------
|
|
|
|
chr13 75553660 ????????????????????????????????????????????????????????????
|
|
3840 ------------------------------------------------------------
|
|
CAG33136. 45 ------------------------------------------------------------
|
|
|
|
chr13 75553720 ????????????????????????????????????????????????????????????
|
|
3900 ------------------------------------------------------------
|
|
CAG33136. 45 ------------------------------------------------------------
|
|
|
|
chr13 75553780 ????????????????????????????????????????????????????????????
|
|
3960 ------------------------------------------------------------
|
|
CAG33136. 45 ------------------------------------------------------------
|
|
|
|
chr13 75553840 ????????????????????????????????????????????????????????????
|
|
4020 ------------------------------------------------------------
|
|
CAG33136. 45 ------------------------------------------------------------
|
|
|
|
chr13 75553900 ????????????????????????????????????????????????????????????
|
|
4080 ------------------------------------------------------------
|
|
CAG33136. 45 ------------------------------------------------------------
|
|
|
|
chr13 75553960 ????????????????????????????????????????????????????????????
|
|
4140 ------------------------------------------------------------
|
|
CAG33136. 45 ------------------------------------------------------------
|
|
|
|
chr13 75554020 ????????????????????????????????????????????????????????????
|
|
4200 ------------------------------------------------------------
|
|
CAG33136. 45 ------------------------------------------------------------
|
|
|
|
chr13 75554080 ????????????????????????????????????????????????????????????
|
|
4260 ------------------------------------------------------------
|
|
CAG33136. 45 ------------------------------------------------------------
|
|
|
|
chr13 75554140 ????????????????????????????????????????????????????????????
|
|
4320 ------------------------------------------------------------
|
|
CAG33136. 45 ------------------------------------------------------------
|
|
|
|
chr13 75554200 ????????????????????????????????????????????????????????????
|
|
4380 ------------------------------------------------------------
|
|
CAG33136. 45 ------------------------------------------------------------
|
|
|
|
chr13 75554260 ????????????????????????????????????????????????????????????
|
|
4440 ------------------------------------------------------------
|
|
CAG33136. 45 ------------------------------------------------------------
|
|
|
|
chr13 75554320 ????????????????????????????????????????????????????????????
|
|
4500 ------------------------------------------------------------
|
|
CAG33136. 45 ------------------------------------------------------------
|
|
|
|
chr13 75554380 ????????????????????????????????????????????????????????????
|
|
4560 ------------------------------------------------------------
|
|
CAG33136. 45 ------------------------------------------------------------
|
|
|
|
chr13 75554440 ????????????????????????????????????????????????????????????
|
|
4620 ------------------------------------------------------------
|
|
CAG33136. 45 ------------------------------------------------------------
|
|
|
|
chr13 75554500 ????????????????????????????????????????????????????????????
|
|
4680 ------------------------------------------------------------
|
|
CAG33136. 45 ------------------------------------------------------------
|
|
|
|
chr13 75554560 ????????????????????????????????????????????????????????????
|
|
4740 ------------------------------------------------------------
|
|
CAG33136. 45 ------------------------------------------------------------
|
|
|
|
chr13 75554620 ????????????????????????????????????????????????????????????
|
|
4800 ------------------------------------------------------------
|
|
CAG33136. 45 ------------------------------------------------------------
|
|
|
|
chr13 75554680 ????????????????????????????????????????????????????????????
|
|
4860 ------------------------------------------------------------
|
|
CAG33136. 45 ------------------------------------------------------------
|
|
|
|
chr13 75554740 ????????????????????????????????????????????????????????????
|
|
4920 ------------------------------------------------------------
|
|
CAG33136. 45 ------------------------------------------------------------
|
|
|
|
chr13 75554800 ????????????????????????????????????????????????????????????
|
|
4980 ------------------------------------------------------------
|
|
CAG33136. 45 ------------------------------------------------------------
|
|
|
|
chr13 75554860 ????????????????????????????????????????????????????????????
|
|
5040 ------------------------------------------------------------
|
|
CAG33136. 45 ------------------------------------------------------------
|
|
|
|
chr13 75554920 ????????????????????????????????????????????????????????????
|
|
5100 ------------------------------------------------------------
|
|
CAG33136. 45 ------------------------------------------------------------
|
|
|
|
chr13 75554980 ????????????????????????????????????????????????????????????
|
|
5160 ------------------------------------------------------------
|
|
CAG33136. 45 ------------------------------------------------------------
|
|
|
|
chr13 75555040 ????????????????????????????????????????????????????????????
|
|
5220 ------------------------------------------------------------
|
|
CAG33136. 45 ------------------------------------------------------------
|
|
|
|
chr13 75555100 ????????????????????????????????????????????????????????????
|
|
5280 ------------------------------------------------------------
|
|
CAG33136. 45 ------------------------------------------------------------
|
|
|
|
chr13 75555160 ????????????????????????????????????????????????????????????
|
|
5340 ------------------------------------------------------------
|
|
CAG33136. 45 ------------------------------------------------------------
|
|
|
|
chr13 75555220 ????????????????????????????????????????????????????????????
|
|
5400 ------------------------------------------------------------
|
|
CAG33136. 45 ------------------------------------------------------------
|
|
|
|
chr13 75555280 ????????????????????????????????????????????????????????????
|
|
5460 ------------------------------------------------------------
|
|
CAG33136. 45 ------------------------------------------------------------
|
|
|
|
chr13 75555340 ????????????????????????????????????????????????????????????
|
|
5520 ------------------------------------------------------------
|
|
CAG33136. 45 ------------------------------------------------------------
|
|
|
|
chr13 75555400 ????????????????????????????????????????????????????????????
|
|
5580 ------------------------------------------------------------
|
|
CAG33136. 45 ------------------------------------------------------------
|
|
|
|
chr13 75555460 ????????????????????????????????????????????????????????????
|
|
5640 ------------------------------------------------------------
|
|
CAG33136. 45 ------------------------------------------------------------
|
|
|
|
chr13 75555520 ????????????????????????????????????????????????????????????
|
|
5700 ------------------------------------------------------------
|
|
CAG33136. 45 ------------------------------------------------------------
|
|
|
|
chr13 75555580 ????????????????????????????????????????????????????????????
|
|
5760 ------------------------------------------------------------
|
|
CAG33136. 45 ------------------------------------------------------------
|
|
|
|
chr13 75555640 ????????????????????????????????????????????????????????????
|
|
5820 ------------------------------------------------------------
|
|
CAG33136. 45 ------------------------------------------------------------
|
|
|
|
chr13 75555700 ????????????????????????????????????????????????????????????
|
|
5880 ------------------------------------------------------------
|
|
CAG33136. 45 ------------------------------------------------------------
|
|
|
|
chr13 75555760 ????????????????????????????????????????????????????????????
|
|
5940 ------------------------------------------------------------
|
|
CAG33136. 45 ------------------------------------------------------------
|
|
|
|
chr13 75555820 ????????????????????????????????????????????????????????????
|
|
6000 ------------------------------------------------------------
|
|
CAG33136. 45 ------------------------------------------------------------
|
|
|
|
chr13 75555880 ????????????????????????????????????????????????????????????
|
|
6060 ------------------------------------------------------------
|
|
CAG33136. 45 ------------------------------------------------------------
|
|
|
|
chr13 75555940 ????????????????????????????????????????????????????????????
|
|
6120 ------------------------------------------------------------
|
|
CAG33136. 45 ------------------------------------------------------------
|
|
|
|
chr13 75556000 ????????????????????????????????????????????????????????????
|
|
6180 ------------------------------------------------------------
|
|
CAG33136. 45 ------------------------------------------------------------
|
|
|
|
chr13 75556060 ????????????????????????????????????????????????????????????
|
|
6240 ------------------------------------------------------------
|
|
CAG33136. 45 ------------------------------------------------------------
|
|
|
|
chr13 75556120 ????????????????????????????????????????????????????????????
|
|
6300 ------------------------------------------------------------
|
|
CAG33136. 45 ------------------------------------------------------------
|
|
|
|
chr13 75556180 ????????????????????????????????????????????????????????????
|
|
6360 ------------------------------------------------------------
|
|
CAG33136. 45 ------------------------------------------------------------
|
|
|
|
chr13 75556240 ????????????????????????????????????????????????????????????
|
|
6420 ------------------------------------------------------------
|
|
CAG33136. 45 ------------------------------------------------------------
|
|
|
|
chr13 75556300 ????????????????????????????????????????????????????????????
|
|
6480 ------------------------------------------------------------
|
|
CAG33136. 45 ------------------------------------------------------------
|
|
|
|
chr13 75556360 ????????????????????????????????????????????????????????????
|
|
6540 ------------------------------------------------------------
|
|
CAG33136. 45 ------------------------------------------------------------
|
|
|
|
chr13 75556420 ????????????????????????????????????????????????????????????
|
|
6600 ------------------------------------------------------------
|
|
CAG33136. 45 ------------------------------------------------------------
|
|
|
|
chr13 75556480 ????????????????????????????????????????????????????????????
|
|
6660 ------------------------------------------------------------
|
|
CAG33136. 45 ------------------------------------------------------------
|
|
|
|
chr13 75556540 ????????????????????????????????????????????????????????????
|
|
6720 ------------------------------------------------------------
|
|
CAG33136. 45 ------------------------------------------------------------
|
|
|
|
chr13 75556600 ????????????????????????????????????????????????????????????
|
|
6780 ------------------------------------------------------------
|
|
CAG33136. 45 ------------------------------------------------------------
|
|
|
|
chr13 75556660 ????????????????????????????????????????????????????????????
|
|
6840 ------------------------------------------------------------
|
|
CAG33136. 45 ------------------------------------------------------------
|
|
|
|
chr13 75556720 ????????????????????????????????????????????????????????????
|
|
6900 ------------------------------------------------------------
|
|
CAG33136. 45 ------------------------------------------------------------
|
|
|
|
chr13 75556780 ????????????????????????????????????????????????????????????
|
|
6960 ------------------------------------------------------------
|
|
CAG33136. 45 ------------------------------------------------------------
|
|
|
|
chr13 75556840 ????????????????????????????????????????????????????????????
|
|
7020 ------------------------------------------------------------
|
|
CAG33136. 45 ------------------------------------------------------------
|
|
|
|
chr13 75556900 ????????????????????????????????????????????????????????????
|
|
7080 ------------------------------------------------------------
|
|
CAG33136. 45 ------------------------------------------------------------
|
|
|
|
chr13 75556960 ????????????????????????????????????????????????????????????
|
|
7140 ------------------------------------------------------------
|
|
CAG33136. 45 ------------------------------------------------------------
|
|
|
|
chr13 75557020 ????????????????????????????????????????????????????????????
|
|
7200 ------------------------------------------------------------
|
|
CAG33136. 45 ------------------------------------------------------------
|
|
|
|
chr13 75557080 ????????????????????????????????????????????????????????????
|
|
7260 ------------------------------------------------------------
|
|
CAG33136. 45 ------------------------------------------------------------
|
|
|
|
chr13 75557140 ????????????????????????????????????????????????????????????
|
|
7320 ------------------------------------------------------------
|
|
CAG33136. 45 ------------------------------------------------------------
|
|
|
|
chr13 75557200 ????????????????????????????????????????????????????????????
|
|
7380 ------------------------------------------------------------
|
|
CAG33136. 45 ------------------------------------------------------------
|
|
|
|
chr13 75557260 ????????????????????????????????????????????????????????????
|
|
7440 ------------------------------------------------------------
|
|
CAG33136. 45 ------------------------------------------------------------
|
|
|
|
chr13 75557320 ????????????????????????????????????????????????????????????
|
|
7500 ------------------------------------------------------------
|
|
CAG33136. 45 ------------------------------------------------------------
|
|
|
|
chr13 75557380 ????????????????????????????????????????????????????????????
|
|
7560 ------------------------------------------------------------
|
|
CAG33136. 45 ------------------------------------------------------------
|
|
|
|
chr13 75557440 ????????????????????????????????????????????????????????????
|
|
7620 ------------------------------------------------------------
|
|
CAG33136. 45 ------------------------------------------------------------
|
|
|
|
chr13 75557500 ????????????????????????????????????????????????????????????
|
|
7680 ------------------------------------------------------------
|
|
CAG33136. 45 ------------------------------------------------------------
|
|
|
|
chr13 75557560 ????????????????????????????????????????????????????????????
|
|
7740 ------------------------------------------------------------
|
|
CAG33136. 45 ------------------------------------------------------------
|
|
|
|
chr13 75557620 ????????????????????????????????????????????????????????????
|
|
7800 ------------------------------------------------------------
|
|
CAG33136. 45 ------------------------------------------------------------
|
|
|
|
chr13 75557680 ????????????????????????????????????????????????????????????
|
|
7860 ------------------------------------------------------------
|
|
CAG33136. 45 ------------------------------------------------------------
|
|
|
|
chr13 75557740 ????????????????????????????????????????????????????????????
|
|
7920 ------------------------------------------------------------
|
|
CAG33136. 45 ------------------------------------------------------------
|
|
|
|
chr13 75557800 ????????????????????????????????????????????????????????????
|
|
7980 ------------------------------------------------------------
|
|
CAG33136. 45 ------------------------------------------------------------
|
|
|
|
chr13 75557860 ????????????????????????????????????????????????????????????
|
|
8040 ------------------------------------------------------------
|
|
CAG33136. 45 ------------------------------------------------------------
|
|
|
|
chr13 75557920 ????????????????????????????????????????????????????????????
|
|
8100 ------------------------------------------------------------
|
|
CAG33136. 45 ------------------------------------------------------------
|
|
|
|
chr13 75557980 ????????????????????????????????????????????????????????????
|
|
8160 ------------------------------------------------------------
|
|
CAG33136. 45 ------------------------------------------------------------
|
|
|
|
chr13 75558040 ????????????????????????????????????????????????????????????
|
|
8220 ------------------------------------------------------------
|
|
CAG33136. 45 ------------------------------------------------------------
|
|
|
|
chr13 75558100 ????????????????????????????????????????????????????????????
|
|
8280 ------------------------------------------------------------
|
|
CAG33136. 45 ------------------------------------------------------------
|
|
|
|
chr13 75558160 ????????????????????????????????????????????????????????????
|
|
8340 ------------------------------------------------------------
|
|
CAG33136. 45 ------------------------------------------------------------
|
|
|
|
chr13 75558220 ????????????????????????????????????????????????????????????
|
|
8400 ------------------------------------------------------------
|
|
CAG33136. 45 ------------------------------------------------------------
|
|
|
|
chr13 75558280 ????????????????????????????????????????????????????????????
|
|
8460 ------------------------------------------------------------
|
|
CAG33136. 45 ------------------------------------------------------------
|
|
|
|
chr13 75558340 ????????????????????????????????????????????????????????????
|
|
8520 ------------------------------------------------------------
|
|
CAG33136. 45 ------------------------------------------------------------
|
|
|
|
chr13 75558400 ????????????????????????????????????????????????????????????
|
|
8580 ------------------------------------------------------------
|
|
CAG33136. 45 ------------------------------------------------------------
|
|
|
|
chr13 75558460 ????????????????????????????????????????????????????????????
|
|
8640 ------------------------------------------------------------
|
|
CAG33136. 45 ------------------------------------------------------------
|
|
|
|
chr13 75558520 ????????????????????????????????????????????????????????????
|
|
8700 ------------------------------------------------------------
|
|
CAG33136. 45 ------------------------------------------------------------
|
|
|
|
chr13 75558580 ????????????????????????????????????????????????????????????
|
|
8760 ------------------------------------------------------------
|
|
CAG33136. 45 ------------------------------------------------------------
|
|
|
|
chr13 75558640 ????????????????????????????????????????????????????????????
|
|
8820 ------------------------------------------------------------
|
|
CAG33136. 45 ------------------------------------------------------------
|
|
|
|
chr13 75558700 ????????????????????????????????????????????????????????????
|
|
8880 ------------------------------------------------------------
|
|
CAG33136. 45 ------------------------------------------------------------
|
|
|
|
chr13 75558760 ????????????????????????????????????????????????????????????
|
|
8940 ------------------------------------------------------------
|
|
CAG33136. 45 ------------------------------------------------------------
|
|
|
|
chr13 75558820 ????????????????????????????????????????????????????????????
|
|
9000 ------------------------------------------------------------
|
|
CAG33136. 45 ------------------------------------------------------------
|
|
|
|
chr13 75558880 ????????????????????????????????????????????????????????????
|
|
9060 ------------------------------------------------------------
|
|
CAG33136. 45 ------------------------------------------------------------
|
|
|
|
chr13 75558940 ????????????????????????????????????????????????????????????
|
|
9120 ------------------------------------------------------------
|
|
CAG33136. 45 ------------------------------------------------------------
|
|
|
|
chr13 75559000 ????????????????????????????????????????????????????????????
|
|
9180 ------------------------------------------------------------
|
|
CAG33136. 45 ------------------------------------------------------------
|
|
|
|
chr13 75559060 ????????????????????????????????????????????????????????????
|
|
9240 ------------------------------------------------------------
|
|
CAG33136. 45 ------------------------------------------------------------
|
|
|
|
chr13 75559120 ????????????????????????????????????????????????????????????
|
|
9300 ------------------------------------------------------------
|
|
CAG33136. 45 ------------------------------------------------------------
|
|
|
|
chr13 75559180 ????????????????????????????????????????????????????????????
|
|
9360 ------------------------------------------------------------
|
|
CAG33136. 45 ------------------------------------------------------------
|
|
|
|
chr13 75559240 ????????????????????????????????????????????????????????????
|
|
9420 ------------------------------------------------------------
|
|
CAG33136. 45 ------------------------------------------------------------
|
|
|
|
chr13 75559300 ????????????????????????????????????????????????????????????
|
|
9480 ------------------------------------------------------------
|
|
CAG33136. 45 ------------------------------------------------------------
|
|
|
|
chr13 75559360 ????????????????????????????????????????????????????????????
|
|
9540 ------------------------------------------------------------
|
|
CAG33136. 45 ------------------------------------------------------------
|
|
|
|
chr13 75559420 ????????????????????????????????????????????????????????????
|
|
9600 ------------------------------------------------------------
|
|
CAG33136. 45 ------------------------------------------------------------
|
|
|
|
chr13 75559480 ????????????????????????????????????????????????????????????
|
|
9660 ------------------------------------------------------------
|
|
CAG33136. 45 ------------------------------------------------------------
|
|
|
|
chr13 75559540 ????????????????????????????????????????????????????????????
|
|
9720 ------------------------------------------------------------
|
|
CAG33136. 45 ------------------------------------------------------------
|
|
|
|
chr13 75559600 ????????????????????????????????????????????????????????????
|
|
9780 ------------------------------------------------------------
|
|
CAG33136. 45 ------------------------------------------------------------
|
|
|
|
chr13 75559660 ????????????????????????????????????????????????????????????
|
|
9840 ------------------------------------------------------------
|
|
CAG33136. 45 ------------------------------------------------------------
|
|
|
|
chr13 75559720 ????????????????????????????????????????????????????????????
|
|
9900 ------------------------------------------------------------
|
|
CAG33136. 45 ------------------------------------------------------------
|
|
|
|
chr13 75559780 ????????????????????????????????????????????????????????????
|
|
9960 ------------------------------------------------------------
|
|
CAG33136. 45 ------------------------------------------------------------
|
|
|
|
chr13 75559840 ????????????????????????????????????????????????????????????
|
|
10020 ------------------------------------------------------------
|
|
CAG33136. 45 ------------------------------------------------------------
|
|
|
|
chr13 75559900 ????????????????????????????????????????????????????????????
|
|
10080 ------------------------------------------------------------
|
|
CAG33136. 45 ------------------------------------------------------------
|
|
|
|
chr13 75559960 ????????????????????????????????????????????????????????????
|
|
10140 ------------------------------------------------------------
|
|
CAG33136. 45 ------------------------------------------------------------
|
|
|
|
chr13 75560020 ????????????????????????????????????????????????????????????
|
|
10200 ------------------------------------------------------------
|
|
CAG33136. 45 ------------------------------------------------------------
|
|
|
|
chr13 75560080 ????????????????????????????????????????????????????????????
|
|
10260 ------------------------------------------------------------
|
|
CAG33136. 45 ------------------------------------------------------------
|
|
|
|
chr13 75560140 ????????????????????????????????????????????????????????????
|
|
10320 ------------------------------------------------------------
|
|
CAG33136. 45 ------------------------------------------------------------
|
|
|
|
chr13 75560200 ????????????????????????????????????????????????????????????
|
|
10380 ------------------------------------------------------------
|
|
CAG33136. 45 ------------------------------------------------------------
|
|
|
|
chr13 75560260 ????????????????????????????????????????????????????????????
|
|
10440 ------------------------------------------------------------
|
|
CAG33136. 45 ------------------------------------------------------------
|
|
|
|
chr13 75560320 ????????????????????????????????????????????????????????????
|
|
10500 ------------------------------------------------------------
|
|
CAG33136. 45 ------------------------------------------------------------
|
|
|
|
chr13 75560380 ????????????????????????????????????????????????????????????
|
|
10560 ------------------------------------------------------------
|
|
CAG33136. 45 ------------------------------------------------------------
|
|
|
|
chr13 75560440 ????????????????????????????????????????????????????????????
|
|
10620 ------------------------------------------------------------
|
|
CAG33136. 45 ------------------------------------------------------------
|
|
|
|
chr13 75560500 ????????????????????????????????????????????????????????????
|
|
10680 ------------------------------------------------------------
|
|
CAG33136. 45 ------------------------------------------------------------
|
|
|
|
chr13 75560560 ????????????????????????????????????????????????????????????
|
|
10740 ------------------------------------------------------------
|
|
CAG33136. 45 ------------------------------------------------------------
|
|
|
|
chr13 75560620 ????????????????????????????????????????????????????????????
|
|
10800 ------------------------------------------------------------
|
|
CAG33136. 45 ------------------------------------------------------------
|
|
|
|
chr13 75560680 ????????????????????????????????????????????????????????????
|
|
10860 ------------------------------------------------------------
|
|
CAG33136. 45 ------------------------------------------------------------
|
|
|
|
chr13 75560740 ????????????????????????????????????????????????????????????
|
|
10920 ------------------------------------------------------------
|
|
CAG33136. 45 ------------------------------------------------------------
|
|
|
|
chr13 75560800 ????????????????????????????????????????????????????????????
|
|
10980 ------------------------------------------------------------
|
|
CAG33136. 45 ------------------------------------------------------------
|
|
|
|
chr13 75560860 ????????????????????????????????????????????????????????????
|
|
11040 ------------------------------------------------------------
|
|
CAG33136. 45 ------------------------------------------------------------
|
|
|
|
chr13 75560920 ????????????????????????????????????????????????????????????
|
|
11100 ------------------------------------------------------------
|
|
CAG33136. 45 ------------------------------------------------------------
|
|
|
|
chr13 75560980 ????????????????????????????????????????????????????????????
|
|
11160 ------------------------------------------------------------
|
|
CAG33136. 45 ------------------------------------------------------------
|
|
|
|
chr13 75561040 ????????????????????????????????????????????????????????????
|
|
11220 ------------------------------------------------------------
|
|
CAG33136. 45 ------------------------------------------------------------
|
|
|
|
chr13 75561100 ????????????????????????????????????????????????????????????
|
|
11280 ------------------------------------------------------------
|
|
CAG33136. 45 ------------------------------------------------------------
|
|
|
|
chr13 75561160 ????????????????????????????????????????????????????????????
|
|
11340 ------------------------------------------------------------
|
|
CAG33136. 45 ------------------------------------------------------------
|
|
|
|
chr13 75561220 ????????????????????????????????????????????????????????????
|
|
11400 ------------------------------------------------------------
|
|
CAG33136. 45 ------------------------------------------------------------
|
|
|
|
chr13 75561280 ????????????????????????????????????????????????????????????
|
|
11460 ------------------------------------------------------------
|
|
CAG33136. 45 ------------------------------------------------------------
|
|
|
|
chr13 75561340 ????????????????????????????????????????????????????????????
|
|
11520 ------------------------------------------------------------
|
|
CAG33136. 45 ------------------------------------------------------------
|
|
|
|
chr13 75561400 ????????????????????????????????????????????????????????????
|
|
11580 ------------------------------------------------------------
|
|
CAG33136. 45 ------------------------------------------------------------
|
|
|
|
chr13 75561460 ????????????????????????????????????????????????????????????
|
|
11640 ------------------------------------------------------------
|
|
CAG33136. 45 ------------------------------------------------------------
|
|
|
|
chr13 75561520 ????????????????????????????????????????????????????????????
|
|
11700 ------------------------------------------------------------
|
|
CAG33136. 45 ------------------------------------------------------------
|
|
|
|
chr13 75561580 ????????????????????????????????????????????????????????????
|
|
11760 ------------------------------------------------------------
|
|
CAG33136. 45 ------------------------------------------------------------
|
|
|
|
chr13 75561640 ????????????????????????????????????????????????????????????
|
|
11820 ------------------------------------------------------------
|
|
CAG33136. 45 ------------------------------------------------------------
|
|
|
|
chr13 75561700 ????????????????????????????????????????????????????????????
|
|
11880 ------------------------------------------------------------
|
|
CAG33136. 45 ------------------------------------------------------------
|
|
|
|
chr13 75561760 ????????????????????????????????????????????????????????????
|
|
11940 ------------------------------------------------------------
|
|
CAG33136. 45 ------------------------------------------------------------
|
|
|
|
chr13 75561820 ????????????????????????????????????????????????????????????
|
|
12000 ------------------------------------------------------------
|
|
CAG33136. 45 ------------------------------------------------------------
|
|
|
|
chr13 75561880 ????????????????????????????????????????????????????????????
|
|
12060 ------------------------------------------------------------
|
|
CAG33136. 45 ------------------------------------------------------------
|
|
|
|
chr13 75561940 ????????????????????????????????????????????????????????????
|
|
12120 ------------------------------------------------------------
|
|
CAG33136. 45 ------------------------------------------------------------
|
|
|
|
chr13 75562000 ????????????????????????????????????????????????????????????
|
|
12180 ------------------------------------------------------------
|
|
CAG33136. 45 ------------------------------------------------------------
|
|
|
|
chr13 75562060 ????????????????????????????????????????????????????????????
|
|
12240 ------------------------------------------------------------
|
|
CAG33136. 45 ------------------------------------------------------------
|
|
|
|
chr13 75562120 ????????????????????????????????????????????????????????????
|
|
12300 ------------------------------------------------------------
|
|
CAG33136. 45 ------------------------------------------------------------
|
|
|
|
chr13 75562180 ????????????????????????????????????????????????????????????
|
|
12360 ------------------------------------------------------------
|
|
CAG33136. 45 ------------------------------------------------------------
|
|
|
|
chr13 75562240 ????????????????????????????????????????????????????????????
|
|
12420 ------------------------------------------------------------
|
|
CAG33136. 45 ------------------------------------------------------------
|
|
|
|
chr13 75562300 ????????????????????????????????????????????????????????????
|
|
12480 ------------------------------------------------------------
|
|
CAG33136. 45 ------------------------------------------------------------
|
|
|
|
chr13 75562360 ????????????????????????????????????????????????????????????
|
|
12540 ------------------------------------------------------------
|
|
CAG33136. 45 ------------------------------------------------------------
|
|
|
|
chr13 75562420 ????????????????????????????????????????????????????????????
|
|
12600 ------------------------------------------------------------
|
|
CAG33136. 45 ------------------------------------------------------------
|
|
|
|
chr13 75562480 ????????????????????????????????????????????????????????????
|
|
12660 ------------------------------------------------------------
|
|
CAG33136. 45 ------------------------------------------------------------
|
|
|
|
chr13 75562540 ????????????????????????????????????????????????????????????
|
|
12720 ------------------------------------------------------------
|
|
CAG33136. 45 ------------------------------------------------------------
|
|
|
|
chr13 75562600 ????????????????????????????????????????????????????????????
|
|
12780 ------------------------------------------------------------
|
|
CAG33136. 45 ------------------------------------------------------------
|
|
|
|
chr13 75562660 ????????????????????????????????????????????????????????????
|
|
12840 ------------------------------------------------------------
|
|
CAG33136. 45 ------------------------------------------------------------
|
|
|
|
chr13 75562720 ????????????????????????????????????????????????????????????
|
|
12900 ------------------------------------------------------------
|
|
CAG33136. 45 ------------------------------------------------------------
|
|
|
|
chr13 75562780 ????????????????????????????????????????????????????????????
|
|
12960 ------------------------------------------------------------
|
|
CAG33136. 45 ------------------------------------------------------------
|
|
|
|
chr13 75562840 ????????????????????????????????????????????????????????????
|
|
13020 ------------------------------------------------------------
|
|
CAG33136. 45 ------------------------------------------------------------
|
|
|
|
chr13 75562900 ????????????????????????????????????????????????????????????
|
|
13080 ------------------------------------------------------------
|
|
CAG33136. 45 ------------------------------------------------------------
|
|
|
|
chr13 75562960 ????????????????????????????????????????????????????????????
|
|
13140 ------------------------------------------------------------
|
|
CAG33136. 45 ------------------------------------------------------------
|
|
|
|
chr13 75563020 ????????????????????????????????????????????????????????????
|
|
13200 ------------------------------------------------------------
|
|
CAG33136. 45 ------------------------------------------------------------
|
|
|
|
chr13 75563080 ????????????????????????????????????????????????????????????
|
|
13260 ------------------------------------------------------------
|
|
CAG33136. 45 ------------------------------------------------------------
|
|
|
|
chr13 75563140 ????????????????????????????????????????????????????????????
|
|
13320 ------------------------------------------------------------
|
|
CAG33136. 45 ------------------------------------------------------------
|
|
|
|
chr13 75563200 ????????????????????????????????????????????????????????????
|
|
13380 ------------------------------------------------------------
|
|
CAG33136. 45 ------------------------------------------------------------
|
|
|
|
chr13 75563260 ????????????????????????????????????????????????????????????
|
|
13440 ------------------------------------------------------------
|
|
CAG33136. 45 ------------------------------------------------------------
|
|
|
|
chr13 75563320 ????????????????????????????????????????????????????????????
|
|
13500 ------------------------------------------------------------
|
|
CAG33136. 45 ------------------------------------------------------------
|
|
|
|
chr13 75563380 ????????????????????????????????????????????????????????????
|
|
13560 ------------------------------------------------------------
|
|
CAG33136. 45 ------------------------------------------------------------
|
|
|
|
chr13 75563440 ????????????????????????????????????????????????????????????
|
|
13620 ------------------------------------------------------------
|
|
CAG33136. 45 ------------------------------------------------------------
|
|
|
|
chr13 75563500 ????????????????????????????????????????????????????????????
|
|
13680 ------------------------------------------------------------
|
|
CAG33136. 45 ------------------------------------------------------------
|
|
|
|
chr13 75563560 ????????????????????????????????????????????????????????????
|
|
13740 ------------------------------------------------------------
|
|
CAG33136. 45 ------------------------------------------------------------
|
|
|
|
chr13 75563620 ????????????????????????????????????????????????????????????
|
|
13800 ------------------------------------------------------------
|
|
CAG33136. 45 ------------------------------------------------------------
|
|
|
|
chr13 75563680 ????????????????????????????????????????????????????????????
|
|
13860 ------------------------------------------------------------
|
|
CAG33136. 45 ------------------------------------------------------------
|
|
|
|
chr13 75563740 ????????????????????????????????????????????????????????????
|
|
13920 ------------------------------------------------------------
|
|
CAG33136. 45 ------------------------------------------------------------
|
|
|
|
chr13 75563800 ????????????????????????????????????????????????????????????
|
|
13980 ------------------------------------------------------------
|
|
CAG33136. 45 ------------------------------------------------------------
|
|
|
|
chr13 75563860 ????????????????????????????????????????????????????????????
|
|
14040 ------------------------------------------------------------
|
|
CAG33136. 45 ------------------------------------------------------------
|
|
|
|
chr13 75563920 ????????????????????????????????????????????????????????????
|
|
14100 ------------------------------------------------------------
|
|
CAG33136. 45 ------------------------------------------------------------
|
|
|
|
chr13 75563980 ????????????????????????????????????????????????????????????
|
|
14160 ------------------------------------------------------------
|
|
CAG33136. 45 ------------------------------------------------------------
|
|
|
|
chr13 75564040 ????????????????????????????????????????????????????????????
|
|
14220 ------------------------------------------------------------
|
|
CAG33136. 45 ------------------------------------------------------------
|
|
|
|
chr13 75564100 ????????????????????????????????????????????????????????????
|
|
14280 ------------------------------------------------------------
|
|
CAG33136. 45 ------------------------------------------------------------
|
|
|
|
chr13 75564160 ????????????????????????????????????????????????????????????
|
|
14340 ------------------------------------------------------------
|
|
CAG33136. 45 ------------------------------------------------------------
|
|
|
|
chr13 75564220 ????????????????????????????????????????????????????????????
|
|
14400 ------------------------------------------------------------
|
|
CAG33136. 45 ------------------------------------------------------------
|
|
|
|
chr13 75564280 ????????????????????????????????????????????????????????????
|
|
14460 ------------------------------------------------------------
|
|
CAG33136. 45 ------------------------------------------------------------
|
|
|
|
chr13 75564340 ????????????????????????????????????????????????????????????
|
|
14520 ------------------------------------------------------------
|
|
CAG33136. 45 ------------------------------------------------------------
|
|
|
|
chr13 75564400 ????????????????????????????????????????????????????????????
|
|
14580 ------------------------------------------------------------
|
|
CAG33136. 45 ------------------------------------------------------------
|
|
|
|
chr13 75564460 ????????????????????????????????????????????????????????????
|
|
14640 ------------------------------------------------------------
|
|
CAG33136. 45 ------------------------------------------------------------
|
|
|
|
chr13 75564520 ????????????????????????????????????????????????????????????
|
|
14700 ------------------------------------------------------------
|
|
CAG33136. 45 ------------------------------------------------------------
|
|
|
|
chr13 75564580 ????????????????????????????????????????????????????????????
|
|
14760 ------------------------------------------------------------
|
|
CAG33136. 45 ------------------------------------------------------------
|
|
|
|
chr13 75564640 ????????????????????????????????????????????????????????????
|
|
14820 ------------------------------------------------------------
|
|
CAG33136. 45 ------------------------------------------------------------
|
|
|
|
chr13 75564700 ????????????????????????????????????????????????????????????
|
|
14880 ------------------------------------------------------------
|
|
CAG33136. 45 ------------------------------------------------------------
|
|
|
|
chr13 75564760 ????????????????????????????????????????????????????????????
|
|
14940 ------------------------------------------------------------
|
|
CAG33136. 45 ------------------------------------------------------------
|
|
|
|
chr13 75564820 ????????????????????????????????????????????????????????????
|
|
15000 ------------------------------------------------------------
|
|
CAG33136. 45 ------------------------------------------------------------
|
|
|
|
chr13 75564880 ????????????????????????????????????????????????????????????
|
|
15060 ------------------------------------------------------------
|
|
CAG33136. 45 ------------------------------------------------------------
|
|
|
|
chr13 75564940 ????????????????????????????????????????????????????????????
|
|
15120 ------------------------------------------------------------
|
|
CAG33136. 45 ------------------------------------------------------------
|
|
|
|
chr13 75565000 ????????????????????????????????????????????????????????????
|
|
15180 ------------------------------------------------------------
|
|
CAG33136. 45 ------------------------------------------------------------
|
|
|
|
chr13 75565060 ????????????????????????????????????????????????????????????
|
|
15240 ------------------------------------------------------------
|
|
CAG33136. 45 ------------------------------------------------------------
|
|
|
|
chr13 75565120 ????????????????????????????????????????????????????????????
|
|
15300 ------------------------------------------------------------
|
|
CAG33136. 45 ------------------------------------------------------------
|
|
|
|
chr13 75565180 ????????????????????????????????????????????????????????????
|
|
15360 ------------------------------------------------------------
|
|
CAG33136. 45 ------------------------------------------------------------
|
|
|
|
chr13 75565240 ????????????????????????????????????????????????????????????
|
|
15420 ------------------------------------------------------------
|
|
CAG33136. 45 ------------------------------------------------------------
|
|
|
|
chr13 75565300 ????????????????????????????????????????????????????????????
|
|
15480 ------------------------------------------------------------
|
|
CAG33136. 45 ------------------------------------------------------------
|
|
|
|
chr13 75565360 ????????????????????????????????????????????????????????????
|
|
15540 ------------------------------------------------------------
|
|
CAG33136. 45 ------------------------------------------------------------
|
|
|
|
chr13 75565420 ????????????????????????????????????????????????????????????
|
|
15600 ------------------------------------------------------------
|
|
CAG33136. 45 ------------------------------------------------------------
|
|
|
|
chr13 75565480 ????????????????????????????????????????????????????????????
|
|
15660 ------------------------------------------------------------
|
|
CAG33136. 45 ------------------------------------------------------------
|
|
|
|
chr13 75565540 ????????????????????????????????????????????????????????????
|
|
15720 ------------------------------------------------------------
|
|
CAG33136. 45 ------------------------------------------------------------
|
|
|
|
chr13 75565600 ????????????????????????????????????????????????????????????
|
|
15780 ------------------------------------------------------------
|
|
CAG33136. 45 ------------------------------------------------------------
|
|
|
|
chr13 75565660 ????????????????????????????????????????????????????????????
|
|
15840 ------------------------------------------------------------
|
|
CAG33136. 45 ------------------------------------------------------------
|
|
|
|
chr13 75565720 ????????????????????????????????????????????????????????????
|
|
15900 ------------------------------------------------------------
|
|
CAG33136. 45 ------------------------------------------------------------
|
|
|
|
chr13 75565780 ????????????????????????????????????????????????????????????
|
|
15960 ------------------------------------------------------------
|
|
CAG33136. 45 ------------------------------------------------------------
|
|
|
|
chr13 75565840 ????????????????????????????????????????????????????????????
|
|
16020 ------------------------------------------------------------
|
|
CAG33136. 45 ------------------------------------------------------------
|
|
|
|
chr13 75565900 ????????????????????????????????????????????????????????????
|
|
16080 ------------------------------------------------------------
|
|
CAG33136. 45 ------------------------------------------------------------
|
|
|
|
chr13 75565960 ????????????????????????????????????????????????????????????
|
|
16140 ------------------------------------------------------------
|
|
CAG33136. 45 ------------------------------------------------------------
|
|
|
|
chr13 75566020 ????????????????????????????????????????????????????????????
|
|
16200 ------------------------------------------------------------
|
|
CAG33136. 45 ------------------------------------------------------------
|
|
|
|
chr13 75566080 ????????????????????????????????????????????????????????????
|
|
16260 ------------------------------------------------------------
|
|
CAG33136. 45 ------------------------------------------------------------
|
|
|
|
chr13 75566140 ????????????????????????????????????????????????????????????
|
|
16320 ------------------------------------------------------------
|
|
CAG33136. 45 ------------------------------------------------------------
|
|
|
|
chr13 75566200 ????????????????????????????????????????????????????????????
|
|
16380 ------------------------------------------------------------
|
|
CAG33136. 45 ------------------------------------------------------------
|
|
|
|
chr13 75566260 ????????????????????????????????????????????????????????????
|
|
16440 ------------------------------------------------------------
|
|
CAG33136. 45 ------------------------------------------------------------
|
|
|
|
chr13 75566320 ????????????????????????????????????????????????????????????
|
|
16500 ------------------------------------------------------------
|
|
CAG33136. 45 ------------------------------------------------------------
|
|
|
|
chr13 75566380 ????????????????????????????????????????????????????????????
|
|
16560 ------------------------------------------------------------
|
|
CAG33136. 45 ------------------------------------------------------------
|
|
|
|
chr13 75566440 ????????????????????????????????????????????????????????????
|
|
16620 ------------------------------------------------------------
|
|
CAG33136. 45 ------------------------------------------------------------
|
|
|
|
chr13 75566500 ????????????????????????????????????????????????????????????
|
|
16680 ------------------------------------------------------------
|
|
CAG33136. 45 ------------------------------------------------------------
|
|
|
|
chr13 75566560 ????????????????????????????????????????????????????????????
|
|
16740 ------------------------------------------------------------
|
|
CAG33136. 45 ------------------------------------------------------------
|
|
|
|
chr13 75566620 ????????????????????????????????????????????????????????????
|
|
16800 ------------------------------------------------------------
|
|
CAG33136. 45 ------------------------------------------------------------
|
|
|
|
chr13 75566680 ????????????????????????????????????????????????????????????
|
|
16860 ------------------------------------------------------------
|
|
CAG33136. 45 ------------------------------------------------------------
|
|
|
|
chr13 75566740 ????????????????????????????????????????????????????????????
|
|
16920 ------------------------------------------------------------
|
|
CAG33136. 45 ------------------------------------------------------------
|
|
|
|
chr13 75566800 ????????????????????????????????????????????????????????????
|
|
16980 ------------------------------------------------------------
|
|
CAG33136. 45 ------------------------------------------------------------
|
|
|
|
chr13 75566860 ????????????????????????????????????????????????????????????
|
|
17040 ------------------------------------------------------------
|
|
CAG33136. 45 ------------------------------------------------------------
|
|
|
|
chr13 75566920 ????????????????????????????????????????????????????????????
|
|
17100 ------------------------------------------------------------
|
|
CAG33136. 45 ------------------------------------------------------------
|
|
|
|
chr13 75566980 ????????????????????????????????????????????????????????????
|
|
17160 ------------------------------------------------------------
|
|
CAG33136. 45 ------------------------------------------------------------
|
|
|
|
chr13 75567040 ????????????????????????????????????????????????????????????
|
|
17220 ------------------------------------------------------------
|
|
CAG33136. 45 ------------------------------------------------------------
|
|
|
|
chr13 75567100 ????????????????????????????????????????????????????????????
|
|
17280 ------------------------------------------------------------
|
|
CAG33136. 45 ------------------------------------------------------------
|
|
|
|
chr13 75567160 ????????????????????????????????????????????????????????????
|
|
17340 ------------------------------------------------------------
|
|
CAG33136. 45 ------------------------------------------------------------
|
|
|
|
chr13 75567220 ????????????????????????????????????????????????????????????
|
|
17400 -----|||||||||||||||||||||||||||||||||||||||||||||||||||||||
|
|
CAG33136. 45 -----???????????????????????????????????????????????????????
|
|
|
|
chr13 75567280 ???????????????????????????????? 75567312
|
|
17460 |||||||||||||||||||||||||||||||| 17492
|
|
CAG33136. 100 ???????????????????????????????? 132
|
|
""",
|
|
)
|
|
self.assertEqual(
|
|
format(alignment, "bed"),
|
|
"""\
|
|
chr13 75549820 75567312 CAG33136.1 986 + 75549820 75567312 0 2 45,87, 0,17405,
|
|
""",
|
|
)
|
|
counts = alignment.counts()
|
|
self.assertEqual(counts.left_insertions, 0)
|
|
self.assertEqual(counts.left_deletions, 0)
|
|
self.assertEqual(counts.right_insertions, 0)
|
|
self.assertEqual(counts.right_deletions, 0)
|
|
self.assertEqual(counts.internal_insertions, 0)
|
|
self.assertEqual(counts.internal_deletions, 17360)
|
|
self.assertEqual(counts.left_gaps, 0)
|
|
self.assertEqual(counts.right_gaps, 0)
|
|
self.assertEqual(counts.internal_gaps, 17360)
|
|
self.assertEqual(counts.insertions, 0)
|
|
self.assertEqual(counts.deletions, 17360)
|
|
self.assertEqual(counts.gaps, 17360)
|
|
self.assertEqual(counts.aligned, 132)
|
|
alignment = next(alignments)
|
|
self.assertEqual(alignment.score, 1000)
|
|
self.assertLess(alignment.coordinates[0, 0], alignment.coordinates[0, -1])
|
|
self.assertLess(alignment.coordinates[1, 0], alignment.coordinates[1, -1])
|
|
self.assertEqual(len(alignment), 2)
|
|
self.assertIs(alignment.sequences[0], alignment.target)
|
|
self.assertIs(alignment.sequences[1], alignment.query)
|
|
self.assertEqual(alignment.target.id, "chr13")
|
|
self.assertEqual(alignment.query.id, "CAG33136.1")
|
|
self.assertTrue(
|
|
np.array_equal(
|
|
alignment.coordinates,
|
|
# fmt: off
|
|
np.array([[75604767, 75604827, 75605728, 75605809],
|
|
[ 0, 60, 60, 141]]),
|
|
# fmt: on
|
|
)
|
|
)
|
|
self.assertEqual(
|
|
str(alignment),
|
|
"""\
|
|
chr13 75604767 ????????????????????????????????????????????????????????????
|
|
0 ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
|
|
CAG33136. 0 ????????????????????????????????????????????????????????????
|
|
|
|
chr13 75604827 ????????????????????????????????????????????????????????????
|
|
60 ------------------------------------------------------------
|
|
CAG33136. 60 ------------------------------------------------------------
|
|
|
|
chr13 75604887 ????????????????????????????????????????????????????????????
|
|
120 ------------------------------------------------------------
|
|
CAG33136. 60 ------------------------------------------------------------
|
|
|
|
chr13 75604947 ????????????????????????????????????????????????????????????
|
|
180 ------------------------------------------------------------
|
|
CAG33136. 60 ------------------------------------------------------------
|
|
|
|
chr13 75605007 ????????????????????????????????????????????????????????????
|
|
240 ------------------------------------------------------------
|
|
CAG33136. 60 ------------------------------------------------------------
|
|
|
|
chr13 75605067 ????????????????????????????????????????????????????????????
|
|
300 ------------------------------------------------------------
|
|
CAG33136. 60 ------------------------------------------------------------
|
|
|
|
chr13 75605127 ????????????????????????????????????????????????????????????
|
|
360 ------------------------------------------------------------
|
|
CAG33136. 60 ------------------------------------------------------------
|
|
|
|
chr13 75605187 ????????????????????????????????????????????????????????????
|
|
420 ------------------------------------------------------------
|
|
CAG33136. 60 ------------------------------------------------------------
|
|
|
|
chr13 75605247 ????????????????????????????????????????????????????????????
|
|
480 ------------------------------------------------------------
|
|
CAG33136. 60 ------------------------------------------------------------
|
|
|
|
chr13 75605307 ????????????????????????????????????????????????????????????
|
|
540 ------------------------------------------------------------
|
|
CAG33136. 60 ------------------------------------------------------------
|
|
|
|
chr13 75605367 ????????????????????????????????????????????????????????????
|
|
600 ------------------------------------------------------------
|
|
CAG33136. 60 ------------------------------------------------------------
|
|
|
|
chr13 75605427 ????????????????????????????????????????????????????????????
|
|
660 ------------------------------------------------------------
|
|
CAG33136. 60 ------------------------------------------------------------
|
|
|
|
chr13 75605487 ????????????????????????????????????????????????????????????
|
|
720 ------------------------------------------------------------
|
|
CAG33136. 60 ------------------------------------------------------------
|
|
|
|
chr13 75605547 ????????????????????????????????????????????????????????????
|
|
780 ------------------------------------------------------------
|
|
CAG33136. 60 ------------------------------------------------------------
|
|
|
|
chr13 75605607 ????????????????????????????????????????????????????????????
|
|
840 ------------------------------------------------------------
|
|
CAG33136. 60 ------------------------------------------------------------
|
|
|
|
chr13 75605667 ????????????????????????????????????????????????????????????
|
|
900 ------------------------------------------------------------
|
|
CAG33136. 60 ------------------------------------------------------------
|
|
|
|
chr13 75605727 ????????????????????????????????????????????????????????????
|
|
960 -|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
|
|
CAG33136. 60 -???????????????????????????????????????????????????????????
|
|
|
|
chr13 75605787 ?????????????????????? 75605809
|
|
1020 |||||||||||||||||||||| 1042
|
|
CAG33136. 119 ?????????????????????? 141
|
|
""",
|
|
)
|
|
self.assertEqual(
|
|
format(alignment, "bed"),
|
|
"""\
|
|
chr13 75604767 75605809 CAG33136.1 1000 + 75604767 75605809 0 2 60,81, 0,961,
|
|
""",
|
|
)
|
|
counts = alignment.counts()
|
|
self.assertEqual(counts.left_insertions, 0)
|
|
self.assertEqual(counts.left_deletions, 0)
|
|
self.assertEqual(counts.right_insertions, 0)
|
|
self.assertEqual(counts.right_deletions, 0)
|
|
self.assertEqual(counts.internal_insertions, 0)
|
|
self.assertEqual(counts.internal_deletions, 901)
|
|
self.assertEqual(counts.left_gaps, 0)
|
|
self.assertEqual(counts.right_gaps, 0)
|
|
self.assertEqual(counts.internal_gaps, 901)
|
|
self.assertEqual(counts.insertions, 0)
|
|
self.assertEqual(counts.deletions, 901)
|
|
self.assertEqual(counts.gaps, 901)
|
|
self.assertEqual(counts.aligned, 141)
|
|
alignment = next(alignments)
|
|
self.assertEqual(alignment.score, 1000)
|
|
self.assertLess(alignment.coordinates[0, 0], alignment.coordinates[0, -1])
|
|
self.assertLess(alignment.coordinates[1, 0], alignment.coordinates[1, -1])
|
|
self.assertEqual(len(alignment), 2)
|
|
self.assertIs(alignment.sequences[0], alignment.target)
|
|
self.assertIs(alignment.sequences[1], alignment.query)
|
|
self.assertEqual(alignment.target.id, "chr13")
|
|
self.assertEqual(alignment.query.id, "CAG33136.1")
|
|
self.assertTrue(
|
|
np.array_equal(
|
|
alignment.coordinates,
|
|
# fmt: off
|
|
np.array([[75594914, 75594989],
|
|
[ 0, 75]]),
|
|
# fmt: on
|
|
)
|
|
)
|
|
self.assertEqual(
|
|
str(alignment),
|
|
"""\
|
|
chr13 75594914 ????????????????????????????????????????????????????????????
|
|
0 ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
|
|
CAG33136. 0 ????????????????????????????????????????????????????????????
|
|
|
|
chr13 75594974 ??????????????? 75594989
|
|
60 ||||||||||||||| 75
|
|
CAG33136. 60 ??????????????? 75
|
|
""",
|
|
)
|
|
self.assertEqual(
|
|
format(alignment, "bed"),
|
|
"""\
|
|
chr13 75594914 75594989 CAG33136.1 1000 + 75594914 75594989 0 1 75, 0,
|
|
""",
|
|
)
|
|
counts = alignment.counts()
|
|
self.assertEqual(counts.left_insertions, 0)
|
|
self.assertEqual(counts.left_deletions, 0)
|
|
self.assertEqual(counts.right_insertions, 0)
|
|
self.assertEqual(counts.right_deletions, 0)
|
|
self.assertEqual(counts.internal_insertions, 0)
|
|
self.assertEqual(counts.internal_deletions, 0)
|
|
self.assertEqual(counts.left_gaps, 0)
|
|
self.assertEqual(counts.right_gaps, 0)
|
|
self.assertEqual(counts.internal_gaps, 0)
|
|
self.assertEqual(counts.insertions, 0)
|
|
self.assertEqual(counts.deletions, 0)
|
|
self.assertEqual(counts.gaps, 0)
|
|
self.assertEqual(counts.aligned, 75)
|
|
alignment = next(alignments)
|
|
self.assertEqual(alignment.score, 1000)
|
|
self.assertLess(alignment.coordinates[0, 0], alignment.coordinates[0, -1])
|
|
self.assertLess(alignment.coordinates[1, 0], alignment.coordinates[1, -1])
|
|
self.assertEqual(len(alignment), 2)
|
|
self.assertIs(alignment.sequences[0], alignment.target)
|
|
self.assertIs(alignment.sequences[1], alignment.query)
|
|
self.assertEqual(alignment.target.id, "chr13")
|
|
self.assertEqual(alignment.query.id, "CAG33136.1")
|
|
self.assertTrue(
|
|
np.array_equal(
|
|
alignment.coordinates,
|
|
# fmt: off
|
|
np.array([[75569459, 75569507],
|
|
[ 0, 48]]),
|
|
# fmt: on
|
|
)
|
|
)
|
|
self.assertEqual(
|
|
str(alignment),
|
|
"""\
|
|
chr13 75569459 ???????????????????????????????????????????????? 75569507
|
|
0 |||||||||||||||||||||||||||||||||||||||||||||||| 48
|
|
CAG33136. 0 ???????????????????????????????????????????????? 48
|
|
""",
|
|
)
|
|
self.assertEqual(
|
|
format(alignment, "bed"),
|
|
"""\
|
|
chr13 75569459 75569507 CAG33136.1 1000 + 75569459 75569507 0 1 48, 0,
|
|
""",
|
|
)
|
|
counts = alignment.counts()
|
|
self.assertEqual(counts.left_insertions, 0)
|
|
self.assertEqual(counts.left_deletions, 0)
|
|
self.assertEqual(counts.right_insertions, 0)
|
|
self.assertEqual(counts.right_deletions, 0)
|
|
self.assertEqual(counts.internal_insertions, 0)
|
|
self.assertEqual(counts.internal_deletions, 0)
|
|
self.assertEqual(counts.left_gaps, 0)
|
|
self.assertEqual(counts.right_gaps, 0)
|
|
self.assertEqual(counts.internal_gaps, 0)
|
|
self.assertEqual(counts.insertions, 0)
|
|
self.assertEqual(counts.deletions, 0)
|
|
self.assertEqual(counts.gaps, 0)
|
|
self.assertEqual(counts.aligned, 48)
|
|
alignment = next(alignments)
|
|
self.assertEqual(alignment.score, 530)
|
|
self.assertLess(alignment.coordinates[0, 0], alignment.coordinates[0, -1])
|
|
self.assertLess(alignment.coordinates[1, 0], alignment.coordinates[1, -1])
|
|
self.assertEqual(len(alignment), 2)
|
|
self.assertIs(alignment.sequences[0], alignment.target)
|
|
self.assertIs(alignment.sequences[1], alignment.query)
|
|
self.assertEqual(alignment.target.id, "chr4")
|
|
self.assertEqual(alignment.query.id, "CAG33136.1")
|
|
self.assertTrue(
|
|
np.array_equal(
|
|
alignment.coordinates,
|
|
# fmt: off
|
|
np.array([[41260685, 41260787],
|
|
[ 0, 102]]),
|
|
# fmt: on
|
|
)
|
|
)
|
|
self.assertEqual(
|
|
str(alignment),
|
|
"""\
|
|
chr4 41260685 ????????????????????????????????????????????????????????????
|
|
0 ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
|
|
CAG33136. 0 ????????????????????????????????????????????????????????????
|
|
|
|
chr4 41260745 ?????????????????????????????????????????? 41260787
|
|
60 |||||||||||||||||||||||||||||||||||||||||| 102
|
|
CAG33136. 60 ?????????????????????????????????????????? 102
|
|
""",
|
|
)
|
|
self.assertEqual(
|
|
format(alignment, "bed"),
|
|
"""\
|
|
chr4 41260685 41260787 CAG33136.1 530 + 41260685 41260787 0 1 102, 0,
|
|
""",
|
|
)
|
|
counts = alignment.counts()
|
|
self.assertEqual(counts.left_insertions, 0)
|
|
self.assertEqual(counts.left_deletions, 0)
|
|
self.assertEqual(counts.right_insertions, 0)
|
|
self.assertEqual(counts.right_deletions, 0)
|
|
self.assertEqual(counts.internal_insertions, 0)
|
|
self.assertEqual(counts.internal_deletions, 0)
|
|
self.assertEqual(counts.left_gaps, 0)
|
|
self.assertEqual(counts.right_gaps, 0)
|
|
self.assertEqual(counts.internal_gaps, 0)
|
|
self.assertEqual(counts.insertions, 0)
|
|
self.assertEqual(counts.deletions, 0)
|
|
self.assertEqual(counts.gaps, 0)
|
|
self.assertEqual(counts.aligned, 102)
|
|
alignment = next(alignments)
|
|
self.assertEqual(alignment.score, 166)
|
|
self.assertLess(alignment.coordinates[0, 0], alignment.coordinates[0, -1])
|
|
self.assertLess(alignment.coordinates[1, 0], alignment.coordinates[1, -1])
|
|
self.assertEqual(len(alignment), 2)
|
|
self.assertIs(alignment.sequences[0], alignment.target)
|
|
self.assertIs(alignment.sequences[1], alignment.query)
|
|
self.assertEqual(alignment.target.id, "chr4")
|
|
self.assertEqual(alignment.query.id, "CAG33136.1")
|
|
self.assertTrue(
|
|
np.array_equal(
|
|
alignment.coordinates,
|
|
# fmt: off
|
|
np.array([[41257605, 41257731, 41263227, 41263290],
|
|
[ 0, 126, 126, 189]]),
|
|
# fmt: on
|
|
)
|
|
)
|
|
self.assertEqual(
|
|
str(alignment),
|
|
"""\
|
|
chr4 41257605 ????????????????????????????????????????????????????????????
|
|
0 ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
|
|
CAG33136. 0 ????????????????????????????????????????????????????????????
|
|
|
|
chr4 41257665 ????????????????????????????????????????????????????????????
|
|
60 ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
|
|
CAG33136. 60 ????????????????????????????????????????????????????????????
|
|
|
|
chr4 41257725 ????????????????????????????????????????????????????????????
|
|
120 ||||||------------------------------------------------------
|
|
CAG33136. 120 ??????------------------------------------------------------
|
|
|
|
chr4 41257785 ????????????????????????????????????????????????????????????
|
|
180 ------------------------------------------------------------
|
|
CAG33136. 126 ------------------------------------------------------------
|
|
|
|
chr4 41257845 ????????????????????????????????????????????????????????????
|
|
240 ------------------------------------------------------------
|
|
CAG33136. 126 ------------------------------------------------------------
|
|
|
|
chr4 41257905 ????????????????????????????????????????????????????????????
|
|
300 ------------------------------------------------------------
|
|
CAG33136. 126 ------------------------------------------------------------
|
|
|
|
chr4 41257965 ????????????????????????????????????????????????????????????
|
|
360 ------------------------------------------------------------
|
|
CAG33136. 126 ------------------------------------------------------------
|
|
|
|
chr4 41258025 ????????????????????????????????????????????????????????????
|
|
420 ------------------------------------------------------------
|
|
CAG33136. 126 ------------------------------------------------------------
|
|
|
|
chr4 41258085 ????????????????????????????????????????????????????????????
|
|
480 ------------------------------------------------------------
|
|
CAG33136. 126 ------------------------------------------------------------
|
|
|
|
chr4 41258145 ????????????????????????????????????????????????????????????
|
|
540 ------------------------------------------------------------
|
|
CAG33136. 126 ------------------------------------------------------------
|
|
|
|
chr4 41258205 ????????????????????????????????????????????????????????????
|
|
600 ------------------------------------------------------------
|
|
CAG33136. 126 ------------------------------------------------------------
|
|
|
|
chr4 41258265 ????????????????????????????????????????????????????????????
|
|
660 ------------------------------------------------------------
|
|
CAG33136. 126 ------------------------------------------------------------
|
|
|
|
chr4 41258325 ????????????????????????????????????????????????????????????
|
|
720 ------------------------------------------------------------
|
|
CAG33136. 126 ------------------------------------------------------------
|
|
|
|
chr4 41258385 ????????????????????????????????????????????????????????????
|
|
780 ------------------------------------------------------------
|
|
CAG33136. 126 ------------------------------------------------------------
|
|
|
|
chr4 41258445 ????????????????????????????????????????????????????????????
|
|
840 ------------------------------------------------------------
|
|
CAG33136. 126 ------------------------------------------------------------
|
|
|
|
chr4 41258505 ????????????????????????????????????????????????????????????
|
|
900 ------------------------------------------------------------
|
|
CAG33136. 126 ------------------------------------------------------------
|
|
|
|
chr4 41258565 ????????????????????????????????????????????????????????????
|
|
960 ------------------------------------------------------------
|
|
CAG33136. 126 ------------------------------------------------------------
|
|
|
|
chr4 41258625 ????????????????????????????????????????????????????????????
|
|
1020 ------------------------------------------------------------
|
|
CAG33136. 126 ------------------------------------------------------------
|
|
|
|
chr4 41258685 ????????????????????????????????????????????????????????????
|
|
1080 ------------------------------------------------------------
|
|
CAG33136. 126 ------------------------------------------------------------
|
|
|
|
chr4 41258745 ????????????????????????????????????????????????????????????
|
|
1140 ------------------------------------------------------------
|
|
CAG33136. 126 ------------------------------------------------------------
|
|
|
|
chr4 41258805 ????????????????????????????????????????????????????????????
|
|
1200 ------------------------------------------------------------
|
|
CAG33136. 126 ------------------------------------------------------------
|
|
|
|
chr4 41258865 ????????????????????????????????????????????????????????????
|
|
1260 ------------------------------------------------------------
|
|
CAG33136. 126 ------------------------------------------------------------
|
|
|
|
chr4 41258925 ????????????????????????????????????????????????????????????
|
|
1320 ------------------------------------------------------------
|
|
CAG33136. 126 ------------------------------------------------------------
|
|
|
|
chr4 41258985 ????????????????????????????????????????????????????????????
|
|
1380 ------------------------------------------------------------
|
|
CAG33136. 126 ------------------------------------------------------------
|
|
|
|
chr4 41259045 ????????????????????????????????????????????????????????????
|
|
1440 ------------------------------------------------------------
|
|
CAG33136. 126 ------------------------------------------------------------
|
|
|
|
chr4 41259105 ????????????????????????????????????????????????????????????
|
|
1500 ------------------------------------------------------------
|
|
CAG33136. 126 ------------------------------------------------------------
|
|
|
|
chr4 41259165 ????????????????????????????????????????????????????????????
|
|
1560 ------------------------------------------------------------
|
|
CAG33136. 126 ------------------------------------------------------------
|
|
|
|
chr4 41259225 ????????????????????????????????????????????????????????????
|
|
1620 ------------------------------------------------------------
|
|
CAG33136. 126 ------------------------------------------------------------
|
|
|
|
chr4 41259285 ????????????????????????????????????????????????????????????
|
|
1680 ------------------------------------------------------------
|
|
CAG33136. 126 ------------------------------------------------------------
|
|
|
|
chr4 41259345 ????????????????????????????????????????????????????????????
|
|
1740 ------------------------------------------------------------
|
|
CAG33136. 126 ------------------------------------------------------------
|
|
|
|
chr4 41259405 ????????????????????????????????????????????????????????????
|
|
1800 ------------------------------------------------------------
|
|
CAG33136. 126 ------------------------------------------------------------
|
|
|
|
chr4 41259465 ????????????????????????????????????????????????????????????
|
|
1860 ------------------------------------------------------------
|
|
CAG33136. 126 ------------------------------------------------------------
|
|
|
|
chr4 41259525 ????????????????????????????????????????????????????????????
|
|
1920 ------------------------------------------------------------
|
|
CAG33136. 126 ------------------------------------------------------------
|
|
|
|
chr4 41259585 ????????????????????????????????????????????????????????????
|
|
1980 ------------------------------------------------------------
|
|
CAG33136. 126 ------------------------------------------------------------
|
|
|
|
chr4 41259645 ????????????????????????????????????????????????????????????
|
|
2040 ------------------------------------------------------------
|
|
CAG33136. 126 ------------------------------------------------------------
|
|
|
|
chr4 41259705 ????????????????????????????????????????????????????????????
|
|
2100 ------------------------------------------------------------
|
|
CAG33136. 126 ------------------------------------------------------------
|
|
|
|
chr4 41259765 ????????????????????????????????????????????????????????????
|
|
2160 ------------------------------------------------------------
|
|
CAG33136. 126 ------------------------------------------------------------
|
|
|
|
chr4 41259825 ????????????????????????????????????????????????????????????
|
|
2220 ------------------------------------------------------------
|
|
CAG33136. 126 ------------------------------------------------------------
|
|
|
|
chr4 41259885 ????????????????????????????????????????????????????????????
|
|
2280 ------------------------------------------------------------
|
|
CAG33136. 126 ------------------------------------------------------------
|
|
|
|
chr4 41259945 ????????????????????????????????????????????????????????????
|
|
2340 ------------------------------------------------------------
|
|
CAG33136. 126 ------------------------------------------------------------
|
|
|
|
chr4 41260005 ????????????????????????????????????????????????????????????
|
|
2400 ------------------------------------------------------------
|
|
CAG33136. 126 ------------------------------------------------------------
|
|
|
|
chr4 41260065 ????????????????????????????????????????????????????????????
|
|
2460 ------------------------------------------------------------
|
|
CAG33136. 126 ------------------------------------------------------------
|
|
|
|
chr4 41260125 ????????????????????????????????????????????????????????????
|
|
2520 ------------------------------------------------------------
|
|
CAG33136. 126 ------------------------------------------------------------
|
|
|
|
chr4 41260185 ????????????????????????????????????????????????????????????
|
|
2580 ------------------------------------------------------------
|
|
CAG33136. 126 ------------------------------------------------------------
|
|
|
|
chr4 41260245 ????????????????????????????????????????????????????????????
|
|
2640 ------------------------------------------------------------
|
|
CAG33136. 126 ------------------------------------------------------------
|
|
|
|
chr4 41260305 ????????????????????????????????????????????????????????????
|
|
2700 ------------------------------------------------------------
|
|
CAG33136. 126 ------------------------------------------------------------
|
|
|
|
chr4 41260365 ????????????????????????????????????????????????????????????
|
|
2760 ------------------------------------------------------------
|
|
CAG33136. 126 ------------------------------------------------------------
|
|
|
|
chr4 41260425 ????????????????????????????????????????????????????????????
|
|
2820 ------------------------------------------------------------
|
|
CAG33136. 126 ------------------------------------------------------------
|
|
|
|
chr4 41260485 ????????????????????????????????????????????????????????????
|
|
2880 ------------------------------------------------------------
|
|
CAG33136. 126 ------------------------------------------------------------
|
|
|
|
chr4 41260545 ????????????????????????????????????????????????????????????
|
|
2940 ------------------------------------------------------------
|
|
CAG33136. 126 ------------------------------------------------------------
|
|
|
|
chr4 41260605 ????????????????????????????????????????????????????????????
|
|
3000 ------------------------------------------------------------
|
|
CAG33136. 126 ------------------------------------------------------------
|
|
|
|
chr4 41260665 ????????????????????????????????????????????????????????????
|
|
3060 ------------------------------------------------------------
|
|
CAG33136. 126 ------------------------------------------------------------
|
|
|
|
chr4 41260725 ????????????????????????????????????????????????????????????
|
|
3120 ------------------------------------------------------------
|
|
CAG33136. 126 ------------------------------------------------------------
|
|
|
|
chr4 41260785 ????????????????????????????????????????????????????????????
|
|
3180 ------------------------------------------------------------
|
|
CAG33136. 126 ------------------------------------------------------------
|
|
|
|
chr4 41260845 ????????????????????????????????????????????????????????????
|
|
3240 ------------------------------------------------------------
|
|
CAG33136. 126 ------------------------------------------------------------
|
|
|
|
chr4 41260905 ????????????????????????????????????????????????????????????
|
|
3300 ------------------------------------------------------------
|
|
CAG33136. 126 ------------------------------------------------------------
|
|
|
|
chr4 41260965 ????????????????????????????????????????????????????????????
|
|
3360 ------------------------------------------------------------
|
|
CAG33136. 126 ------------------------------------------------------------
|
|
|
|
chr4 41261025 ????????????????????????????????????????????????????????????
|
|
3420 ------------------------------------------------------------
|
|
CAG33136. 126 ------------------------------------------------------------
|
|
|
|
chr4 41261085 ????????????????????????????????????????????????????????????
|
|
3480 ------------------------------------------------------------
|
|
CAG33136. 126 ------------------------------------------------------------
|
|
|
|
chr4 41261145 ????????????????????????????????????????????????????????????
|
|
3540 ------------------------------------------------------------
|
|
CAG33136. 126 ------------------------------------------------------------
|
|
|
|
chr4 41261205 ????????????????????????????????????????????????????????????
|
|
3600 ------------------------------------------------------------
|
|
CAG33136. 126 ------------------------------------------------------------
|
|
|
|
chr4 41261265 ????????????????????????????????????????????????????????????
|
|
3660 ------------------------------------------------------------
|
|
CAG33136. 126 ------------------------------------------------------------
|
|
|
|
chr4 41261325 ????????????????????????????????????????????????????????????
|
|
3720 ------------------------------------------------------------
|
|
CAG33136. 126 ------------------------------------------------------------
|
|
|
|
chr4 41261385 ????????????????????????????????????????????????????????????
|
|
3780 ------------------------------------------------------------
|
|
CAG33136. 126 ------------------------------------------------------------
|
|
|
|
chr4 41261445 ????????????????????????????????????????????????????????????
|
|
3840 ------------------------------------------------------------
|
|
CAG33136. 126 ------------------------------------------------------------
|
|
|
|
chr4 41261505 ????????????????????????????????????????????????????????????
|
|
3900 ------------------------------------------------------------
|
|
CAG33136. 126 ------------------------------------------------------------
|
|
|
|
chr4 41261565 ????????????????????????????????????????????????????????????
|
|
3960 ------------------------------------------------------------
|
|
CAG33136. 126 ------------------------------------------------------------
|
|
|
|
chr4 41261625 ????????????????????????????????????????????????????????????
|
|
4020 ------------------------------------------------------------
|
|
CAG33136. 126 ------------------------------------------------------------
|
|
|
|
chr4 41261685 ????????????????????????????????????????????????????????????
|
|
4080 ------------------------------------------------------------
|
|
CAG33136. 126 ------------------------------------------------------------
|
|
|
|
chr4 41261745 ????????????????????????????????????????????????????????????
|
|
4140 ------------------------------------------------------------
|
|
CAG33136. 126 ------------------------------------------------------------
|
|
|
|
chr4 41261805 ????????????????????????????????????????????????????????????
|
|
4200 ------------------------------------------------------------
|
|
CAG33136. 126 ------------------------------------------------------------
|
|
|
|
chr4 41261865 ????????????????????????????????????????????????????????????
|
|
4260 ------------------------------------------------------------
|
|
CAG33136. 126 ------------------------------------------------------------
|
|
|
|
chr4 41261925 ????????????????????????????????????????????????????????????
|
|
4320 ------------------------------------------------------------
|
|
CAG33136. 126 ------------------------------------------------------------
|
|
|
|
chr4 41261985 ????????????????????????????????????????????????????????????
|
|
4380 ------------------------------------------------------------
|
|
CAG33136. 126 ------------------------------------------------------------
|
|
|
|
chr4 41262045 ????????????????????????????????????????????????????????????
|
|
4440 ------------------------------------------------------------
|
|
CAG33136. 126 ------------------------------------------------------------
|
|
|
|
chr4 41262105 ????????????????????????????????????????????????????????????
|
|
4500 ------------------------------------------------------------
|
|
CAG33136. 126 ------------------------------------------------------------
|
|
|
|
chr4 41262165 ????????????????????????????????????????????????????????????
|
|
4560 ------------------------------------------------------------
|
|
CAG33136. 126 ------------------------------------------------------------
|
|
|
|
chr4 41262225 ????????????????????????????????????????????????????????????
|
|
4620 ------------------------------------------------------------
|
|
CAG33136. 126 ------------------------------------------------------------
|
|
|
|
chr4 41262285 ????????????????????????????????????????????????????????????
|
|
4680 ------------------------------------------------------------
|
|
CAG33136. 126 ------------------------------------------------------------
|
|
|
|
chr4 41262345 ????????????????????????????????????????????????????????????
|
|
4740 ------------------------------------------------------------
|
|
CAG33136. 126 ------------------------------------------------------------
|
|
|
|
chr4 41262405 ????????????????????????????????????????????????????????????
|
|
4800 ------------------------------------------------------------
|
|
CAG33136. 126 ------------------------------------------------------------
|
|
|
|
chr4 41262465 ????????????????????????????????????????????????????????????
|
|
4860 ------------------------------------------------------------
|
|
CAG33136. 126 ------------------------------------------------------------
|
|
|
|
chr4 41262525 ????????????????????????????????????????????????????????????
|
|
4920 ------------------------------------------------------------
|
|
CAG33136. 126 ------------------------------------------------------------
|
|
|
|
chr4 41262585 ????????????????????????????????????????????????????????????
|
|
4980 ------------------------------------------------------------
|
|
CAG33136. 126 ------------------------------------------------------------
|
|
|
|
chr4 41262645 ????????????????????????????????????????????????????????????
|
|
5040 ------------------------------------------------------------
|
|
CAG33136. 126 ------------------------------------------------------------
|
|
|
|
chr4 41262705 ????????????????????????????????????????????????????????????
|
|
5100 ------------------------------------------------------------
|
|
CAG33136. 126 ------------------------------------------------------------
|
|
|
|
chr4 41262765 ????????????????????????????????????????????????????????????
|
|
5160 ------------------------------------------------------------
|
|
CAG33136. 126 ------------------------------------------------------------
|
|
|
|
chr4 41262825 ????????????????????????????????????????????????????????????
|
|
5220 ------------------------------------------------------------
|
|
CAG33136. 126 ------------------------------------------------------------
|
|
|
|
chr4 41262885 ????????????????????????????????????????????????????????????
|
|
5280 ------------------------------------------------------------
|
|
CAG33136. 126 ------------------------------------------------------------
|
|
|
|
chr4 41262945 ????????????????????????????????????????????????????????????
|
|
5340 ------------------------------------------------------------
|
|
CAG33136. 126 ------------------------------------------------------------
|
|
|
|
chr4 41263005 ????????????????????????????????????????????????????????????
|
|
5400 ------------------------------------------------------------
|
|
CAG33136. 126 ------------------------------------------------------------
|
|
|
|
chr4 41263065 ????????????????????????????????????????????????????????????
|
|
5460 ------------------------------------------------------------
|
|
CAG33136. 126 ------------------------------------------------------------
|
|
|
|
chr4 41263125 ????????????????????????????????????????????????????????????
|
|
5520 ------------------------------------------------------------
|
|
CAG33136. 126 ------------------------------------------------------------
|
|
|
|
chr4 41263185 ????????????????????????????????????????????????????????????
|
|
5580 ------------------------------------------||||||||||||||||||
|
|
CAG33136. 126 ------------------------------------------??????????????????
|
|
|
|
chr4 41263245 ????????????????????????????????????????????? 41263290
|
|
5640 ||||||||||||||||||||||||||||||||||||||||||||| 5685
|
|
CAG33136. 144 ????????????????????????????????????????????? 189
|
|
""",
|
|
)
|
|
self.assertEqual(
|
|
format(alignment, "bed"),
|
|
"""\
|
|
chr4 41257605 41263290 CAG33136.1 166 + 41257605 41263290 0 2 126,63, 0,5622,
|
|
""",
|
|
)
|
|
counts = alignment.counts()
|
|
self.assertEqual(counts.left_insertions, 0)
|
|
self.assertEqual(counts.left_deletions, 0)
|
|
self.assertEqual(counts.right_insertions, 0)
|
|
self.assertEqual(counts.right_deletions, 0)
|
|
self.assertEqual(counts.internal_insertions, 0)
|
|
self.assertEqual(counts.internal_deletions, 5496)
|
|
self.assertEqual(counts.left_gaps, 0)
|
|
self.assertEqual(counts.right_gaps, 0)
|
|
self.assertEqual(counts.internal_gaps, 5496)
|
|
self.assertEqual(counts.insertions, 0)
|
|
self.assertEqual(counts.deletions, 5496)
|
|
self.assertEqual(counts.gaps, 5496)
|
|
self.assertEqual(counts.aligned, 189)
|
|
self.assertRaises(StopIteration, next, alignments)
|
|
|
|
def test_writing_psl_35_001(self):
|
|
"""Test writing the alignments in psl_35_001.bed."""
|
|
path = "Blat/psl_35_001.bed"
|
|
with open(path) as stream:
|
|
original_data = stream.read()
|
|
alignments = Align.parse(path, "bed")
|
|
stream = StringIO()
|
|
n = Align.write(alignments, stream, "bed")
|
|
self.assertEqual(n, 8)
|
|
stream.seek(0)
|
|
written_data = stream.read()
|
|
stream.close()
|
|
self.assertEqual(original_data, written_data)
|
|
|
|
def test_reading_psl_35_002(self):
|
|
"""Test parsing psl_35_002.bed."""
|
|
path = "Blat/psl_35_002.bed"
|
|
alignments = Align.parse(path, "bed")
|
|
alignment = next(alignments)
|
|
self.assertEqual(alignment.score, 972)
|
|
self.assertLess(alignment.coordinates[0, 0], alignment.coordinates[0, -1])
|
|
self.assertLess(alignment.coordinates[1, 0], alignment.coordinates[1, -1])
|
|
self.assertEqual(len(alignment), 2)
|
|
self.assertIs(alignment.sequences[0], alignment.target)
|
|
self.assertIs(alignment.sequences[1], alignment.query)
|
|
self.assertEqual(alignment.target.id, "KI537979")
|
|
self.assertEqual(alignment.query.id, "CAG33136.1")
|
|
self.assertTrue(
|
|
np.array_equal(
|
|
alignment.coordinates,
|
|
# fmt: off
|
|
np.array([[9712654, 9712786, 9715941, 9716097, 9716445, 9716532, 9718374,
|
|
9718422, 9739264, 9739339, 9743706, 9743766, 9744511, 9744592],
|
|
[ 0, 132, 132, 288, 288, 375, 375,
|
|
423, 423, 498, 498, 558, 558, 639]]),
|
|
# fmt: on
|
|
)
|
|
)
|
|
self.assertEqual(
|
|
str(alignment),
|
|
"""\
|
|
KI537979 9712654 ????????????????????????????????????????????????????????????
|
|
0 ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
|
|
CAG33136. 0 ????????????????????????????????????????????????????????????
|
|
|
|
KI537979 9712714 ????????????????????????????????????????????????????????????
|
|
60 ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
|
|
CAG33136. 60 ????????????????????????????????????????????????????????????
|
|
|
|
KI537979 9712774 ????????????????????????????????????????????????????????????
|
|
120 ||||||||||||------------------------------------------------
|
|
CAG33136. 120 ????????????------------------------------------------------
|
|
|
|
KI537979 9712834 ????????????????????????????????????????????????????????????
|
|
180 ------------------------------------------------------------
|
|
CAG33136. 132 ------------------------------------------------------------
|
|
|
|
KI537979 9712894 ????????????????????????????????????????????????????????????
|
|
240 ------------------------------------------------------------
|
|
CAG33136. 132 ------------------------------------------------------------
|
|
|
|
KI537979 9712954 ????????????????????????????????????????????????????????????
|
|
300 ------------------------------------------------------------
|
|
CAG33136. 132 ------------------------------------------------------------
|
|
|
|
KI537979 9713014 ????????????????????????????????????????????????????????????
|
|
360 ------------------------------------------------------------
|
|
CAG33136. 132 ------------------------------------------------------------
|
|
|
|
KI537979 9713074 ????????????????????????????????????????????????????????????
|
|
420 ------------------------------------------------------------
|
|
CAG33136. 132 ------------------------------------------------------------
|
|
|
|
KI537979 9713134 ????????????????????????????????????????????????????????????
|
|
480 ------------------------------------------------------------
|
|
CAG33136. 132 ------------------------------------------------------------
|
|
|
|
KI537979 9713194 ????????????????????????????????????????????????????????????
|
|
540 ------------------------------------------------------------
|
|
CAG33136. 132 ------------------------------------------------------------
|
|
|
|
KI537979 9713254 ????????????????????????????????????????????????????????????
|
|
600 ------------------------------------------------------------
|
|
CAG33136. 132 ------------------------------------------------------------
|
|
|
|
KI537979 9713314 ????????????????????????????????????????????????????????????
|
|
660 ------------------------------------------------------------
|
|
CAG33136. 132 ------------------------------------------------------------
|
|
|
|
KI537979 9713374 ????????????????????????????????????????????????????????????
|
|
720 ------------------------------------------------------------
|
|
CAG33136. 132 ------------------------------------------------------------
|
|
|
|
KI537979 9713434 ????????????????????????????????????????????????????????????
|
|
780 ------------------------------------------------------------
|
|
CAG33136. 132 ------------------------------------------------------------
|
|
|
|
KI537979 9713494 ????????????????????????????????????????????????????????????
|
|
840 ------------------------------------------------------------
|
|
CAG33136. 132 ------------------------------------------------------------
|
|
|
|
KI537979 9713554 ????????????????????????????????????????????????????????????
|
|
900 ------------------------------------------------------------
|
|
CAG33136. 132 ------------------------------------------------------------
|
|
|
|
KI537979 9713614 ????????????????????????????????????????????????????????????
|
|
960 ------------------------------------------------------------
|
|
CAG33136. 132 ------------------------------------------------------------
|
|
|
|
KI537979 9713674 ????????????????????????????????????????????????????????????
|
|
1020 ------------------------------------------------------------
|
|
CAG33136. 132 ------------------------------------------------------------
|
|
|
|
KI537979 9713734 ????????????????????????????????????????????????????????????
|
|
1080 ------------------------------------------------------------
|
|
CAG33136. 132 ------------------------------------------------------------
|
|
|
|
KI537979 9713794 ????????????????????????????????????????????????????????????
|
|
1140 ------------------------------------------------------------
|
|
CAG33136. 132 ------------------------------------------------------------
|
|
|
|
KI537979 9713854 ????????????????????????????????????????????????????????????
|
|
1200 ------------------------------------------------------------
|
|
CAG33136. 132 ------------------------------------------------------------
|
|
|
|
KI537979 9713914 ????????????????????????????????????????????????????????????
|
|
1260 ------------------------------------------------------------
|
|
CAG33136. 132 ------------------------------------------------------------
|
|
|
|
KI537979 9713974 ????????????????????????????????????????????????????????????
|
|
1320 ------------------------------------------------------------
|
|
CAG33136. 132 ------------------------------------------------------------
|
|
|
|
KI537979 9714034 ????????????????????????????????????????????????????????????
|
|
1380 ------------------------------------------------------------
|
|
CAG33136. 132 ------------------------------------------------------------
|
|
|
|
KI537979 9714094 ????????????????????????????????????????????????????????????
|
|
1440 ------------------------------------------------------------
|
|
CAG33136. 132 ------------------------------------------------------------
|
|
|
|
KI537979 9714154 ????????????????????????????????????????????????????????????
|
|
1500 ------------------------------------------------------------
|
|
CAG33136. 132 ------------------------------------------------------------
|
|
|
|
KI537979 9714214 ????????????????????????????????????????????????????????????
|
|
1560 ------------------------------------------------------------
|
|
CAG33136. 132 ------------------------------------------------------------
|
|
|
|
KI537979 9714274 ????????????????????????????????????????????????????????????
|
|
1620 ------------------------------------------------------------
|
|
CAG33136. 132 ------------------------------------------------------------
|
|
|
|
KI537979 9714334 ????????????????????????????????????????????????????????????
|
|
1680 ------------------------------------------------------------
|
|
CAG33136. 132 ------------------------------------------------------------
|
|
|
|
KI537979 9714394 ????????????????????????????????????????????????????????????
|
|
1740 ------------------------------------------------------------
|
|
CAG33136. 132 ------------------------------------------------------------
|
|
|
|
KI537979 9714454 ????????????????????????????????????????????????????????????
|
|
1800 ------------------------------------------------------------
|
|
CAG33136. 132 ------------------------------------------------------------
|
|
|
|
KI537979 9714514 ????????????????????????????????????????????????????????????
|
|
1860 ------------------------------------------------------------
|
|
CAG33136. 132 ------------------------------------------------------------
|
|
|
|
KI537979 9714574 ????????????????????????????????????????????????????????????
|
|
1920 ------------------------------------------------------------
|
|
CAG33136. 132 ------------------------------------------------------------
|
|
|
|
KI537979 9714634 ????????????????????????????????????????????????????????????
|
|
1980 ------------------------------------------------------------
|
|
CAG33136. 132 ------------------------------------------------------------
|
|
|
|
KI537979 9714694 ????????????????????????????????????????????????????????????
|
|
2040 ------------------------------------------------------------
|
|
CAG33136. 132 ------------------------------------------------------------
|
|
|
|
KI537979 9714754 ????????????????????????????????????????????????????????????
|
|
2100 ------------------------------------------------------------
|
|
CAG33136. 132 ------------------------------------------------------------
|
|
|
|
KI537979 9714814 ????????????????????????????????????????????????????????????
|
|
2160 ------------------------------------------------------------
|
|
CAG33136. 132 ------------------------------------------------------------
|
|
|
|
KI537979 9714874 ????????????????????????????????????????????????????????????
|
|
2220 ------------------------------------------------------------
|
|
CAG33136. 132 ------------------------------------------------------------
|
|
|
|
KI537979 9714934 ????????????????????????????????????????????????????????????
|
|
2280 ------------------------------------------------------------
|
|
CAG33136. 132 ------------------------------------------------------------
|
|
|
|
KI537979 9714994 ????????????????????????????????????????????????????????????
|
|
2340 ------------------------------------------------------------
|
|
CAG33136. 132 ------------------------------------------------------------
|
|
|
|
KI537979 9715054 ????????????????????????????????????????????????????????????
|
|
2400 ------------------------------------------------------------
|
|
CAG33136. 132 ------------------------------------------------------------
|
|
|
|
KI537979 9715114 ????????????????????????????????????????????????????????????
|
|
2460 ------------------------------------------------------------
|
|
CAG33136. 132 ------------------------------------------------------------
|
|
|
|
KI537979 9715174 ????????????????????????????????????????????????????????????
|
|
2520 ------------------------------------------------------------
|
|
CAG33136. 132 ------------------------------------------------------------
|
|
|
|
KI537979 9715234 ????????????????????????????????????????????????????????????
|
|
2580 ------------------------------------------------------------
|
|
CAG33136. 132 ------------------------------------------------------------
|
|
|
|
KI537979 9715294 ????????????????????????????????????????????????????????????
|
|
2640 ------------------------------------------------------------
|
|
CAG33136. 132 ------------------------------------------------------------
|
|
|
|
KI537979 9715354 ????????????????????????????????????????????????????????????
|
|
2700 ------------------------------------------------------------
|
|
CAG33136. 132 ------------------------------------------------------------
|
|
|
|
KI537979 9715414 ????????????????????????????????????????????????????????????
|
|
2760 ------------------------------------------------------------
|
|
CAG33136. 132 ------------------------------------------------------------
|
|
|
|
KI537979 9715474 ????????????????????????????????????????????????????????????
|
|
2820 ------------------------------------------------------------
|
|
CAG33136. 132 ------------------------------------------------------------
|
|
|
|
KI537979 9715534 ????????????????????????????????????????????????????????????
|
|
2880 ------------------------------------------------------------
|
|
CAG33136. 132 ------------------------------------------------------------
|
|
|
|
KI537979 9715594 ????????????????????????????????????????????????????????????
|
|
2940 ------------------------------------------------------------
|
|
CAG33136. 132 ------------------------------------------------------------
|
|
|
|
KI537979 9715654 ????????????????????????????????????????????????????????????
|
|
3000 ------------------------------------------------------------
|
|
CAG33136. 132 ------------------------------------------------------------
|
|
|
|
KI537979 9715714 ????????????????????????????????????????????????????????????
|
|
3060 ------------------------------------------------------------
|
|
CAG33136. 132 ------------------------------------------------------------
|
|
|
|
KI537979 9715774 ????????????????????????????????????????????????????????????
|
|
3120 ------------------------------------------------------------
|
|
CAG33136. 132 ------------------------------------------------------------
|
|
|
|
KI537979 9715834 ????????????????????????????????????????????????????????????
|
|
3180 ------------------------------------------------------------
|
|
CAG33136. 132 ------------------------------------------------------------
|
|
|
|
KI537979 9715894 ????????????????????????????????????????????????????????????
|
|
3240 -----------------------------------------------|||||||||||||
|
|
CAG33136. 132 -----------------------------------------------?????????????
|
|
|
|
KI537979 9715954 ????????????????????????????????????????????????????????????
|
|
3300 ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
|
|
CAG33136. 145 ????????????????????????????????????????????????????????????
|
|
|
|
KI537979 9716014 ????????????????????????????????????????????????????????????
|
|
3360 ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
|
|
CAG33136. 205 ????????????????????????????????????????????????????????????
|
|
|
|
KI537979 9716074 ????????????????????????????????????????????????????????????
|
|
3420 |||||||||||||||||||||||-------------------------------------
|
|
CAG33136. 265 ???????????????????????-------------------------------------
|
|
|
|
KI537979 9716134 ????????????????????????????????????????????????????????????
|
|
3480 ------------------------------------------------------------
|
|
CAG33136. 288 ------------------------------------------------------------
|
|
|
|
KI537979 9716194 ????????????????????????????????????????????????????????????
|
|
3540 ------------------------------------------------------------
|
|
CAG33136. 288 ------------------------------------------------------------
|
|
|
|
KI537979 9716254 ????????????????????????????????????????????????????????????
|
|
3600 ------------------------------------------------------------
|
|
CAG33136. 288 ------------------------------------------------------------
|
|
|
|
KI537979 9716314 ????????????????????????????????????????????????????????????
|
|
3660 ------------------------------------------------------------
|
|
CAG33136. 288 ------------------------------------------------------------
|
|
|
|
KI537979 9716374 ????????????????????????????????????????????????????????????
|
|
3720 ------------------------------------------------------------
|
|
CAG33136. 288 ------------------------------------------------------------
|
|
|
|
KI537979 9716434 ????????????????????????????????????????????????????????????
|
|
3780 -----------|||||||||||||||||||||||||||||||||||||||||||||||||
|
|
CAG33136. 288 -----------?????????????????????????????????????????????????
|
|
|
|
KI537979 9716494 ????????????????????????????????????????????????????????????
|
|
3840 ||||||||||||||||||||||||||||||||||||||----------------------
|
|
CAG33136. 337 ??????????????????????????????????????----------------------
|
|
|
|
KI537979 9716554 ????????????????????????????????????????????????????????????
|
|
3900 ------------------------------------------------------------
|
|
CAG33136. 375 ------------------------------------------------------------
|
|
|
|
KI537979 9716614 ????????????????????????????????????????????????????????????
|
|
3960 ------------------------------------------------------------
|
|
CAG33136. 375 ------------------------------------------------------------
|
|
|
|
KI537979 9716674 ????????????????????????????????????????????????????????????
|
|
4020 ------------------------------------------------------------
|
|
CAG33136. 375 ------------------------------------------------------------
|
|
|
|
KI537979 9716734 ????????????????????????????????????????????????????????????
|
|
4080 ------------------------------------------------------------
|
|
CAG33136. 375 ------------------------------------------------------------
|
|
|
|
KI537979 9716794 ????????????????????????????????????????????????????????????
|
|
4140 ------------------------------------------------------------
|
|
CAG33136. 375 ------------------------------------------------------------
|
|
|
|
KI537979 9716854 ????????????????????????????????????????????????????????????
|
|
4200 ------------------------------------------------------------
|
|
CAG33136. 375 ------------------------------------------------------------
|
|
|
|
KI537979 9716914 ????????????????????????????????????????????????????????????
|
|
4260 ------------------------------------------------------------
|
|
CAG33136. 375 ------------------------------------------------------------
|
|
|
|
KI537979 9716974 ????????????????????????????????????????????????????????????
|
|
4320 ------------------------------------------------------------
|
|
CAG33136. 375 ------------------------------------------------------------
|
|
|
|
KI537979 9717034 ????????????????????????????????????????????????????????????
|
|
4380 ------------------------------------------------------------
|
|
CAG33136. 375 ------------------------------------------------------------
|
|
|
|
KI537979 9717094 ????????????????????????????????????????????????????????????
|
|
4440 ------------------------------------------------------------
|
|
CAG33136. 375 ------------------------------------------------------------
|
|
|
|
KI537979 9717154 ????????????????????????????????????????????????????????????
|
|
4500 ------------------------------------------------------------
|
|
CAG33136. 375 ------------------------------------------------------------
|
|
|
|
KI537979 9717214 ????????????????????????????????????????????????????????????
|
|
4560 ------------------------------------------------------------
|
|
CAG33136. 375 ------------------------------------------------------------
|
|
|
|
KI537979 9717274 ????????????????????????????????????????????????????????????
|
|
4620 ------------------------------------------------------------
|
|
CAG33136. 375 ------------------------------------------------------------
|
|
|
|
KI537979 9717334 ????????????????????????????????????????????????????????????
|
|
4680 ------------------------------------------------------------
|
|
CAG33136. 375 ------------------------------------------------------------
|
|
|
|
KI537979 9717394 ????????????????????????????????????????????????????????????
|
|
4740 ------------------------------------------------------------
|
|
CAG33136. 375 ------------------------------------------------------------
|
|
|
|
KI537979 9717454 ????????????????????????????????????????????????????????????
|
|
4800 ------------------------------------------------------------
|
|
CAG33136. 375 ------------------------------------------------------------
|
|
|
|
KI537979 9717514 ????????????????????????????????????????????????????????????
|
|
4860 ------------------------------------------------------------
|
|
CAG33136. 375 ------------------------------------------------------------
|
|
|
|
KI537979 9717574 ????????????????????????????????????????????????????????????
|
|
4920 ------------------------------------------------------------
|
|
CAG33136. 375 ------------------------------------------------------------
|
|
|
|
KI537979 9717634 ????????????????????????????????????????????????????????????
|
|
4980 ------------------------------------------------------------
|
|
CAG33136. 375 ------------------------------------------------------------
|
|
|
|
KI537979 9717694 ????????????????????????????????????????????????????????????
|
|
5040 ------------------------------------------------------------
|
|
CAG33136. 375 ------------------------------------------------------------
|
|
|
|
KI537979 9717754 ????????????????????????????????????????????????????????????
|
|
5100 ------------------------------------------------------------
|
|
CAG33136. 375 ------------------------------------------------------------
|
|
|
|
KI537979 9717814 ????????????????????????????????????????????????????????????
|
|
5160 ------------------------------------------------------------
|
|
CAG33136. 375 ------------------------------------------------------------
|
|
|
|
KI537979 9717874 ????????????????????????????????????????????????????????????
|
|
5220 ------------------------------------------------------------
|
|
CAG33136. 375 ------------------------------------------------------------
|
|
|
|
KI537979 9717934 ????????????????????????????????????????????????????????????
|
|
5280 ------------------------------------------------------------
|
|
CAG33136. 375 ------------------------------------------------------------
|
|
|
|
KI537979 9717994 ????????????????????????????????????????????????????????????
|
|
5340 ------------------------------------------------------------
|
|
CAG33136. 375 ------------------------------------------------------------
|
|
|
|
KI537979 9718054 ????????????????????????????????????????????????????????????
|
|
5400 ------------------------------------------------------------
|
|
CAG33136. 375 ------------------------------------------------------------
|
|
|
|
KI537979 9718114 ????????????????????????????????????????????????????????????
|
|
5460 ------------------------------------------------------------
|
|
CAG33136. 375 ------------------------------------------------------------
|
|
|
|
KI537979 9718174 ????????????????????????????????????????????????????????????
|
|
5520 ------------------------------------------------------------
|
|
CAG33136. 375 ------------------------------------------------------------
|
|
|
|
KI537979 9718234 ????????????????????????????????????????????????????????????
|
|
5580 ------------------------------------------------------------
|
|
CAG33136. 375 ------------------------------------------------------------
|
|
|
|
KI537979 9718294 ????????????????????????????????????????????????????????????
|
|
5640 ------------------------------------------------------------
|
|
CAG33136. 375 ------------------------------------------------------------
|
|
|
|
KI537979 9718354 ????????????????????????????????????????????????????????????
|
|
5700 --------------------||||||||||||||||||||||||||||||||||||||||
|
|
CAG33136. 375 --------------------????????????????????????????????????????
|
|
|
|
KI537979 9718414 ????????????????????????????????????????????????????????????
|
|
5760 ||||||||----------------------------------------------------
|
|
CAG33136. 415 ????????----------------------------------------------------
|
|
|
|
KI537979 9718474 ????????????????????????????????????????????????????????????
|
|
5820 ------------------------------------------------------------
|
|
CAG33136. 423 ------------------------------------------------------------
|
|
|
|
KI537979 9718534 ????????????????????????????????????????????????????????????
|
|
5880 ------------------------------------------------------------
|
|
CAG33136. 423 ------------------------------------------------------------
|
|
|
|
KI537979 9718594 ????????????????????????????????????????????????????????????
|
|
5940 ------------------------------------------------------------
|
|
CAG33136. 423 ------------------------------------------------------------
|
|
|
|
KI537979 9718654 ????????????????????????????????????????????????????????????
|
|
6000 ------------------------------------------------------------
|
|
CAG33136. 423 ------------------------------------------------------------
|
|
|
|
KI537979 9718714 ????????????????????????????????????????????????????????????
|
|
6060 ------------------------------------------------------------
|
|
CAG33136. 423 ------------------------------------------------------------
|
|
|
|
KI537979 9718774 ????????????????????????????????????????????????????????????
|
|
6120 ------------------------------------------------------------
|
|
CAG33136. 423 ------------------------------------------------------------
|
|
|
|
KI537979 9718834 ????????????????????????????????????????????????????????????
|
|
6180 ------------------------------------------------------------
|
|
CAG33136. 423 ------------------------------------------------------------
|
|
|
|
KI537979 9718894 ????????????????????????????????????????????????????????????
|
|
6240 ------------------------------------------------------------
|
|
CAG33136. 423 ------------------------------------------------------------
|
|
|
|
KI537979 9718954 ????????????????????????????????????????????????????????????
|
|
6300 ------------------------------------------------------------
|
|
CAG33136. 423 ------------------------------------------------------------
|
|
|
|
KI537979 9719014 ????????????????????????????????????????????????????????????
|
|
6360 ------------------------------------------------------------
|
|
CAG33136. 423 ------------------------------------------------------------
|
|
|
|
KI537979 9719074 ????????????????????????????????????????????????????????????
|
|
6420 ------------------------------------------------------------
|
|
CAG33136. 423 ------------------------------------------------------------
|
|
|
|
KI537979 9719134 ????????????????????????????????????????????????????????????
|
|
6480 ------------------------------------------------------------
|
|
CAG33136. 423 ------------------------------------------------------------
|
|
|
|
KI537979 9719194 ????????????????????????????????????????????????????????????
|
|
6540 ------------------------------------------------------------
|
|
CAG33136. 423 ------------------------------------------------------------
|
|
|
|
KI537979 9719254 ????????????????????????????????????????????????????????????
|
|
6600 ------------------------------------------------------------
|
|
CAG33136. 423 ------------------------------------------------------------
|
|
|
|
KI537979 9719314 ????????????????????????????????????????????????????????????
|
|
6660 ------------------------------------------------------------
|
|
CAG33136. 423 ------------------------------------------------------------
|
|
|
|
KI537979 9719374 ????????????????????????????????????????????????????????????
|
|
6720 ------------------------------------------------------------
|
|
CAG33136. 423 ------------------------------------------------------------
|
|
|
|
KI537979 9719434 ????????????????????????????????????????????????????????????
|
|
6780 ------------------------------------------------------------
|
|
CAG33136. 423 ------------------------------------------------------------
|
|
|
|
KI537979 9719494 ????????????????????????????????????????????????????????????
|
|
6840 ------------------------------------------------------------
|
|
CAG33136. 423 ------------------------------------------------------------
|
|
|
|
KI537979 9719554 ????????????????????????????????????????????????????????????
|
|
6900 ------------------------------------------------------------
|
|
CAG33136. 423 ------------------------------------------------------------
|
|
|
|
KI537979 9719614 ????????????????????????????????????????????????????????????
|
|
6960 ------------------------------------------------------------
|
|
CAG33136. 423 ------------------------------------------------------------
|
|
|
|
KI537979 9719674 ????????????????????????????????????????????????????????????
|
|
7020 ------------------------------------------------------------
|
|
CAG33136. 423 ------------------------------------------------------------
|
|
|
|
KI537979 9719734 ????????????????????????????????????????????????????????????
|
|
7080 ------------------------------------------------------------
|
|
CAG33136. 423 ------------------------------------------------------------
|
|
|
|
KI537979 9719794 ????????????????????????????????????????????????????????????
|
|
7140 ------------------------------------------------------------
|
|
CAG33136. 423 ------------------------------------------------------------
|
|
|
|
KI537979 9719854 ????????????????????????????????????????????????????????????
|
|
7200 ------------------------------------------------------------
|
|
CAG33136. 423 ------------------------------------------------------------
|
|
|
|
KI537979 9719914 ????????????????????????????????????????????????????????????
|
|
7260 ------------------------------------------------------------
|
|
CAG33136. 423 ------------------------------------------------------------
|
|
|
|
KI537979 9719974 ????????????????????????????????????????????????????????????
|
|
7320 ------------------------------------------------------------
|
|
CAG33136. 423 ------------------------------------------------------------
|
|
|
|
KI537979 9720034 ????????????????????????????????????????????????????????????
|
|
7380 ------------------------------------------------------------
|
|
CAG33136. 423 ------------------------------------------------------------
|
|
|
|
KI537979 9720094 ????????????????????????????????????????????????????????????
|
|
7440 ------------------------------------------------------------
|
|
CAG33136. 423 ------------------------------------------------------------
|
|
|
|
KI537979 9720154 ????????????????????????????????????????????????????????????
|
|
7500 ------------------------------------------------------------
|
|
CAG33136. 423 ------------------------------------------------------------
|
|
|
|
KI537979 9720214 ????????????????????????????????????????????????????????????
|
|
7560 ------------------------------------------------------------
|
|
CAG33136. 423 ------------------------------------------------------------
|
|
|
|
KI537979 9720274 ????????????????????????????????????????????????????????????
|
|
7620 ------------------------------------------------------------
|
|
CAG33136. 423 ------------------------------------------------------------
|
|
|
|
KI537979 9720334 ????????????????????????????????????????????????????????????
|
|
7680 ------------------------------------------------------------
|
|
CAG33136. 423 ------------------------------------------------------------
|
|
|
|
KI537979 9720394 ????????????????????????????????????????????????????????????
|
|
7740 ------------------------------------------------------------
|
|
CAG33136. 423 ------------------------------------------------------------
|
|
|
|
KI537979 9720454 ????????????????????????????????????????????????????????????
|
|
7800 ------------------------------------------------------------
|
|
CAG33136. 423 ------------------------------------------------------------
|
|
|
|
KI537979 9720514 ????????????????????????????????????????????????????????????
|
|
7860 ------------------------------------------------------------
|
|
CAG33136. 423 ------------------------------------------------------------
|
|
|
|
KI537979 9720574 ????????????????????????????????????????????????????????????
|
|
7920 ------------------------------------------------------------
|
|
CAG33136. 423 ------------------------------------------------------------
|
|
|
|
KI537979 9720634 ????????????????????????????????????????????????????????????
|
|
7980 ------------------------------------------------------------
|
|
CAG33136. 423 ------------------------------------------------------------
|
|
|
|
KI537979 9720694 ????????????????????????????????????????????????????????????
|
|
8040 ------------------------------------------------------------
|
|
CAG33136. 423 ------------------------------------------------------------
|
|
|
|
KI537979 9720754 ????????????????????????????????????????????????????????????
|
|
8100 ------------------------------------------------------------
|
|
CAG33136. 423 ------------------------------------------------------------
|
|
|
|
KI537979 9720814 ????????????????????????????????????????????????????????????
|
|
8160 ------------------------------------------------------------
|
|
CAG33136. 423 ------------------------------------------------------------
|
|
|
|
KI537979 9720874 ????????????????????????????????????????????????????????????
|
|
8220 ------------------------------------------------------------
|
|
CAG33136. 423 ------------------------------------------------------------
|
|
|
|
KI537979 9720934 ????????????????????????????????????????????????????????????
|
|
8280 ------------------------------------------------------------
|
|
CAG33136. 423 ------------------------------------------------------------
|
|
|
|
KI537979 9720994 ????????????????????????????????????????????????????????????
|
|
8340 ------------------------------------------------------------
|
|
CAG33136. 423 ------------------------------------------------------------
|
|
|
|
KI537979 9721054 ????????????????????????????????????????????????????????????
|
|
8400 ------------------------------------------------------------
|
|
CAG33136. 423 ------------------------------------------------------------
|
|
|
|
KI537979 9721114 ????????????????????????????????????????????????????????????
|
|
8460 ------------------------------------------------------------
|
|
CAG33136. 423 ------------------------------------------------------------
|
|
|
|
KI537979 9721174 ????????????????????????????????????????????????????????????
|
|
8520 ------------------------------------------------------------
|
|
CAG33136. 423 ------------------------------------------------------------
|
|
|
|
KI537979 9721234 ????????????????????????????????????????????????????????????
|
|
8580 ------------------------------------------------------------
|
|
CAG33136. 423 ------------------------------------------------------------
|
|
|
|
KI537979 9721294 ????????????????????????????????????????????????????????????
|
|
8640 ------------------------------------------------------------
|
|
CAG33136. 423 ------------------------------------------------------------
|
|
|
|
KI537979 9721354 ????????????????????????????????????????????????????????????
|
|
8700 ------------------------------------------------------------
|
|
CAG33136. 423 ------------------------------------------------------------
|
|
|
|
KI537979 9721414 ????????????????????????????????????????????????????????????
|
|
8760 ------------------------------------------------------------
|
|
CAG33136. 423 ------------------------------------------------------------
|
|
|
|
KI537979 9721474 ????????????????????????????????????????????????????????????
|
|
8820 ------------------------------------------------------------
|
|
CAG33136. 423 ------------------------------------------------------------
|
|
|
|
KI537979 9721534 ????????????????????????????????????????????????????????????
|
|
8880 ------------------------------------------------------------
|
|
CAG33136. 423 ------------------------------------------------------------
|
|
|
|
KI537979 9721594 ????????????????????????????????????????????????????????????
|
|
8940 ------------------------------------------------------------
|
|
CAG33136. 423 ------------------------------------------------------------
|
|
|
|
KI537979 9721654 ????????????????????????????????????????????????????????????
|
|
9000 ------------------------------------------------------------
|
|
CAG33136. 423 ------------------------------------------------------------
|
|
|
|
KI537979 9721714 ????????????????????????????????????????????????????????????
|
|
9060 ------------------------------------------------------------
|
|
CAG33136. 423 ------------------------------------------------------------
|
|
|
|
KI537979 9721774 ????????????????????????????????????????????????????????????
|
|
9120 ------------------------------------------------------------
|
|
CAG33136. 423 ------------------------------------------------------------
|
|
|
|
KI537979 9721834 ????????????????????????????????????????????????????????????
|
|
9180 ------------------------------------------------------------
|
|
CAG33136. 423 ------------------------------------------------------------
|
|
|
|
KI537979 9721894 ????????????????????????????????????????????????????????????
|
|
9240 ------------------------------------------------------------
|
|
CAG33136. 423 ------------------------------------------------------------
|
|
|
|
KI537979 9721954 ????????????????????????????????????????????????????????????
|
|
9300 ------------------------------------------------------------
|
|
CAG33136. 423 ------------------------------------------------------------
|
|
|
|
KI537979 9722014 ????????????????????????????????????????????????????????????
|
|
9360 ------------------------------------------------------------
|
|
CAG33136. 423 ------------------------------------------------------------
|
|
|
|
KI537979 9722074 ????????????????????????????????????????????????????????????
|
|
9420 ------------------------------------------------------------
|
|
CAG33136. 423 ------------------------------------------------------------
|
|
|
|
KI537979 9722134 ????????????????????????????????????????????????????????????
|
|
9480 ------------------------------------------------------------
|
|
CAG33136. 423 ------------------------------------------------------------
|
|
|
|
KI537979 9722194 ????????????????????????????????????????????????????????????
|
|
9540 ------------------------------------------------------------
|
|
CAG33136. 423 ------------------------------------------------------------
|
|
|
|
KI537979 9722254 ????????????????????????????????????????????????????????????
|
|
9600 ------------------------------------------------------------
|
|
CAG33136. 423 ------------------------------------------------------------
|
|
|
|
KI537979 9722314 ????????????????????????????????????????????????????????????
|
|
9660 ------------------------------------------------------------
|
|
CAG33136. 423 ------------------------------------------------------------
|
|
|
|
KI537979 9722374 ????????????????????????????????????????????????????????????
|
|
9720 ------------------------------------------------------------
|
|
CAG33136. 423 ------------------------------------------------------------
|
|
|
|
KI537979 9722434 ????????????????????????????????????????????????????????????
|
|
9780 ------------------------------------------------------------
|
|
CAG33136. 423 ------------------------------------------------------------
|
|
|
|
KI537979 9722494 ????????????????????????????????????????????????????????????
|
|
9840 ------------------------------------------------------------
|
|
CAG33136. 423 ------------------------------------------------------------
|
|
|
|
KI537979 9722554 ????????????????????????????????????????????????????????????
|
|
9900 ------------------------------------------------------------
|
|
CAG33136. 423 ------------------------------------------------------------
|
|
|
|
KI537979 9722614 ????????????????????????????????????????????????????????????
|
|
9960 ------------------------------------------------------------
|
|
CAG33136. 423 ------------------------------------------------------------
|
|
|
|
KI537979 9722674 ????????????????????????????????????????????????????????????
|
|
10020 ------------------------------------------------------------
|
|
CAG33136. 423 ------------------------------------------------------------
|
|
|
|
KI537979 9722734 ????????????????????????????????????????????????????????????
|
|
10080 ------------------------------------------------------------
|
|
CAG33136. 423 ------------------------------------------------------------
|
|
|
|
KI537979 9722794 ????????????????????????????????????????????????????????????
|
|
10140 ------------------------------------------------------------
|
|
CAG33136. 423 ------------------------------------------------------------
|
|
|
|
KI537979 9722854 ????????????????????????????????????????????????????????????
|
|
10200 ------------------------------------------------------------
|
|
CAG33136. 423 ------------------------------------------------------------
|
|
|
|
KI537979 9722914 ????????????????????????????????????????????????????????????
|
|
10260 ------------------------------------------------------------
|
|
CAG33136. 423 ------------------------------------------------------------
|
|
|
|
KI537979 9722974 ????????????????????????????????????????????????????????????
|
|
10320 ------------------------------------------------------------
|
|
CAG33136. 423 ------------------------------------------------------------
|
|
|
|
KI537979 9723034 ????????????????????????????????????????????????????????????
|
|
10380 ------------------------------------------------------------
|
|
CAG33136. 423 ------------------------------------------------------------
|
|
|
|
KI537979 9723094 ????????????????????????????????????????????????????????????
|
|
10440 ------------------------------------------------------------
|
|
CAG33136. 423 ------------------------------------------------------------
|
|
|
|
KI537979 9723154 ????????????????????????????????????????????????????????????
|
|
10500 ------------------------------------------------------------
|
|
CAG33136. 423 ------------------------------------------------------------
|
|
|
|
KI537979 9723214 ????????????????????????????????????????????????????????????
|
|
10560 ------------------------------------------------------------
|
|
CAG33136. 423 ------------------------------------------------------------
|
|
|
|
KI537979 9723274 ????????????????????????????????????????????????????????????
|
|
10620 ------------------------------------------------------------
|
|
CAG33136. 423 ------------------------------------------------------------
|
|
|
|
KI537979 9723334 ????????????????????????????????????????????????????????????
|
|
10680 ------------------------------------------------------------
|
|
CAG33136. 423 ------------------------------------------------------------
|
|
|
|
KI537979 9723394 ????????????????????????????????????????????????????????????
|
|
10740 ------------------------------------------------------------
|
|
CAG33136. 423 ------------------------------------------------------------
|
|
|
|
KI537979 9723454 ????????????????????????????????????????????????????????????
|
|
10800 ------------------------------------------------------------
|
|
CAG33136. 423 ------------------------------------------------------------
|
|
|
|
KI537979 9723514 ????????????????????????????????????????????????????????????
|
|
10860 ------------------------------------------------------------
|
|
CAG33136. 423 ------------------------------------------------------------
|
|
|
|
KI537979 9723574 ????????????????????????????????????????????????????????????
|
|
10920 ------------------------------------------------------------
|
|
CAG33136. 423 ------------------------------------------------------------
|
|
|
|
KI537979 9723634 ????????????????????????????????????????????????????????????
|
|
10980 ------------------------------------------------------------
|
|
CAG33136. 423 ------------------------------------------------------------
|
|
|
|
KI537979 9723694 ????????????????????????????????????????????????????????????
|
|
11040 ------------------------------------------------------------
|
|
CAG33136. 423 ------------------------------------------------------------
|
|
|
|
KI537979 9723754 ????????????????????????????????????????????????????????????
|
|
11100 ------------------------------------------------------------
|
|
CAG33136. 423 ------------------------------------------------------------
|
|
|
|
KI537979 9723814 ????????????????????????????????????????????????????????????
|
|
11160 ------------------------------------------------------------
|
|
CAG33136. 423 ------------------------------------------------------------
|
|
|
|
KI537979 9723874 ????????????????????????????????????????????????????????????
|
|
11220 ------------------------------------------------------------
|
|
CAG33136. 423 ------------------------------------------------------------
|
|
|
|
KI537979 9723934 ????????????????????????????????????????????????????????????
|
|
11280 ------------------------------------------------------------
|
|
CAG33136. 423 ------------------------------------------------------------
|
|
|
|
KI537979 9723994 ????????????????????????????????????????????????????????????
|
|
11340 ------------------------------------------------------------
|
|
CAG33136. 423 ------------------------------------------------------------
|
|
|
|
KI537979 9724054 ????????????????????????????????????????????????????????????
|
|
11400 ------------------------------------------------------------
|
|
CAG33136. 423 ------------------------------------------------------------
|
|
|
|
KI537979 9724114 ????????????????????????????????????????????????????????????
|
|
11460 ------------------------------------------------------------
|
|
CAG33136. 423 ------------------------------------------------------------
|
|
|
|
KI537979 9724174 ????????????????????????????????????????????????????????????
|
|
11520 ------------------------------------------------------------
|
|
CAG33136. 423 ------------------------------------------------------------
|
|
|
|
KI537979 9724234 ????????????????????????????????????????????????????????????
|
|
11580 ------------------------------------------------------------
|
|
CAG33136. 423 ------------------------------------------------------------
|
|
|
|
KI537979 9724294 ????????????????????????????????????????????????????????????
|
|
11640 ------------------------------------------------------------
|
|
CAG33136. 423 ------------------------------------------------------------
|
|
|
|
KI537979 9724354 ????????????????????????????????????????????????????????????
|
|
11700 ------------------------------------------------------------
|
|
CAG33136. 423 ------------------------------------------------------------
|
|
|
|
KI537979 9724414 ????????????????????????????????????????????????????????????
|
|
11760 ------------------------------------------------------------
|
|
CAG33136. 423 ------------------------------------------------------------
|
|
|
|
KI537979 9724474 ????????????????????????????????????????????????????????????
|
|
11820 ------------------------------------------------------------
|
|
CAG33136. 423 ------------------------------------------------------------
|
|
|
|
KI537979 9724534 ????????????????????????????????????????????????????????????
|
|
11880 ------------------------------------------------------------
|
|
CAG33136. 423 ------------------------------------------------------------
|
|
|
|
KI537979 9724594 ????????????????????????????????????????????????????????????
|
|
11940 ------------------------------------------------------------
|
|
CAG33136. 423 ------------------------------------------------------------
|
|
|
|
KI537979 9724654 ????????????????????????????????????????????????????????????
|
|
12000 ------------------------------------------------------------
|
|
CAG33136. 423 ------------------------------------------------------------
|
|
|
|
KI537979 9724714 ????????????????????????????????????????????????????????????
|
|
12060 ------------------------------------------------------------
|
|
CAG33136. 423 ------------------------------------------------------------
|
|
|
|
KI537979 9724774 ????????????????????????????????????????????????????????????
|
|
12120 ------------------------------------------------------------
|
|
CAG33136. 423 ------------------------------------------------------------
|
|
|
|
KI537979 9724834 ????????????????????????????????????????????????????????????
|
|
12180 ------------------------------------------------------------
|
|
CAG33136. 423 ------------------------------------------------------------
|
|
|
|
KI537979 9724894 ????????????????????????????????????????????????????????????
|
|
12240 ------------------------------------------------------------
|
|
CAG33136. 423 ------------------------------------------------------------
|
|
|
|
KI537979 9724954 ????????????????????????????????????????????????????????????
|
|
12300 ------------------------------------------------------------
|
|
CAG33136. 423 ------------------------------------------------------------
|
|
|
|
KI537979 9725014 ????????????????????????????????????????????????????????????
|
|
12360 ------------------------------------------------------------
|
|
CAG33136. 423 ------------------------------------------------------------
|
|
|
|
KI537979 9725074 ????????????????????????????????????????????????????????????
|
|
12420 ------------------------------------------------------------
|
|
CAG33136. 423 ------------------------------------------------------------
|
|
|
|
KI537979 9725134 ????????????????????????????????????????????????????????????
|
|
12480 ------------------------------------------------------------
|
|
CAG33136. 423 ------------------------------------------------------------
|
|
|
|
KI537979 9725194 ????????????????????????????????????????????????????????????
|
|
12540 ------------------------------------------------------------
|
|
CAG33136. 423 ------------------------------------------------------------
|
|
|
|
KI537979 9725254 ????????????????????????????????????????????????????????????
|
|
12600 ------------------------------------------------------------
|
|
CAG33136. 423 ------------------------------------------------------------
|
|
|
|
KI537979 9725314 ????????????????????????????????????????????????????????????
|
|
12660 ------------------------------------------------------------
|
|
CAG33136. 423 ------------------------------------------------------------
|
|
|
|
KI537979 9725374 ????????????????????????????????????????????????????????????
|
|
12720 ------------------------------------------------------------
|
|
CAG33136. 423 ------------------------------------------------------------
|
|
|
|
KI537979 9725434 ????????????????????????????????????????????????????????????
|
|
12780 ------------------------------------------------------------
|
|
CAG33136. 423 ------------------------------------------------------------
|
|
|
|
KI537979 9725494 ????????????????????????????????????????????????????????????
|
|
12840 ------------------------------------------------------------
|
|
CAG33136. 423 ------------------------------------------------------------
|
|
|
|
KI537979 9725554 ????????????????????????????????????????????????????????????
|
|
12900 ------------------------------------------------------------
|
|
CAG33136. 423 ------------------------------------------------------------
|
|
|
|
KI537979 9725614 ????????????????????????????????????????????????????????????
|
|
12960 ------------------------------------------------------------
|
|
CAG33136. 423 ------------------------------------------------------------
|
|
|
|
KI537979 9725674 ????????????????????????????????????????????????????????????
|
|
13020 ------------------------------------------------------------
|
|
CAG33136. 423 ------------------------------------------------------------
|
|
|
|
KI537979 9725734 ????????????????????????????????????????????????????????????
|
|
13080 ------------------------------------------------------------
|
|
CAG33136. 423 ------------------------------------------------------------
|
|
|
|
KI537979 9725794 ????????????????????????????????????????????????????????????
|
|
13140 ------------------------------------------------------------
|
|
CAG33136. 423 ------------------------------------------------------------
|
|
|
|
KI537979 9725854 ????????????????????????????????????????????????????????????
|
|
13200 ------------------------------------------------------------
|
|
CAG33136. 423 ------------------------------------------------------------
|
|
|
|
KI537979 9725914 ????????????????????????????????????????????????????????????
|
|
13260 ------------------------------------------------------------
|
|
CAG33136. 423 ------------------------------------------------------------
|
|
|
|
KI537979 9725974 ????????????????????????????????????????????????????????????
|
|
13320 ------------------------------------------------------------
|
|
CAG33136. 423 ------------------------------------------------------------
|
|
|
|
KI537979 9726034 ????????????????????????????????????????????????????????????
|
|
13380 ------------------------------------------------------------
|
|
CAG33136. 423 ------------------------------------------------------------
|
|
|
|
KI537979 9726094 ????????????????????????????????????????????????????????????
|
|
13440 ------------------------------------------------------------
|
|
CAG33136. 423 ------------------------------------------------------------
|
|
|
|
KI537979 9726154 ????????????????????????????????????????????????????????????
|
|
13500 ------------------------------------------------------------
|
|
CAG33136. 423 ------------------------------------------------------------
|
|
|
|
KI537979 9726214 ????????????????????????????????????????????????????????????
|
|
13560 ------------------------------------------------------------
|
|
CAG33136. 423 ------------------------------------------------------------
|
|
|
|
KI537979 9726274 ????????????????????????????????????????????????????????????
|
|
13620 ------------------------------------------------------------
|
|
CAG33136. 423 ------------------------------------------------------------
|
|
|
|
KI537979 9726334 ????????????????????????????????????????????????????????????
|
|
13680 ------------------------------------------------------------
|
|
CAG33136. 423 ------------------------------------------------------------
|
|
|
|
KI537979 9726394 ????????????????????????????????????????????????????????????
|
|
13740 ------------------------------------------------------------
|
|
CAG33136. 423 ------------------------------------------------------------
|
|
|
|
KI537979 9726454 ????????????????????????????????????????????????????????????
|
|
13800 ------------------------------------------------------------
|
|
CAG33136. 423 ------------------------------------------------------------
|
|
|
|
KI537979 9726514 ????????????????????????????????????????????????????????????
|
|
13860 ------------------------------------------------------------
|
|
CAG33136. 423 ------------------------------------------------------------
|
|
|
|
KI537979 9726574 ????????????????????????????????????????????????????????????
|
|
13920 ------------------------------------------------------------
|
|
CAG33136. 423 ------------------------------------------------------------
|
|
|
|
KI537979 9726634 ????????????????????????????????????????????????????????????
|
|
13980 ------------------------------------------------------------
|
|
CAG33136. 423 ------------------------------------------------------------
|
|
|
|
KI537979 9726694 ????????????????????????????????????????????????????????????
|
|
14040 ------------------------------------------------------------
|
|
CAG33136. 423 ------------------------------------------------------------
|
|
|
|
KI537979 9726754 ????????????????????????????????????????????????????????????
|
|
14100 ------------------------------------------------------------
|
|
CAG33136. 423 ------------------------------------------------------------
|
|
|
|
KI537979 9726814 ????????????????????????????????????????????????????????????
|
|
14160 ------------------------------------------------------------
|
|
CAG33136. 423 ------------------------------------------------------------
|
|
|
|
KI537979 9726874 ????????????????????????????????????????????????????????????
|
|
14220 ------------------------------------------------------------
|
|
CAG33136. 423 ------------------------------------------------------------
|
|
|
|
KI537979 9726934 ????????????????????????????????????????????????????????????
|
|
14280 ------------------------------------------------------------
|
|
CAG33136. 423 ------------------------------------------------------------
|
|
|
|
KI537979 9726994 ????????????????????????????????????????????????????????????
|
|
14340 ------------------------------------------------------------
|
|
CAG33136. 423 ------------------------------------------------------------
|
|
|
|
KI537979 9727054 ????????????????????????????????????????????????????????????
|
|
14400 ------------------------------------------------------------
|
|
CAG33136. 423 ------------------------------------------------------------
|
|
|
|
KI537979 9727114 ????????????????????????????????????????????????????????????
|
|
14460 ------------------------------------------------------------
|
|
CAG33136. 423 ------------------------------------------------------------
|
|
|
|
KI537979 9727174 ????????????????????????????????????????????????????????????
|
|
14520 ------------------------------------------------------------
|
|
CAG33136. 423 ------------------------------------------------------------
|
|
|
|
KI537979 9727234 ????????????????????????????????????????????????????????????
|
|
14580 ------------------------------------------------------------
|
|
CAG33136. 423 ------------------------------------------------------------
|
|
|
|
KI537979 9727294 ????????????????????????????????????????????????????????????
|
|
14640 ------------------------------------------------------------
|
|
CAG33136. 423 ------------------------------------------------------------
|
|
|
|
KI537979 9727354 ????????????????????????????????????????????????????????????
|
|
14700 ------------------------------------------------------------
|
|
CAG33136. 423 ------------------------------------------------------------
|
|
|
|
KI537979 9727414 ????????????????????????????????????????????????????????????
|
|
14760 ------------------------------------------------------------
|
|
CAG33136. 423 ------------------------------------------------------------
|
|
|
|
KI537979 9727474 ????????????????????????????????????????????????????????????
|
|
14820 ------------------------------------------------------------
|
|
CAG33136. 423 ------------------------------------------------------------
|
|
|
|
KI537979 9727534 ????????????????????????????????????????????????????????????
|
|
14880 ------------------------------------------------------------
|
|
CAG33136. 423 ------------------------------------------------------------
|
|
|
|
KI537979 9727594 ????????????????????????????????????????????????????????????
|
|
14940 ------------------------------------------------------------
|
|
CAG33136. 423 ------------------------------------------------------------
|
|
|
|
KI537979 9727654 ????????????????????????????????????????????????????????????
|
|
15000 ------------------------------------------------------------
|
|
CAG33136. 423 ------------------------------------------------------------
|
|
|
|
KI537979 9727714 ????????????????????????????????????????????????????????????
|
|
15060 ------------------------------------------------------------
|
|
CAG33136. 423 ------------------------------------------------------------
|
|
|
|
KI537979 9727774 ????????????????????????????????????????????????????????????
|
|
15120 ------------------------------------------------------------
|
|
CAG33136. 423 ------------------------------------------------------------
|
|
|
|
KI537979 9727834 ????????????????????????????????????????????????????????????
|
|
15180 ------------------------------------------------------------
|
|
CAG33136. 423 ------------------------------------------------------------
|
|
|
|
KI537979 9727894 ????????????????????????????????????????????????????????????
|
|
15240 ------------------------------------------------------------
|
|
CAG33136. 423 ------------------------------------------------------------
|
|
|
|
KI537979 9727954 ????????????????????????????????????????????????????????????
|
|
15300 ------------------------------------------------------------
|
|
CAG33136. 423 ------------------------------------------------------------
|
|
|
|
KI537979 9728014 ????????????????????????????????????????????????????????????
|
|
15360 ------------------------------------------------------------
|
|
CAG33136. 423 ------------------------------------------------------------
|
|
|
|
KI537979 9728074 ????????????????????????????????????????????????????????????
|
|
15420 ------------------------------------------------------------
|
|
CAG33136. 423 ------------------------------------------------------------
|
|
|
|
KI537979 9728134 ????????????????????????????????????????????????????????????
|
|
15480 ------------------------------------------------------------
|
|
CAG33136. 423 ------------------------------------------------------------
|
|
|
|
KI537979 9728194 ????????????????????????????????????????????????????????????
|
|
15540 ------------------------------------------------------------
|
|
CAG33136. 423 ------------------------------------------------------------
|
|
|
|
KI537979 9728254 ????????????????????????????????????????????????????????????
|
|
15600 ------------------------------------------------------------
|
|
CAG33136. 423 ------------------------------------------------------------
|
|
|
|
KI537979 9728314 ????????????????????????????????????????????????????????????
|
|
15660 ------------------------------------------------------------
|
|
CAG33136. 423 ------------------------------------------------------------
|
|
|
|
KI537979 9728374 ????????????????????????????????????????????????????????????
|
|
15720 ------------------------------------------------------------
|
|
CAG33136. 423 ------------------------------------------------------------
|
|
|
|
KI537979 9728434 ????????????????????????????????????????????????????????????
|
|
15780 ------------------------------------------------------------
|
|
CAG33136. 423 ------------------------------------------------------------
|
|
|
|
KI537979 9728494 ????????????????????????????????????????????????????????????
|
|
15840 ------------------------------------------------------------
|
|
CAG33136. 423 ------------------------------------------------------------
|
|
|
|
KI537979 9728554 ????????????????????????????????????????????????????????????
|
|
15900 ------------------------------------------------------------
|
|
CAG33136. 423 ------------------------------------------------------------
|
|
|
|
KI537979 9728614 ????????????????????????????????????????????????????????????
|
|
15960 ------------------------------------------------------------
|
|
CAG33136. 423 ------------------------------------------------------------
|
|
|
|
KI537979 9728674 ????????????????????????????????????????????????????????????
|
|
16020 ------------------------------------------------------------
|
|
CAG33136. 423 ------------------------------------------------------------
|
|
|
|
KI537979 9728734 ????????????????????????????????????????????????????????????
|
|
16080 ------------------------------------------------------------
|
|
CAG33136. 423 ------------------------------------------------------------
|
|
|
|
KI537979 9728794 ????????????????????????????????????????????????????????????
|
|
16140 ------------------------------------------------------------
|
|
CAG33136. 423 ------------------------------------------------------------
|
|
|
|
KI537979 9728854 ????????????????????????????????????????????????????????????
|
|
16200 ------------------------------------------------------------
|
|
CAG33136. 423 ------------------------------------------------------------
|
|
|
|
KI537979 9728914 ????????????????????????????????????????????????????????????
|
|
16260 ------------------------------------------------------------
|
|
CAG33136. 423 ------------------------------------------------------------
|
|
|
|
KI537979 9728974 ????????????????????????????????????????????????????????????
|
|
16320 ------------------------------------------------------------
|
|
CAG33136. 423 ------------------------------------------------------------
|
|
|
|
KI537979 9729034 ????????????????????????????????????????????????????????????
|
|
16380 ------------------------------------------------------------
|
|
CAG33136. 423 ------------------------------------------------------------
|
|
|
|
KI537979 9729094 ????????????????????????????????????????????????????????????
|
|
16440 ------------------------------------------------------------
|
|
CAG33136. 423 ------------------------------------------------------------
|
|
|
|
KI537979 9729154 ????????????????????????????????????????????????????????????
|
|
16500 ------------------------------------------------------------
|
|
CAG33136. 423 ------------------------------------------------------------
|
|
|
|
KI537979 9729214 ????????????????????????????????????????????????????????????
|
|
16560 ------------------------------------------------------------
|
|
CAG33136. 423 ------------------------------------------------------------
|
|
|
|
KI537979 9729274 ????????????????????????????????????????????????????????????
|
|
16620 ------------------------------------------------------------
|
|
CAG33136. 423 ------------------------------------------------------------
|
|
|
|
KI537979 9729334 ????????????????????????????????????????????????????????????
|
|
16680 ------------------------------------------------------------
|
|
CAG33136. 423 ------------------------------------------------------------
|
|
|
|
KI537979 9729394 ????????????????????????????????????????????????????????????
|
|
16740 ------------------------------------------------------------
|
|
CAG33136. 423 ------------------------------------------------------------
|
|
|
|
KI537979 9729454 ????????????????????????????????????????????????????????????
|
|
16800 ------------------------------------------------------------
|
|
CAG33136. 423 ------------------------------------------------------------
|
|
|
|
KI537979 9729514 ????????????????????????????????????????????????????????????
|
|
16860 ------------------------------------------------------------
|
|
CAG33136. 423 ------------------------------------------------------------
|
|
|
|
KI537979 9729574 ????????????????????????????????????????????????????????????
|
|
16920 ------------------------------------------------------------
|
|
CAG33136. 423 ------------------------------------------------------------
|
|
|
|
KI537979 9729634 ????????????????????????????????????????????????????????????
|
|
16980 ------------------------------------------------------------
|
|
CAG33136. 423 ------------------------------------------------------------
|
|
|
|
KI537979 9729694 ????????????????????????????????????????????????????????????
|
|
17040 ------------------------------------------------------------
|
|
CAG33136. 423 ------------------------------------------------------------
|
|
|
|
KI537979 9729754 ????????????????????????????????????????????????????????????
|
|
17100 ------------------------------------------------------------
|
|
CAG33136. 423 ------------------------------------------------------------
|
|
|
|
KI537979 9729814 ????????????????????????????????????????????????????????????
|
|
17160 ------------------------------------------------------------
|
|
CAG33136. 423 ------------------------------------------------------------
|
|
|
|
KI537979 9729874 ????????????????????????????????????????????????????????????
|
|
17220 ------------------------------------------------------------
|
|
CAG33136. 423 ------------------------------------------------------------
|
|
|
|
KI537979 9729934 ????????????????????????????????????????????????????????????
|
|
17280 ------------------------------------------------------------
|
|
CAG33136. 423 ------------------------------------------------------------
|
|
|
|
KI537979 9729994 ????????????????????????????????????????????????????????????
|
|
17340 ------------------------------------------------------------
|
|
CAG33136. 423 ------------------------------------------------------------
|
|
|
|
KI537979 9730054 ????????????????????????????????????????????????????????????
|
|
17400 ------------------------------------------------------------
|
|
CAG33136. 423 ------------------------------------------------------------
|
|
|
|
KI537979 9730114 ????????????????????????????????????????????????????????????
|
|
17460 ------------------------------------------------------------
|
|
CAG33136. 423 ------------------------------------------------------------
|
|
|
|
KI537979 9730174 ????????????????????????????????????????????????????????????
|
|
17520 ------------------------------------------------------------
|
|
CAG33136. 423 ------------------------------------------------------------
|
|
|
|
KI537979 9730234 ????????????????????????????????????????????????????????????
|
|
17580 ------------------------------------------------------------
|
|
CAG33136. 423 ------------------------------------------------------------
|
|
|
|
KI537979 9730294 ????????????????????????????????????????????????????????????
|
|
17640 ------------------------------------------------------------
|
|
CAG33136. 423 ------------------------------------------------------------
|
|
|
|
KI537979 9730354 ????????????????????????????????????????????????????????????
|
|
17700 ------------------------------------------------------------
|
|
CAG33136. 423 ------------------------------------------------------------
|
|
|
|
KI537979 9730414 ????????????????????????????????????????????????????????????
|
|
17760 ------------------------------------------------------------
|
|
CAG33136. 423 ------------------------------------------------------------
|
|
|
|
KI537979 9730474 ????????????????????????????????????????????????????????????
|
|
17820 ------------------------------------------------------------
|
|
CAG33136. 423 ------------------------------------------------------------
|
|
|
|
KI537979 9730534 ????????????????????????????????????????????????????????????
|
|
17880 ------------------------------------------------------------
|
|
CAG33136. 423 ------------------------------------------------------------
|
|
|
|
KI537979 9730594 ????????????????????????????????????????????????????????????
|
|
17940 ------------------------------------------------------------
|
|
CAG33136. 423 ------------------------------------------------------------
|
|
|
|
KI537979 9730654 ????????????????????????????????????????????????????????????
|
|
18000 ------------------------------------------------------------
|
|
CAG33136. 423 ------------------------------------------------------------
|
|
|
|
KI537979 9730714 ????????????????????????????????????????????????????????????
|
|
18060 ------------------------------------------------------------
|
|
CAG33136. 423 ------------------------------------------------------------
|
|
|
|
KI537979 9730774 ????????????????????????????????????????????????????????????
|
|
18120 ------------------------------------------------------------
|
|
CAG33136. 423 ------------------------------------------------------------
|
|
|
|
KI537979 9730834 ????????????????????????????????????????????????????????????
|
|
18180 ------------------------------------------------------------
|
|
CAG33136. 423 ------------------------------------------------------------
|
|
|
|
KI537979 9730894 ????????????????????????????????????????????????????????????
|
|
18240 ------------------------------------------------------------
|
|
CAG33136. 423 ------------------------------------------------------------
|
|
|
|
KI537979 9730954 ????????????????????????????????????????????????????????????
|
|
18300 ------------------------------------------------------------
|
|
CAG33136. 423 ------------------------------------------------------------
|
|
|
|
KI537979 9731014 ????????????????????????????????????????????????????????????
|
|
18360 ------------------------------------------------------------
|
|
CAG33136. 423 ------------------------------------------------------------
|
|
|
|
KI537979 9731074 ????????????????????????????????????????????????????????????
|
|
18420 ------------------------------------------------------------
|
|
CAG33136. 423 ------------------------------------------------------------
|
|
|
|
KI537979 9731134 ????????????????????????????????????????????????????????????
|
|
18480 ------------------------------------------------------------
|
|
CAG33136. 423 ------------------------------------------------------------
|
|
|
|
KI537979 9731194 ????????????????????????????????????????????????????????????
|
|
18540 ------------------------------------------------------------
|
|
CAG33136. 423 ------------------------------------------------------------
|
|
|
|
KI537979 9731254 ????????????????????????????????????????????????????????????
|
|
18600 ------------------------------------------------------------
|
|
CAG33136. 423 ------------------------------------------------------------
|
|
|
|
KI537979 9731314 ????????????????????????????????????????????????????????????
|
|
18660 ------------------------------------------------------------
|
|
CAG33136. 423 ------------------------------------------------------------
|
|
|
|
KI537979 9731374 ????????????????????????????????????????????????????????????
|
|
18720 ------------------------------------------------------------
|
|
CAG33136. 423 ------------------------------------------------------------
|
|
|
|
KI537979 9731434 ????????????????????????????????????????????????????????????
|
|
18780 ------------------------------------------------------------
|
|
CAG33136. 423 ------------------------------------------------------------
|
|
|
|
KI537979 9731494 ????????????????????????????????????????????????????????????
|
|
18840 ------------------------------------------------------------
|
|
CAG33136. 423 ------------------------------------------------------------
|
|
|
|
KI537979 9731554 ????????????????????????????????????????????????????????????
|
|
18900 ------------------------------------------------------------
|
|
CAG33136. 423 ------------------------------------------------------------
|
|
|
|
KI537979 9731614 ????????????????????????????????????????????????????????????
|
|
18960 ------------------------------------------------------------
|
|
CAG33136. 423 ------------------------------------------------------------
|
|
|
|
KI537979 9731674 ????????????????????????????????????????????????????????????
|
|
19020 ------------------------------------------------------------
|
|
CAG33136. 423 ------------------------------------------------------------
|
|
|
|
KI537979 9731734 ????????????????????????????????????????????????????????????
|
|
19080 ------------------------------------------------------------
|
|
CAG33136. 423 ------------------------------------------------------------
|
|
|
|
KI537979 9731794 ????????????????????????????????????????????????????????????
|
|
19140 ------------------------------------------------------------
|
|
CAG33136. 423 ------------------------------------------------------------
|
|
|
|
KI537979 9731854 ????????????????????????????????????????????????????????????
|
|
19200 ------------------------------------------------------------
|
|
CAG33136. 423 ------------------------------------------------------------
|
|
|
|
KI537979 9731914 ????????????????????????????????????????????????????????????
|
|
19260 ------------------------------------------------------------
|
|
CAG33136. 423 ------------------------------------------------------------
|
|
|
|
KI537979 9731974 ????????????????????????????????????????????????????????????
|
|
19320 ------------------------------------------------------------
|
|
CAG33136. 423 ------------------------------------------------------------
|
|
|
|
KI537979 9732034 ????????????????????????????????????????????????????????????
|
|
19380 ------------------------------------------------------------
|
|
CAG33136. 423 ------------------------------------------------------------
|
|
|
|
KI537979 9732094 ????????????????????????????????????????????????????????????
|
|
19440 ------------------------------------------------------------
|
|
CAG33136. 423 ------------------------------------------------------------
|
|
|
|
KI537979 9732154 ????????????????????????????????????????????????????????????
|
|
19500 ------------------------------------------------------------
|
|
CAG33136. 423 ------------------------------------------------------------
|
|
|
|
KI537979 9732214 ????????????????????????????????????????????????????????????
|
|
19560 ------------------------------------------------------------
|
|
CAG33136. 423 ------------------------------------------------------------
|
|
|
|
KI537979 9732274 ????????????????????????????????????????????????????????????
|
|
19620 ------------------------------------------------------------
|
|
CAG33136. 423 ------------------------------------------------------------
|
|
|
|
KI537979 9732334 ????????????????????????????????????????????????????????????
|
|
19680 ------------------------------------------------------------
|
|
CAG33136. 423 ------------------------------------------------------------
|
|
|
|
KI537979 9732394 ????????????????????????????????????????????????????????????
|
|
19740 ------------------------------------------------------------
|
|
CAG33136. 423 ------------------------------------------------------------
|
|
|
|
KI537979 9732454 ????????????????????????????????????????????????????????????
|
|
19800 ------------------------------------------------------------
|
|
CAG33136. 423 ------------------------------------------------------------
|
|
|
|
KI537979 9732514 ????????????????????????????????????????????????????????????
|
|
19860 ------------------------------------------------------------
|
|
CAG33136. 423 ------------------------------------------------------------
|
|
|
|
KI537979 9732574 ????????????????????????????????????????????????????????????
|
|
19920 ------------------------------------------------------------
|
|
CAG33136. 423 ------------------------------------------------------------
|
|
|
|
KI537979 9732634 ????????????????????????????????????????????????????????????
|
|
19980 ------------------------------------------------------------
|
|
CAG33136. 423 ------------------------------------------------------------
|
|
|
|
KI537979 9732694 ????????????????????????????????????????????????????????????
|
|
20040 ------------------------------------------------------------
|
|
CAG33136. 423 ------------------------------------------------------------
|
|
|
|
KI537979 9732754 ????????????????????????????????????????????????????????????
|
|
20100 ------------------------------------------------------------
|
|
CAG33136. 423 ------------------------------------------------------------
|
|
|
|
KI537979 9732814 ????????????????????????????????????????????????????????????
|
|
20160 ------------------------------------------------------------
|
|
CAG33136. 423 ------------------------------------------------------------
|
|
|
|
KI537979 9732874 ????????????????????????????????????????????????????????????
|
|
20220 ------------------------------------------------------------
|
|
CAG33136. 423 ------------------------------------------------------------
|
|
|
|
KI537979 9732934 ????????????????????????????????????????????????????????????
|
|
20280 ------------------------------------------------------------
|
|
CAG33136. 423 ------------------------------------------------------------
|
|
|
|
KI537979 9732994 ????????????????????????????????????????????????????????????
|
|
20340 ------------------------------------------------------------
|
|
CAG33136. 423 ------------------------------------------------------------
|
|
|
|
KI537979 9733054 ????????????????????????????????????????????????????????????
|
|
20400 ------------------------------------------------------------
|
|
CAG33136. 423 ------------------------------------------------------------
|
|
|
|
KI537979 9733114 ????????????????????????????????????????????????????????????
|
|
20460 ------------------------------------------------------------
|
|
CAG33136. 423 ------------------------------------------------------------
|
|
|
|
KI537979 9733174 ????????????????????????????????????????????????????????????
|
|
20520 ------------------------------------------------------------
|
|
CAG33136. 423 ------------------------------------------------------------
|
|
|
|
KI537979 9733234 ????????????????????????????????????????????????????????????
|
|
20580 ------------------------------------------------------------
|
|
CAG33136. 423 ------------------------------------------------------------
|
|
|
|
KI537979 9733294 ????????????????????????????????????????????????????????????
|
|
20640 ------------------------------------------------------------
|
|
CAG33136. 423 ------------------------------------------------------------
|
|
|
|
KI537979 9733354 ????????????????????????????????????????????????????????????
|
|
20700 ------------------------------------------------------------
|
|
CAG33136. 423 ------------------------------------------------------------
|
|
|
|
KI537979 9733414 ????????????????????????????????????????????????????????????
|
|
20760 ------------------------------------------------------------
|
|
CAG33136. 423 ------------------------------------------------------------
|
|
|
|
KI537979 9733474 ????????????????????????????????????????????????????????????
|
|
20820 ------------------------------------------------------------
|
|
CAG33136. 423 ------------------------------------------------------------
|
|
|
|
KI537979 9733534 ????????????????????????????????????????????????????????????
|
|
20880 ------------------------------------------------------------
|
|
CAG33136. 423 ------------------------------------------------------------
|
|
|
|
KI537979 9733594 ????????????????????????????????????????????????????????????
|
|
20940 ------------------------------------------------------------
|
|
CAG33136. 423 ------------------------------------------------------------
|
|
|
|
KI537979 9733654 ????????????????????????????????????????????????????????????
|
|
21000 ------------------------------------------------------------
|
|
CAG33136. 423 ------------------------------------------------------------
|
|
|
|
KI537979 9733714 ????????????????????????????????????????????????????????????
|
|
21060 ------------------------------------------------------------
|
|
CAG33136. 423 ------------------------------------------------------------
|
|
|
|
KI537979 9733774 ????????????????????????????????????????????????????????????
|
|
21120 ------------------------------------------------------------
|
|
CAG33136. 423 ------------------------------------------------------------
|
|
|
|
KI537979 9733834 ????????????????????????????????????????????????????????????
|
|
21180 ------------------------------------------------------------
|
|
CAG33136. 423 ------------------------------------------------------------
|
|
|
|
KI537979 9733894 ????????????????????????????????????????????????????????????
|
|
21240 ------------------------------------------------------------
|
|
CAG33136. 423 ------------------------------------------------------------
|
|
|
|
KI537979 9733954 ????????????????????????????????????????????????????????????
|
|
21300 ------------------------------------------------------------
|
|
CAG33136. 423 ------------------------------------------------------------
|
|
|
|
KI537979 9734014 ????????????????????????????????????????????????????????????
|
|
21360 ------------------------------------------------------------
|
|
CAG33136. 423 ------------------------------------------------------------
|
|
|
|
KI537979 9734074 ????????????????????????????????????????????????????????????
|
|
21420 ------------------------------------------------------------
|
|
CAG33136. 423 ------------------------------------------------------------
|
|
|
|
KI537979 9734134 ????????????????????????????????????????????????????????????
|
|
21480 ------------------------------------------------------------
|
|
CAG33136. 423 ------------------------------------------------------------
|
|
|
|
KI537979 9734194 ????????????????????????????????????????????????????????????
|
|
21540 ------------------------------------------------------------
|
|
CAG33136. 423 ------------------------------------------------------------
|
|
|
|
KI537979 9734254 ????????????????????????????????????????????????????????????
|
|
21600 ------------------------------------------------------------
|
|
CAG33136. 423 ------------------------------------------------------------
|
|
|
|
KI537979 9734314 ????????????????????????????????????????????????????????????
|
|
21660 ------------------------------------------------------------
|
|
CAG33136. 423 ------------------------------------------------------------
|
|
|
|
KI537979 9734374 ????????????????????????????????????????????????????????????
|
|
21720 ------------------------------------------------------------
|
|
CAG33136. 423 ------------------------------------------------------------
|
|
|
|
KI537979 9734434 ????????????????????????????????????????????????????????????
|
|
21780 ------------------------------------------------------------
|
|
CAG33136. 423 ------------------------------------------------------------
|
|
|
|
KI537979 9734494 ????????????????????????????????????????????????????????????
|
|
21840 ------------------------------------------------------------
|
|
CAG33136. 423 ------------------------------------------------------------
|
|
|
|
KI537979 9734554 ????????????????????????????????????????????????????????????
|
|
21900 ------------------------------------------------------------
|
|
CAG33136. 423 ------------------------------------------------------------
|
|
|
|
KI537979 9734614 ????????????????????????????????????????????????????????????
|
|
21960 ------------------------------------------------------------
|
|
CAG33136. 423 ------------------------------------------------------------
|
|
|
|
KI537979 9734674 ????????????????????????????????????????????????????????????
|
|
22020 ------------------------------------------------------------
|
|
CAG33136. 423 ------------------------------------------------------------
|
|
|
|
KI537979 9734734 ????????????????????????????????????????????????????????????
|
|
22080 ------------------------------------------------------------
|
|
CAG33136. 423 ------------------------------------------------------------
|
|
|
|
KI537979 9734794 ????????????????????????????????????????????????????????????
|
|
22140 ------------------------------------------------------------
|
|
CAG33136. 423 ------------------------------------------------------------
|
|
|
|
KI537979 9734854 ????????????????????????????????????????????????????????????
|
|
22200 ------------------------------------------------------------
|
|
CAG33136. 423 ------------------------------------------------------------
|
|
|
|
KI537979 9734914 ????????????????????????????????????????????????????????????
|
|
22260 ------------------------------------------------------------
|
|
CAG33136. 423 ------------------------------------------------------------
|
|
|
|
KI537979 9734974 ????????????????????????????????????????????????????????????
|
|
22320 ------------------------------------------------------------
|
|
CAG33136. 423 ------------------------------------------------------------
|
|
|
|
KI537979 9735034 ????????????????????????????????????????????????????????????
|
|
22380 ------------------------------------------------------------
|
|
CAG33136. 423 ------------------------------------------------------------
|
|
|
|
KI537979 9735094 ????????????????????????????????????????????????????????????
|
|
22440 ------------------------------------------------------------
|
|
CAG33136. 423 ------------------------------------------------------------
|
|
|
|
KI537979 9735154 ????????????????????????????????????????????????????????????
|
|
22500 ------------------------------------------------------------
|
|
CAG33136. 423 ------------------------------------------------------------
|
|
|
|
KI537979 9735214 ????????????????????????????????????????????????????????????
|
|
22560 ------------------------------------------------------------
|
|
CAG33136. 423 ------------------------------------------------------------
|
|
|
|
KI537979 9735274 ????????????????????????????????????????????????????????????
|
|
22620 ------------------------------------------------------------
|
|
CAG33136. 423 ------------------------------------------------------------
|
|
|
|
KI537979 9735334 ????????????????????????????????????????????????????????????
|
|
22680 ------------------------------------------------------------
|
|
CAG33136. 423 ------------------------------------------------------------
|
|
|
|
KI537979 9735394 ????????????????????????????????????????????????????????????
|
|
22740 ------------------------------------------------------------
|
|
CAG33136. 423 ------------------------------------------------------------
|
|
|
|
KI537979 9735454 ????????????????????????????????????????????????????????????
|
|
22800 ------------------------------------------------------------
|
|
CAG33136. 423 ------------------------------------------------------------
|
|
|
|
KI537979 9735514 ????????????????????????????????????????????????????????????
|
|
22860 ------------------------------------------------------------
|
|
CAG33136. 423 ------------------------------------------------------------
|
|
|
|
KI537979 9735574 ????????????????????????????????????????????????????????????
|
|
22920 ------------------------------------------------------------
|
|
CAG33136. 423 ------------------------------------------------------------
|
|
|
|
KI537979 9735634 ????????????????????????????????????????????????????????????
|
|
22980 ------------------------------------------------------------
|
|
CAG33136. 423 ------------------------------------------------------------
|
|
|
|
KI537979 9735694 ????????????????????????????????????????????????????????????
|
|
23040 ------------------------------------------------------------
|
|
CAG33136. 423 ------------------------------------------------------------
|
|
|
|
KI537979 9735754 ????????????????????????????????????????????????????????????
|
|
23100 ------------------------------------------------------------
|
|
CAG33136. 423 ------------------------------------------------------------
|
|
|
|
KI537979 9735814 ????????????????????????????????????????????????????????????
|
|
23160 ------------------------------------------------------------
|
|
CAG33136. 423 ------------------------------------------------------------
|
|
|
|
KI537979 9735874 ????????????????????????????????????????????????????????????
|
|
23220 ------------------------------------------------------------
|
|
CAG33136. 423 ------------------------------------------------------------
|
|
|
|
KI537979 9735934 ????????????????????????????????????????????????????????????
|
|
23280 ------------------------------------------------------------
|
|
CAG33136. 423 ------------------------------------------------------------
|
|
|
|
KI537979 9735994 ????????????????????????????????????????????????????????????
|
|
23340 ------------------------------------------------------------
|
|
CAG33136. 423 ------------------------------------------------------------
|
|
|
|
KI537979 9736054 ????????????????????????????????????????????????????????????
|
|
23400 ------------------------------------------------------------
|
|
CAG33136. 423 ------------------------------------------------------------
|
|
|
|
KI537979 9736114 ????????????????????????????????????????????????????????????
|
|
23460 ------------------------------------------------------------
|
|
CAG33136. 423 ------------------------------------------------------------
|
|
|
|
KI537979 9736174 ????????????????????????????????????????????????????????????
|
|
23520 ------------------------------------------------------------
|
|
CAG33136. 423 ------------------------------------------------------------
|
|
|
|
KI537979 9736234 ????????????????????????????????????????????????????????????
|
|
23580 ------------------------------------------------------------
|
|
CAG33136. 423 ------------------------------------------------------------
|
|
|
|
KI537979 9736294 ????????????????????????????????????????????????????????????
|
|
23640 ------------------------------------------------------------
|
|
CAG33136. 423 ------------------------------------------------------------
|
|
|
|
KI537979 9736354 ????????????????????????????????????????????????????????????
|
|
23700 ------------------------------------------------------------
|
|
CAG33136. 423 ------------------------------------------------------------
|
|
|
|
KI537979 9736414 ????????????????????????????????????????????????????????????
|
|
23760 ------------------------------------------------------------
|
|
CAG33136. 423 ------------------------------------------------------------
|
|
|
|
KI537979 9736474 ????????????????????????????????????????????????????????????
|
|
23820 ------------------------------------------------------------
|
|
CAG33136. 423 ------------------------------------------------------------
|
|
|
|
KI537979 9736534 ????????????????????????????????????????????????????????????
|
|
23880 ------------------------------------------------------------
|
|
CAG33136. 423 ------------------------------------------------------------
|
|
|
|
KI537979 9736594 ????????????????????????????????????????????????????????????
|
|
23940 ------------------------------------------------------------
|
|
CAG33136. 423 ------------------------------------------------------------
|
|
|
|
KI537979 9736654 ????????????????????????????????????????????????????????????
|
|
24000 ------------------------------------------------------------
|
|
CAG33136. 423 ------------------------------------------------------------
|
|
|
|
KI537979 9736714 ????????????????????????????????????????????????????????????
|
|
24060 ------------------------------------------------------------
|
|
CAG33136. 423 ------------------------------------------------------------
|
|
|
|
KI537979 9736774 ????????????????????????????????????????????????????????????
|
|
24120 ------------------------------------------------------------
|
|
CAG33136. 423 ------------------------------------------------------------
|
|
|
|
KI537979 9736834 ????????????????????????????????????????????????????????????
|
|
24180 ------------------------------------------------------------
|
|
CAG33136. 423 ------------------------------------------------------------
|
|
|
|
KI537979 9736894 ????????????????????????????????????????????????????????????
|
|
24240 ------------------------------------------------------------
|
|
CAG33136. 423 ------------------------------------------------------------
|
|
|
|
KI537979 9736954 ????????????????????????????????????????????????????????????
|
|
24300 ------------------------------------------------------------
|
|
CAG33136. 423 ------------------------------------------------------------
|
|
|
|
KI537979 9737014 ????????????????????????????????????????????????????????????
|
|
24360 ------------------------------------------------------------
|
|
CAG33136. 423 ------------------------------------------------------------
|
|
|
|
KI537979 9737074 ????????????????????????????????????????????????????????????
|
|
24420 ------------------------------------------------------------
|
|
CAG33136. 423 ------------------------------------------------------------
|
|
|
|
KI537979 9737134 ????????????????????????????????????????????????????????????
|
|
24480 ------------------------------------------------------------
|
|
CAG33136. 423 ------------------------------------------------------------
|
|
|
|
KI537979 9737194 ????????????????????????????????????????????????????????????
|
|
24540 ------------------------------------------------------------
|
|
CAG33136. 423 ------------------------------------------------------------
|
|
|
|
KI537979 9737254 ????????????????????????????????????????????????????????????
|
|
24600 ------------------------------------------------------------
|
|
CAG33136. 423 ------------------------------------------------------------
|
|
|
|
KI537979 9737314 ????????????????????????????????????????????????????????????
|
|
24660 ------------------------------------------------------------
|
|
CAG33136. 423 ------------------------------------------------------------
|
|
|
|
KI537979 9737374 ????????????????????????????????????????????????????????????
|
|
24720 ------------------------------------------------------------
|
|
CAG33136. 423 ------------------------------------------------------------
|
|
|
|
KI537979 9737434 ????????????????????????????????????????????????????????????
|
|
24780 ------------------------------------------------------------
|
|
CAG33136. 423 ------------------------------------------------------------
|
|
|
|
KI537979 9737494 ????????????????????????????????????????????????????????????
|
|
24840 ------------------------------------------------------------
|
|
CAG33136. 423 ------------------------------------------------------------
|
|
|
|
KI537979 9737554 ????????????????????????????????????????????????????????????
|
|
24900 ------------------------------------------------------------
|
|
CAG33136. 423 ------------------------------------------------------------
|
|
|
|
KI537979 9737614 ????????????????????????????????????????????????????????????
|
|
24960 ------------------------------------------------------------
|
|
CAG33136. 423 ------------------------------------------------------------
|
|
|
|
KI537979 9737674 ????????????????????????????????????????????????????????????
|
|
25020 ------------------------------------------------------------
|
|
CAG33136. 423 ------------------------------------------------------------
|
|
|
|
KI537979 9737734 ????????????????????????????????????????????????????????????
|
|
25080 ------------------------------------------------------------
|
|
CAG33136. 423 ------------------------------------------------------------
|
|
|
|
KI537979 9737794 ????????????????????????????????????????????????????????????
|
|
25140 ------------------------------------------------------------
|
|
CAG33136. 423 ------------------------------------------------------------
|
|
|
|
KI537979 9737854 ????????????????????????????????????????????????????????????
|
|
25200 ------------------------------------------------------------
|
|
CAG33136. 423 ------------------------------------------------------------
|
|
|
|
KI537979 9737914 ????????????????????????????????????????????????????????????
|
|
25260 ------------------------------------------------------------
|
|
CAG33136. 423 ------------------------------------------------------------
|
|
|
|
KI537979 9737974 ????????????????????????????????????????????????????????????
|
|
25320 ------------------------------------------------------------
|
|
CAG33136. 423 ------------------------------------------------------------
|
|
|
|
KI537979 9738034 ????????????????????????????????????????????????????????????
|
|
25380 ------------------------------------------------------------
|
|
CAG33136. 423 ------------------------------------------------------------
|
|
|
|
KI537979 9738094 ????????????????????????????????????????????????????????????
|
|
25440 ------------------------------------------------------------
|
|
CAG33136. 423 ------------------------------------------------------------
|
|
|
|
KI537979 9738154 ????????????????????????????????????????????????????????????
|
|
25500 ------------------------------------------------------------
|
|
CAG33136. 423 ------------------------------------------------------------
|
|
|
|
KI537979 9738214 ????????????????????????????????????????????????????????????
|
|
25560 ------------------------------------------------------------
|
|
CAG33136. 423 ------------------------------------------------------------
|
|
|
|
KI537979 9738274 ????????????????????????????????????????????????????????????
|
|
25620 ------------------------------------------------------------
|
|
CAG33136. 423 ------------------------------------------------------------
|
|
|
|
KI537979 9738334 ????????????????????????????????????????????????????????????
|
|
25680 ------------------------------------------------------------
|
|
CAG33136. 423 ------------------------------------------------------------
|
|
|
|
KI537979 9738394 ????????????????????????????????????????????????????????????
|
|
25740 ------------------------------------------------------------
|
|
CAG33136. 423 ------------------------------------------------------------
|
|
|
|
KI537979 9738454 ????????????????????????????????????????????????????????????
|
|
25800 ------------------------------------------------------------
|
|
CAG33136. 423 ------------------------------------------------------------
|
|
|
|
KI537979 9738514 ????????????????????????????????????????????????????????????
|
|
25860 ------------------------------------------------------------
|
|
CAG33136. 423 ------------------------------------------------------------
|
|
|
|
KI537979 9738574 ????????????????????????????????????????????????????????????
|
|
25920 ------------------------------------------------------------
|
|
CAG33136. 423 ------------------------------------------------------------
|
|
|
|
KI537979 9738634 ????????????????????????????????????????????????????????????
|
|
25980 ------------------------------------------------------------
|
|
CAG33136. 423 ------------------------------------------------------------
|
|
|
|
KI537979 9738694 ????????????????????????????????????????????????????????????
|
|
26040 ------------------------------------------------------------
|
|
CAG33136. 423 ------------------------------------------------------------
|
|
|
|
KI537979 9738754 ????????????????????????????????????????????????????????????
|
|
26100 ------------------------------------------------------------
|
|
CAG33136. 423 ------------------------------------------------------------
|
|
|
|
KI537979 9738814 ????????????????????????????????????????????????????????????
|
|
26160 ------------------------------------------------------------
|
|
CAG33136. 423 ------------------------------------------------------------
|
|
|
|
KI537979 9738874 ????????????????????????????????????????????????????????????
|
|
26220 ------------------------------------------------------------
|
|
CAG33136. 423 ------------------------------------------------------------
|
|
|
|
KI537979 9738934 ????????????????????????????????????????????????????????????
|
|
26280 ------------------------------------------------------------
|
|
CAG33136. 423 ------------------------------------------------------------
|
|
|
|
KI537979 9738994 ????????????????????????????????????????????????????????????
|
|
26340 ------------------------------------------------------------
|
|
CAG33136. 423 ------------------------------------------------------------
|
|
|
|
KI537979 9739054 ????????????????????????????????????????????????????????????
|
|
26400 ------------------------------------------------------------
|
|
CAG33136. 423 ------------------------------------------------------------
|
|
|
|
KI537979 9739114 ????????????????????????????????????????????????????????????
|
|
26460 ------------------------------------------------------------
|
|
CAG33136. 423 ------------------------------------------------------------
|
|
|
|
KI537979 9739174 ????????????????????????????????????????????????????????????
|
|
26520 ------------------------------------------------------------
|
|
CAG33136. 423 ------------------------------------------------------------
|
|
|
|
KI537979 9739234 ????????????????????????????????????????????????????????????
|
|
26580 ------------------------------||||||||||||||||||||||||||||||
|
|
CAG33136. 423 ------------------------------??????????????????????????????
|
|
|
|
KI537979 9739294 ????????????????????????????????????????????????????????????
|
|
26640 |||||||||||||||||||||||||||||||||||||||||||||---------------
|
|
CAG33136. 453 ?????????????????????????????????????????????---------------
|
|
|
|
KI537979 9739354 ????????????????????????????????????????????????????????????
|
|
26700 ------------------------------------------------------------
|
|
CAG33136. 498 ------------------------------------------------------------
|
|
|
|
KI537979 9739414 ????????????????????????????????????????????????????????????
|
|
26760 ------------------------------------------------------------
|
|
CAG33136. 498 ------------------------------------------------------------
|
|
|
|
KI537979 9739474 ????????????????????????????????????????????????????????????
|
|
26820 ------------------------------------------------------------
|
|
CAG33136. 498 ------------------------------------------------------------
|
|
|
|
KI537979 9739534 ????????????????????????????????????????????????????????????
|
|
26880 ------------------------------------------------------------
|
|
CAG33136. 498 ------------------------------------------------------------
|
|
|
|
KI537979 9739594 ????????????????????????????????????????????????????????????
|
|
26940 ------------------------------------------------------------
|
|
CAG33136. 498 ------------------------------------------------------------
|
|
|
|
KI537979 9739654 ????????????????????????????????????????????????????????????
|
|
27000 ------------------------------------------------------------
|
|
CAG33136. 498 ------------------------------------------------------------
|
|
|
|
KI537979 9739714 ????????????????????????????????????????????????????????????
|
|
27060 ------------------------------------------------------------
|
|
CAG33136. 498 ------------------------------------------------------------
|
|
|
|
KI537979 9739774 ????????????????????????????????????????????????????????????
|
|
27120 ------------------------------------------------------------
|
|
CAG33136. 498 ------------------------------------------------------------
|
|
|
|
KI537979 9739834 ????????????????????????????????????????????????????????????
|
|
27180 ------------------------------------------------------------
|
|
CAG33136. 498 ------------------------------------------------------------
|
|
|
|
KI537979 9739894 ????????????????????????????????????????????????????????????
|
|
27240 ------------------------------------------------------------
|
|
CAG33136. 498 ------------------------------------------------------------
|
|
|
|
KI537979 9739954 ????????????????????????????????????????????????????????????
|
|
27300 ------------------------------------------------------------
|
|
CAG33136. 498 ------------------------------------------------------------
|
|
|
|
KI537979 9740014 ????????????????????????????????????????????????????????????
|
|
27360 ------------------------------------------------------------
|
|
CAG33136. 498 ------------------------------------------------------------
|
|
|
|
KI537979 9740074 ????????????????????????????????????????????????????????????
|
|
27420 ------------------------------------------------------------
|
|
CAG33136. 498 ------------------------------------------------------------
|
|
|
|
KI537979 9740134 ????????????????????????????????????????????????????????????
|
|
27480 ------------------------------------------------------------
|
|
CAG33136. 498 ------------------------------------------------------------
|
|
|
|
KI537979 9740194 ????????????????????????????????????????????????????????????
|
|
27540 ------------------------------------------------------------
|
|
CAG33136. 498 ------------------------------------------------------------
|
|
|
|
KI537979 9740254 ????????????????????????????????????????????????????????????
|
|
27600 ------------------------------------------------------------
|
|
CAG33136. 498 ------------------------------------------------------------
|
|
|
|
KI537979 9740314 ????????????????????????????????????????????????????????????
|
|
27660 ------------------------------------------------------------
|
|
CAG33136. 498 ------------------------------------------------------------
|
|
|
|
KI537979 9740374 ????????????????????????????????????????????????????????????
|
|
27720 ------------------------------------------------------------
|
|
CAG33136. 498 ------------------------------------------------------------
|
|
|
|
KI537979 9740434 ????????????????????????????????????????????????????????????
|
|
27780 ------------------------------------------------------------
|
|
CAG33136. 498 ------------------------------------------------------------
|
|
|
|
KI537979 9740494 ????????????????????????????????????????????????????????????
|
|
27840 ------------------------------------------------------------
|
|
CAG33136. 498 ------------------------------------------------------------
|
|
|
|
KI537979 9740554 ????????????????????????????????????????????????????????????
|
|
27900 ------------------------------------------------------------
|
|
CAG33136. 498 ------------------------------------------------------------
|
|
|
|
KI537979 9740614 ????????????????????????????????????????????????????????????
|
|
27960 ------------------------------------------------------------
|
|
CAG33136. 498 ------------------------------------------------------------
|
|
|
|
KI537979 9740674 ????????????????????????????????????????????????????????????
|
|
28020 ------------------------------------------------------------
|
|
CAG33136. 498 ------------------------------------------------------------
|
|
|
|
KI537979 9740734 ????????????????????????????????????????????????????????????
|
|
28080 ------------------------------------------------------------
|
|
CAG33136. 498 ------------------------------------------------------------
|
|
|
|
KI537979 9740794 ????????????????????????????????????????????????????????????
|
|
28140 ------------------------------------------------------------
|
|
CAG33136. 498 ------------------------------------------------------------
|
|
|
|
KI537979 9740854 ????????????????????????????????????????????????????????????
|
|
28200 ------------------------------------------------------------
|
|
CAG33136. 498 ------------------------------------------------------------
|
|
|
|
KI537979 9740914 ????????????????????????????????????????????????????????????
|
|
28260 ------------------------------------------------------------
|
|
CAG33136. 498 ------------------------------------------------------------
|
|
|
|
KI537979 9740974 ????????????????????????????????????????????????????????????
|
|
28320 ------------------------------------------------------------
|
|
CAG33136. 498 ------------------------------------------------------------
|
|
|
|
KI537979 9741034 ????????????????????????????????????????????????????????????
|
|
28380 ------------------------------------------------------------
|
|
CAG33136. 498 ------------------------------------------------------------
|
|
|
|
KI537979 9741094 ????????????????????????????????????????????????????????????
|
|
28440 ------------------------------------------------------------
|
|
CAG33136. 498 ------------------------------------------------------------
|
|
|
|
KI537979 9741154 ????????????????????????????????????????????????????????????
|
|
28500 ------------------------------------------------------------
|
|
CAG33136. 498 ------------------------------------------------------------
|
|
|
|
KI537979 9741214 ????????????????????????????????????????????????????????????
|
|
28560 ------------------------------------------------------------
|
|
CAG33136. 498 ------------------------------------------------------------
|
|
|
|
KI537979 9741274 ????????????????????????????????????????????????????????????
|
|
28620 ------------------------------------------------------------
|
|
CAG33136. 498 ------------------------------------------------------------
|
|
|
|
KI537979 9741334 ????????????????????????????????????????????????????????????
|
|
28680 ------------------------------------------------------------
|
|
CAG33136. 498 ------------------------------------------------------------
|
|
|
|
KI537979 9741394 ????????????????????????????????????????????????????????????
|
|
28740 ------------------------------------------------------------
|
|
CAG33136. 498 ------------------------------------------------------------
|
|
|
|
KI537979 9741454 ????????????????????????????????????????????????????????????
|
|
28800 ------------------------------------------------------------
|
|
CAG33136. 498 ------------------------------------------------------------
|
|
|
|
KI537979 9741514 ????????????????????????????????????????????????????????????
|
|
28860 ------------------------------------------------------------
|
|
CAG33136. 498 ------------------------------------------------------------
|
|
|
|
KI537979 9741574 ????????????????????????????????????????????????????????????
|
|
28920 ------------------------------------------------------------
|
|
CAG33136. 498 ------------------------------------------------------------
|
|
|
|
KI537979 9741634 ????????????????????????????????????????????????????????????
|
|
28980 ------------------------------------------------------------
|
|
CAG33136. 498 ------------------------------------------------------------
|
|
|
|
KI537979 9741694 ????????????????????????????????????????????????????????????
|
|
29040 ------------------------------------------------------------
|
|
CAG33136. 498 ------------------------------------------------------------
|
|
|
|
KI537979 9741754 ????????????????????????????????????????????????????????????
|
|
29100 ------------------------------------------------------------
|
|
CAG33136. 498 ------------------------------------------------------------
|
|
|
|
KI537979 9741814 ????????????????????????????????????????????????????????????
|
|
29160 ------------------------------------------------------------
|
|
CAG33136. 498 ------------------------------------------------------------
|
|
|
|
KI537979 9741874 ????????????????????????????????????????????????????????????
|
|
29220 ------------------------------------------------------------
|
|
CAG33136. 498 ------------------------------------------------------------
|
|
|
|
KI537979 9741934 ????????????????????????????????????????????????????????????
|
|
29280 ------------------------------------------------------------
|
|
CAG33136. 498 ------------------------------------------------------------
|
|
|
|
KI537979 9741994 ????????????????????????????????????????????????????????????
|
|
29340 ------------------------------------------------------------
|
|
CAG33136. 498 ------------------------------------------------------------
|
|
|
|
KI537979 9742054 ????????????????????????????????????????????????????????????
|
|
29400 ------------------------------------------------------------
|
|
CAG33136. 498 ------------------------------------------------------------
|
|
|
|
KI537979 9742114 ????????????????????????????????????????????????????????????
|
|
29460 ------------------------------------------------------------
|
|
CAG33136. 498 ------------------------------------------------------------
|
|
|
|
KI537979 9742174 ????????????????????????????????????????????????????????????
|
|
29520 ------------------------------------------------------------
|
|
CAG33136. 498 ------------------------------------------------------------
|
|
|
|
KI537979 9742234 ????????????????????????????????????????????????????????????
|
|
29580 ------------------------------------------------------------
|
|
CAG33136. 498 ------------------------------------------------------------
|
|
|
|
KI537979 9742294 ????????????????????????????????????????????????????????????
|
|
29640 ------------------------------------------------------------
|
|
CAG33136. 498 ------------------------------------------------------------
|
|
|
|
KI537979 9742354 ????????????????????????????????????????????????????????????
|
|
29700 ------------------------------------------------------------
|
|
CAG33136. 498 ------------------------------------------------------------
|
|
|
|
KI537979 9742414 ????????????????????????????????????????????????????????????
|
|
29760 ------------------------------------------------------------
|
|
CAG33136. 498 ------------------------------------------------------------
|
|
|
|
KI537979 9742474 ????????????????????????????????????????????????????????????
|
|
29820 ------------------------------------------------------------
|
|
CAG33136. 498 ------------------------------------------------------------
|
|
|
|
KI537979 9742534 ????????????????????????????????????????????????????????????
|
|
29880 ------------------------------------------------------------
|
|
CAG33136. 498 ------------------------------------------------------------
|
|
|
|
KI537979 9742594 ????????????????????????????????????????????????????????????
|
|
29940 ------------------------------------------------------------
|
|
CAG33136. 498 ------------------------------------------------------------
|
|
|
|
KI537979 9742654 ????????????????????????????????????????????????????????????
|
|
30000 ------------------------------------------------------------
|
|
CAG33136. 498 ------------------------------------------------------------
|
|
|
|
KI537979 9742714 ????????????????????????????????????????????????????????????
|
|
30060 ------------------------------------------------------------
|
|
CAG33136. 498 ------------------------------------------------------------
|
|
|
|
KI537979 9742774 ????????????????????????????????????????????????????????????
|
|
30120 ------------------------------------------------------------
|
|
CAG33136. 498 ------------------------------------------------------------
|
|
|
|
KI537979 9742834 ????????????????????????????????????????????????????????????
|
|
30180 ------------------------------------------------------------
|
|
CAG33136. 498 ------------------------------------------------------------
|
|
|
|
KI537979 9742894 ????????????????????????????????????????????????????????????
|
|
30240 ------------------------------------------------------------
|
|
CAG33136. 498 ------------------------------------------------------------
|
|
|
|
KI537979 9742954 ????????????????????????????????????????????????????????????
|
|
30300 ------------------------------------------------------------
|
|
CAG33136. 498 ------------------------------------------------------------
|
|
|
|
KI537979 9743014 ????????????????????????????????????????????????????????????
|
|
30360 ------------------------------------------------------------
|
|
CAG33136. 498 ------------------------------------------------------------
|
|
|
|
KI537979 9743074 ????????????????????????????????????????????????????????????
|
|
30420 ------------------------------------------------------------
|
|
CAG33136. 498 ------------------------------------------------------------
|
|
|
|
KI537979 9743134 ????????????????????????????????????????????????????????????
|
|
30480 ------------------------------------------------------------
|
|
CAG33136. 498 ------------------------------------------------------------
|
|
|
|
KI537979 9743194 ????????????????????????????????????????????????????????????
|
|
30540 ------------------------------------------------------------
|
|
CAG33136. 498 ------------------------------------------------------------
|
|
|
|
KI537979 9743254 ????????????????????????????????????????????????????????????
|
|
30600 ------------------------------------------------------------
|
|
CAG33136. 498 ------------------------------------------------------------
|
|
|
|
KI537979 9743314 ????????????????????????????????????????????????????????????
|
|
30660 ------------------------------------------------------------
|
|
CAG33136. 498 ------------------------------------------------------------
|
|
|
|
KI537979 9743374 ????????????????????????????????????????????????????????????
|
|
30720 ------------------------------------------------------------
|
|
CAG33136. 498 ------------------------------------------------------------
|
|
|
|
KI537979 9743434 ????????????????????????????????????????????????????????????
|
|
30780 ------------------------------------------------------------
|
|
CAG33136. 498 ------------------------------------------------------------
|
|
|
|
KI537979 9743494 ????????????????????????????????????????????????????????????
|
|
30840 ------------------------------------------------------------
|
|
CAG33136. 498 ------------------------------------------------------------
|
|
|
|
KI537979 9743554 ????????????????????????????????????????????????????????????
|
|
30900 ------------------------------------------------------------
|
|
CAG33136. 498 ------------------------------------------------------------
|
|
|
|
KI537979 9743614 ????????????????????????????????????????????????????????????
|
|
30960 ------------------------------------------------------------
|
|
CAG33136. 498 ------------------------------------------------------------
|
|
|
|
KI537979 9743674 ????????????????????????????????????????????????????????????
|
|
31020 --------------------------------||||||||||||||||||||||||||||
|
|
CAG33136. 498 --------------------------------????????????????????????????
|
|
|
|
KI537979 9743734 ????????????????????????????????????????????????????????????
|
|
31080 ||||||||||||||||||||||||||||||||----------------------------
|
|
CAG33136. 526 ????????????????????????????????----------------------------
|
|
|
|
KI537979 9743794 ????????????????????????????????????????????????????????????
|
|
31140 ------------------------------------------------------------
|
|
CAG33136. 558 ------------------------------------------------------------
|
|
|
|
KI537979 9743854 ????????????????????????????????????????????????????????????
|
|
31200 ------------------------------------------------------------
|
|
CAG33136. 558 ------------------------------------------------------------
|
|
|
|
KI537979 9743914 ????????????????????????????????????????????????????????????
|
|
31260 ------------------------------------------------------------
|
|
CAG33136. 558 ------------------------------------------------------------
|
|
|
|
KI537979 9743974 ????????????????????????????????????????????????????????????
|
|
31320 ------------------------------------------------------------
|
|
CAG33136. 558 ------------------------------------------------------------
|
|
|
|
KI537979 9744034 ????????????????????????????????????????????????????????????
|
|
31380 ------------------------------------------------------------
|
|
CAG33136. 558 ------------------------------------------------------------
|
|
|
|
KI537979 9744094 ????????????????????????????????????????????????????????????
|
|
31440 ------------------------------------------------------------
|
|
CAG33136. 558 ------------------------------------------------------------
|
|
|
|
KI537979 9744154 ????????????????????????????????????????????????????????????
|
|
31500 ------------------------------------------------------------
|
|
CAG33136. 558 ------------------------------------------------------------
|
|
|
|
KI537979 9744214 ????????????????????????????????????????????????????????????
|
|
31560 ------------------------------------------------------------
|
|
CAG33136. 558 ------------------------------------------------------------
|
|
|
|
KI537979 9744274 ????????????????????????????????????????????????????????????
|
|
31620 ------------------------------------------------------------
|
|
CAG33136. 558 ------------------------------------------------------------
|
|
|
|
KI537979 9744334 ????????????????????????????????????????????????????????????
|
|
31680 ------------------------------------------------------------
|
|
CAG33136. 558 ------------------------------------------------------------
|
|
|
|
KI537979 9744394 ????????????????????????????????????????????????????????????
|
|
31740 ------------------------------------------------------------
|
|
CAG33136. 558 ------------------------------------------------------------
|
|
|
|
KI537979 9744454 ????????????????????????????????????????????????????????????
|
|
31800 ---------------------------------------------------------|||
|
|
CAG33136. 558 ---------------------------------------------------------???
|
|
|
|
KI537979 9744514 ????????????????????????????????????????????????????????????
|
|
31860 ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
|
|
CAG33136. 561 ????????????????????????????????????????????????????????????
|
|
|
|
KI537979 9744574 ?????????????????? 9744592
|
|
31920 |||||||||||||||||| 31938
|
|
CAG33136. 621 ?????????????????? 639
|
|
""",
|
|
)
|
|
self.assertEqual(
|
|
format(alignment, "bed"),
|
|
"""\
|
|
KI537979 9712654 9744592 CAG33136.1 972 + 9712654 9744592 0 7 132,156,87,48,75,60,81, 0,3287,3791,5720,26610,31052,31857,
|
|
""",
|
|
)
|
|
counts = alignment.counts()
|
|
self.assertEqual(counts.left_insertions, 0)
|
|
self.assertEqual(counts.left_deletions, 0)
|
|
self.assertEqual(counts.right_insertions, 0)
|
|
self.assertEqual(counts.right_deletions, 0)
|
|
self.assertEqual(counts.internal_insertions, 0)
|
|
self.assertEqual(counts.internal_deletions, 31299)
|
|
self.assertEqual(counts.left_gaps, 0)
|
|
self.assertEqual(counts.right_gaps, 0)
|
|
self.assertEqual(counts.internal_gaps, 31299)
|
|
self.assertEqual(counts.insertions, 0)
|
|
self.assertEqual(counts.deletions, 31299)
|
|
self.assertEqual(counts.gaps, 31299)
|
|
self.assertEqual(counts.aligned, 639)
|
|
alignment = next(alignments)
|
|
self.assertEqual(alignment.score, 792)
|
|
self.assertLess(alignment.coordinates[0, 0], alignment.coordinates[0, -1])
|
|
self.assertLess(alignment.coordinates[1, 0], alignment.coordinates[1, -1])
|
|
self.assertEqual(len(alignment), 2)
|
|
self.assertIs(alignment.sequences[0], alignment.target)
|
|
self.assertIs(alignment.sequences[1], alignment.query)
|
|
self.assertEqual(alignment.target.id, "KI538594")
|
|
self.assertEqual(alignment.query.id, "CAG33136.1")
|
|
self.assertTrue(
|
|
np.array_equal(
|
|
alignment.coordinates,
|
|
# fmt: off
|
|
np.array([[2103463, 2103523, 2103522, 2104149],
|
|
[ 0, 60, 60, 687]]),
|
|
# fmt: on
|
|
)
|
|
)
|
|
self.assertEqual(
|
|
str(alignment),
|
|
"""\
|
|
KI538594 2103463 ????????????????????????????????????????????????????????????
|
|
0 ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
|
|
CAG33136. 0 ????????????????????????????????????????????????????????????
|
|
|
|
KI538594 2103523
|
|
60
|
|
CAG33136. 60
|
|
|
|
KI538594 2103522 ????????????????????????????????????????????????????????????
|
|
60 ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
|
|
CAG33136. 60 ????????????????????????????????????????????????????????????
|
|
|
|
KI538594 2103582 ????????????????????????????????????????????????????????????
|
|
120 ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
|
|
CAG33136. 120 ????????????????????????????????????????????????????????????
|
|
|
|
KI538594 2103642 ????????????????????????????????????????????????????????????
|
|
180 ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
|
|
CAG33136. 180 ????????????????????????????????????????????????????????????
|
|
|
|
KI538594 2103702 ????????????????????????????????????????????????????????????
|
|
240 ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
|
|
CAG33136. 240 ????????????????????????????????????????????????????????????
|
|
|
|
KI538594 2103762 ????????????????????????????????????????????????????????????
|
|
300 ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
|
|
CAG33136. 300 ????????????????????????????????????????????????????????????
|
|
|
|
KI538594 2103822 ????????????????????????????????????????????????????????????
|
|
360 ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
|
|
CAG33136. 360 ????????????????????????????????????????????????????????????
|
|
|
|
KI538594 2103882 ????????????????????????????????????????????????????????????
|
|
420 ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
|
|
CAG33136. 420 ????????????????????????????????????????????????????????????
|
|
|
|
KI538594 2103942 ????????????????????????????????????????????????????????????
|
|
480 ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
|
|
CAG33136. 480 ????????????????????????????????????????????????????????????
|
|
|
|
KI538594 2104002 ????????????????????????????????????????????????????????????
|
|
540 ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
|
|
CAG33136. 540 ????????????????????????????????????????????????????????????
|
|
|
|
KI538594 2104062 ????????????????????????????????????????????????????????????
|
|
600 ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
|
|
CAG33136. 600 ????????????????????????????????????????????????????????????
|
|
|
|
KI538594 2104122 ??????????????????????????? 2104149
|
|
660 ||||||||||||||||||||||||||| 687
|
|
CAG33136. 660 ??????????????????????????? 687
|
|
""",
|
|
)
|
|
self.assertEqual(
|
|
format(alignment, "bed"),
|
|
"""\
|
|
KI538594 2103463 2104149 CAG33136.1 792 + 2103463 2104149 0 2 60,627, 0,59,
|
|
""",
|
|
)
|
|
counts = alignment.counts()
|
|
self.assertEqual(counts.left_insertions, 0)
|
|
self.assertEqual(counts.left_deletions, 0)
|
|
self.assertEqual(counts.right_insertions, 0)
|
|
self.assertEqual(counts.right_deletions, 0)
|
|
self.assertEqual(counts.internal_insertions, 0)
|
|
self.assertEqual(counts.internal_deletions, -1)
|
|
self.assertEqual(counts.left_gaps, 0)
|
|
self.assertEqual(counts.right_gaps, 0)
|
|
self.assertEqual(counts.internal_gaps, -1)
|
|
self.assertEqual(counts.insertions, 0)
|
|
self.assertEqual(counts.deletions, -1)
|
|
self.assertEqual(counts.gaps, -1)
|
|
self.assertEqual(counts.aligned, 687)
|
|
alignment = next(alignments)
|
|
self.assertEqual(alignment.score, 902)
|
|
self.assertLess(alignment.coordinates[0, 0], alignment.coordinates[0, -1])
|
|
self.assertGreater(alignment.coordinates[1, 0], alignment.coordinates[1, -1])
|
|
self.assertEqual(len(alignment), 2)
|
|
self.assertIs(alignment.sequences[0], alignment.target)
|
|
self.assertIs(alignment.sequences[1], alignment.query)
|
|
self.assertEqual(alignment.target.id, "KI537194")
|
|
self.assertEqual(alignment.query.id, "CAG33136.1")
|
|
self.assertTrue(
|
|
np.array_equal(
|
|
alignment.coordinates,
|
|
# fmt: off
|
|
np.array([[20872390, 20872471, 20872472, 20873021],
|
|
[ 630, 549, 549, 0]]),
|
|
# fmt: on
|
|
)
|
|
)
|
|
self.assertEqual(
|
|
str(alignment),
|
|
"""\
|
|
KI537194 20872390 ????????????????????????????????????????????????????????????
|
|
0 ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
|
|
CAG33136. 630 ????????????????????????????????????????????????????????????
|
|
|
|
KI537194 20872450 ????????????????????????????????????????????????????????????
|
|
60 |||||||||||||||||||||-||||||||||||||||||||||||||||||||||||||
|
|
CAG33136. 570 ?????????????????????-??????????????????????????????????????
|
|
|
|
KI537194 20872510 ????????????????????????????????????????????????????????????
|
|
120 ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
|
|
CAG33136. 511 ????????????????????????????????????????????????????????????
|
|
|
|
KI537194 20872570 ????????????????????????????????????????????????????????????
|
|
180 ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
|
|
CAG33136. 451 ????????????????????????????????????????????????????????????
|
|
|
|
KI537194 20872630 ????????????????????????????????????????????????????????????
|
|
240 ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
|
|
CAG33136. 391 ????????????????????????????????????????????????????????????
|
|
|
|
KI537194 20872690 ????????????????????????????????????????????????????????????
|
|
300 ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
|
|
CAG33136. 331 ????????????????????????????????????????????????????????????
|
|
|
|
KI537194 20872750 ????????????????????????????????????????????????????????????
|
|
360 ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
|
|
CAG33136. 271 ????????????????????????????????????????????????????????????
|
|
|
|
KI537194 20872810 ????????????????????????????????????????????????????????????
|
|
420 ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
|
|
CAG33136. 211 ????????????????????????????????????????????????????????????
|
|
|
|
KI537194 20872870 ????????????????????????????????????????????????????????????
|
|
480 ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
|
|
CAG33136. 151 ????????????????????????????????????????????????????????????
|
|
|
|
KI537194 20872930 ????????????????????????????????????????????????????????????
|
|
540 ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
|
|
CAG33136. 91 ????????????????????????????????????????????????????????????
|
|
|
|
KI537194 20872990 ??????????????????????????????? 20873021
|
|
600 ||||||||||||||||||||||||||||||| 631
|
|
CAG33136. 31 ??????????????????????????????? 0
|
|
""",
|
|
)
|
|
self.assertEqual(
|
|
format(alignment, "bed"),
|
|
"""\
|
|
KI537194 20872390 20873021 CAG33136.1 902 - 20872390 20873021 0 2 81,549, 0,82,
|
|
""",
|
|
)
|
|
counts = alignment.counts()
|
|
self.assertEqual(counts.left_insertions, 0)
|
|
self.assertEqual(counts.left_deletions, 0)
|
|
self.assertEqual(counts.right_insertions, 0)
|
|
self.assertEqual(counts.right_deletions, 0)
|
|
self.assertEqual(counts.internal_insertions, 0)
|
|
self.assertEqual(counts.internal_deletions, 1)
|
|
self.assertEqual(counts.left_gaps, 0)
|
|
self.assertEqual(counts.right_gaps, 0)
|
|
self.assertEqual(counts.internal_gaps, 1)
|
|
self.assertEqual(counts.insertions, 0)
|
|
self.assertEqual(counts.deletions, 1)
|
|
self.assertEqual(counts.gaps, 1)
|
|
self.assertEqual(counts.aligned, 630)
|
|
self.assertRaises(StopIteration, next, alignments)
|
|
|
|
def test_writing_psl_35_002(self):
|
|
"""Test writing the alignments in psl_35_002.bed."""
|
|
path = "Blat/psl_35_002.bed"
|
|
with open(path) as stream:
|
|
original_data = stream.read()
|
|
alignments = Align.parse(path, "bed")
|
|
stream = StringIO()
|
|
n = Align.write(alignments, stream, "bed")
|
|
self.assertEqual(n, 3)
|
|
stream.seek(0)
|
|
written_data = stream.read()
|
|
stream.close()
|
|
self.assertEqual(original_data, written_data)
|
|
|
|
|
|
class TestAlign_bed12(unittest.TestCase):
|
|
def test_reading(self):
|
|
"""Test parsing alignments in file formats BED3 through BED12."""
|
|
for bedN in (3, 4, 5, 6, 7, 8, 9, 12):
|
|
filename = "bed%d.bed" % bedN
|
|
path = os.path.join("Blat", filename)
|
|
alignments = Align.parse(path, "bed")
|
|
alignment = next(alignments)
|
|
if bedN >= 5:
|
|
self.assertEqual(alignment.score, 960, msg=filename)
|
|
self.assertEqual(alignment.shape, (2, 4000), msg=filename)
|
|
self.assertLess(
|
|
alignment.coordinates[0, 0], alignment.coordinates[0, -1], msg=filename
|
|
)
|
|
self.assertLess(
|
|
alignment.coordinates[1, 0], alignment.coordinates[1, -1], msg=filename
|
|
)
|
|
self.assertEqual(len(alignment), 2, msg=filename)
|
|
self.assertIs(alignment.sequences[0], alignment.target, msg=filename)
|
|
self.assertIs(alignment.sequences[1], alignment.query, msg=filename)
|
|
self.assertEqual(alignment.target.id, "chr22", msg=filename)
|
|
if bedN >= 4:
|
|
self.assertEqual(alignment.query.id, "mRNA1", msg=filename)
|
|
else:
|
|
self.assertIsNone(alignment.query.id, msg=filename)
|
|
if bedN == 12:
|
|
self.assertTrue(
|
|
np.array_equal(
|
|
alignment.coordinates,
|
|
# fmt: off
|
|
np.array([[1000, 1567, 4512, 5000],
|
|
[ 0, 567, 567, 1055]]),
|
|
# fmt: on
|
|
),
|
|
msg=filename,
|
|
)
|
|
else:
|
|
self.assertTrue(
|
|
np.array_equal(
|
|
alignment.coordinates,
|
|
np.array([[1000, 5000], [0, 4000]]),
|
|
),
|
|
msg=filename,
|
|
)
|
|
if bedN >= 7:
|
|
self.assertEqual(alignment.thickStart, 1200, msg=filename)
|
|
if bedN >= 8:
|
|
self.assertEqual(alignment.thickEnd, 4900, msg=filename)
|
|
if bedN >= 9:
|
|
self.assertEqual(alignment.itemRgb, "255,0,0", msg=filename)
|
|
words = [
|
|
"chr22",
|
|
"1000",
|
|
"5000",
|
|
"mRNA1",
|
|
"960",
|
|
"+",
|
|
"1200",
|
|
"4900",
|
|
"255,0,0",
|
|
"2",
|
|
"567,488,",
|
|
"0,3512,",
|
|
]
|
|
self.assertEqual(
|
|
alignment.format("bed", bedN), "\t".join(words[:bedN]) + "\n"
|
|
)
|
|
print(bedN, alignment.coordinates)
|
|
counts = alignment.counts()
|
|
self.assertEqual(counts.left_insertions, 0)
|
|
self.assertEqual(counts.left_deletions, 0)
|
|
self.assertEqual(counts.right_insertions, 0)
|
|
self.assertEqual(counts.right_deletions, 0)
|
|
self.assertEqual(counts.internal_insertions, 0)
|
|
if bedN == 12:
|
|
self.assertEqual(counts.internal_deletions, 2945)
|
|
self.assertEqual(counts.internal_gaps, 2945)
|
|
self.assertEqual(counts.deletions, 2945)
|
|
self.assertEqual(counts.gaps, 2945)
|
|
self.assertEqual(counts.aligned, 1055)
|
|
else:
|
|
self.assertEqual(counts.internal_deletions, 0)
|
|
self.assertEqual(counts.internal_gaps, 0)
|
|
self.assertEqual(counts.deletions, 0)
|
|
self.assertEqual(counts.gaps, 0)
|
|
self.assertEqual(counts.aligned, 4000)
|
|
self.assertEqual(counts.left_gaps, 0)
|
|
self.assertEqual(counts.right_gaps, 0)
|
|
self.assertEqual(counts.insertions, 0)
|
|
alignment = next(alignments)
|
|
if bedN >= 5:
|
|
self.assertEqual(alignment.score, 900, msg=filename)
|
|
self.assertEqual(alignment.shape, (2, 4000), msg=filename)
|
|
self.assertLess(
|
|
alignment.coordinates[0, 0], alignment.coordinates[0, -1], msg=filename
|
|
)
|
|
if bedN >= 6:
|
|
self.assertGreater(
|
|
alignment.coordinates[1, 0],
|
|
alignment.coordinates[1, -1],
|
|
msg=filename,
|
|
)
|
|
else:
|
|
self.assertLess(
|
|
alignment.coordinates[1, 0],
|
|
alignment.coordinates[1, -1],
|
|
msg=filename,
|
|
)
|
|
self.assertEqual(len(alignment), 2, msg=filename)
|
|
self.assertIs(alignment.sequences[0], alignment.target, msg=filename)
|
|
self.assertIs(alignment.sequences[1], alignment.query, msg=filename)
|
|
self.assertEqual(alignment.target.id, "chr22", msg=filename)
|
|
if bedN >= 4:
|
|
self.assertEqual(alignment.query.id, "mRNA2", msg=filename)
|
|
else:
|
|
self.assertIsNone(alignment.query.id, msg=filename)
|
|
if bedN == 12:
|
|
self.assertTrue(
|
|
np.array_equal(
|
|
alignment.coordinates,
|
|
# fmt: off
|
|
np.array([[2000, 2433, 5601, 6000],
|
|
[ 832, 399, 399, 0]])
|
|
# fmt: on
|
|
),
|
|
msg=filename,
|
|
)
|
|
elif bedN >= 6:
|
|
self.assertTrue(
|
|
np.array_equal(
|
|
alignment.coordinates,
|
|
np.array([[2000, 6000], [4000, 0]]),
|
|
),
|
|
msg=filename,
|
|
)
|
|
else:
|
|
self.assertTrue(
|
|
np.array_equal(
|
|
alignment.coordinates,
|
|
np.array([[2000, 6000], [0, 4000]]),
|
|
),
|
|
msg=filename,
|
|
)
|
|
if bedN >= 7:
|
|
self.assertEqual(alignment.thickStart, 2300, msg=filename)
|
|
if bedN >= 8:
|
|
self.assertEqual(alignment.thickEnd, 5960, msg=filename)
|
|
if bedN >= 9:
|
|
self.assertEqual(alignment.itemRgb, "0,255,0", msg=filename)
|
|
words = [
|
|
"chr22",
|
|
"2000",
|
|
"6000",
|
|
"mRNA2",
|
|
"900",
|
|
"-",
|
|
"2300",
|
|
"5960",
|
|
"0,255,0",
|
|
"2",
|
|
"433,399,",
|
|
"0,3601,",
|
|
]
|
|
self.assertEqual(
|
|
alignment.format("bed", bedN), "\t".join(words[:bedN]) + "\n"
|
|
)
|
|
counts = alignment.counts()
|
|
self.assertEqual(counts.left_insertions, 0)
|
|
self.assertEqual(counts.left_deletions, 0)
|
|
self.assertEqual(counts.right_insertions, 0)
|
|
self.assertEqual(counts.right_deletions, 0)
|
|
self.assertEqual(counts.internal_insertions, 0)
|
|
if bedN == 12:
|
|
self.assertEqual(counts.internal_deletions, 3168)
|
|
self.assertEqual(counts.deletions, 3168)
|
|
self.assertEqual(counts.internal_gaps, 3168)
|
|
self.assertEqual(counts.gaps, 3168)
|
|
self.assertEqual(counts.aligned, 832)
|
|
else:
|
|
self.assertEqual(counts.internal_deletions, 0)
|
|
self.assertEqual(counts.deletions, 0)
|
|
self.assertEqual(counts.internal_gaps, 0)
|
|
self.assertEqual(counts.gaps, 0)
|
|
self.assertEqual(counts.aligned, 4000)
|
|
self.assertEqual(counts.left_gaps, 0)
|
|
self.assertEqual(counts.right_gaps, 0)
|
|
self.assertEqual(counts.insertions, 0)
|
|
with self.assertRaises(StopIteration) as cm:
|
|
next(alignments)
|
|
self.fail(f"More than two alignments reported in {filename}")
|
|
|
|
def test_writing(self):
|
|
"""Test writing the alignments in bed12.bed as BED3 through BED12."""
|
|
for bedN in (3, 4, 5, 6, 7, 8, 9, 12):
|
|
filename = "bed%d.bed" % bedN
|
|
path = os.path.join("Blat", filename)
|
|
with open(path) as stream:
|
|
original_data = stream.read()
|
|
alignments = Align.parse(path, "bed")
|
|
stream = StringIO()
|
|
n = Align.write(alignments, stream, "bed", bedN=bedN)
|
|
self.assertEqual(n, 2, msg=filename)
|
|
stream.seek(0)
|
|
written_data = stream.read()
|
|
stream.close()
|
|
self.assertEqual(original_data, written_data, msg=filename)
|
|
|
|
|
|
class TestAlign_strand(unittest.TestCase):
|
|
def test_format(self):
|
|
"""Test alignment with the target on the opposite strand."""
|
|
sequences = ["AACAGCAGCGTGTCG", "CAGCTAGCGAA"]
|
|
coordinates = np.array(
|
|
[[0, 2, 2, 3, 4, 6, 6, 9, 10, 12, 15], [11, 11, 9, 8, 8, 6, 5, 2, 2, 0, 0]]
|
|
)
|
|
alignment = Alignment(sequences, coordinates)
|
|
alignment.score = 8
|
|
line = """\
|
|
target 2 12 query 8 - 2 12 0 4 1,2,3,2, 0,2,4,8,
|
|
"""
|
|
self.assertEqual(
|
|
str(alignment),
|
|
"""\
|
|
target 0 AA--CAGC-AGCGTGTCG 15
|
|
0 ----|-||-|||-||--- 18
|
|
query 11 --TTC-GCTAGC-TG--- 0
|
|
""",
|
|
)
|
|
self.assertEqual(format(alignment, "bed"), line)
|
|
alignment.coordinates = alignment.coordinates[:, ::-1]
|
|
self.assertEqual(
|
|
str(alignment),
|
|
"""\
|
|
target 15 CGACACGCT-GCTG--TT 0
|
|
0 ---||-|||-||-|---- 18
|
|
query 0 ---CA-GCTAGC-GAA-- 11
|
|
""",
|
|
)
|
|
self.assertEqual(format(alignment, "bed"), line)
|
|
alignment.coordinates = alignment.coordinates[:, ::-1]
|
|
line = """\
|
|
target 3 13 query 0 - 3 13 0 4 2,3,2,1, 0,3,6,9,
|
|
"""
|
|
alignment = alignment.reverse_complement()
|
|
self.assertEqual(
|
|
str(alignment),
|
|
"""\
|
|
target 0 CGACACGCT-GCTG--TT 15
|
|
0 ---||-|||-||-|---- 18
|
|
query 11 ---CA-GCTAGC-GAA-- 0
|
|
""",
|
|
)
|
|
self.assertEqual(format(alignment, "bed"), line)
|
|
alignment.coordinates = alignment.coordinates[:, ::-1]
|
|
self.assertEqual(
|
|
str(alignment),
|
|
"""\
|
|
target 15 AA--CAGC-AGCGTGTCG 0
|
|
0 ----|-||-|||-||--- 18
|
|
query 0 --TTC-GCTAGC-TG--- 11
|
|
""",
|
|
)
|
|
self.assertEqual(format(alignment, "bed"), line)
|
|
|
|
|
|
class TestAlign_searching(unittest.TestCase):
|
|
path = "Blat/bigbedtest.bed"
|
|
|
|
def check_alignments(self, alignments):
|
|
alignment = next(alignments)
|
|
self.assertEqual(alignment.score, 1)
|
|
self.assertEqual(alignment.shape, (2, 90))
|
|
self.assertEqual(len(alignment), 2)
|
|
self.assertIs(alignment.sequences[0], alignment.target)
|
|
self.assertIs(alignment.sequences[1], alignment.query)
|
|
self.assertEqual(alignment.target.id, "chr1")
|
|
self.assertEqual(alignment.query.id, "name1")
|
|
self.assertTrue(
|
|
np.array_equal(alignment.coordinates, np.array([[10, 100], [0, 90]]))
|
|
)
|
|
counts = alignment.counts()
|
|
self.assertEqual(counts.left_insertions, 0)
|
|
self.assertEqual(counts.left_deletions, 0)
|
|
self.assertEqual(counts.right_insertions, 0)
|
|
self.assertEqual(counts.right_deletions, 0)
|
|
self.assertEqual(counts.internal_insertions, 0)
|
|
self.assertEqual(counts.internal_deletions, 0)
|
|
self.assertEqual(counts.left_gaps, 0)
|
|
self.assertEqual(counts.right_gaps, 0)
|
|
self.assertEqual(counts.internal_gaps, 0)
|
|
self.assertEqual(counts.insertions, 0)
|
|
self.assertEqual(counts.deletions, 0)
|
|
self.assertEqual(counts.gaps, 0)
|
|
self.assertEqual(counts.aligned, 90)
|
|
alignment = next(alignments)
|
|
self.assertEqual(alignment.score, 2)
|
|
self.assertEqual(alignment.shape, (2, 10))
|
|
self.assertEqual(len(alignment), 2)
|
|
self.assertIs(alignment.sequences[0], alignment.target)
|
|
self.assertIs(alignment.sequences[1], alignment.query)
|
|
self.assertEqual(alignment.target.id, "chr1")
|
|
self.assertEqual(alignment.query.id, "name2")
|
|
self.assertTrue(
|
|
np.array_equal(alignment.coordinates, np.array([[29, 39], [10, 0]]))
|
|
)
|
|
counts = alignment.counts()
|
|
self.assertEqual(counts.left_insertions, 0)
|
|
self.assertEqual(counts.left_deletions, 0)
|
|
self.assertEqual(counts.right_insertions, 0)
|
|
self.assertEqual(counts.right_deletions, 0)
|
|
self.assertEqual(counts.internal_insertions, 0)
|
|
self.assertEqual(counts.internal_deletions, 0)
|
|
self.assertEqual(counts.left_gaps, 0)
|
|
self.assertEqual(counts.right_gaps, 0)
|
|
self.assertEqual(counts.internal_gaps, 0)
|
|
self.assertEqual(counts.insertions, 0)
|
|
self.assertEqual(counts.deletions, 0)
|
|
self.assertEqual(counts.gaps, 0)
|
|
self.assertEqual(counts.aligned, 10)
|
|
alignment = next(alignments)
|
|
self.assertEqual(alignment.score, 3)
|
|
self.assertEqual(alignment.shape, (2, 100))
|
|
self.assertEqual(len(alignment), 2)
|
|
self.assertIs(alignment.sequences[0], alignment.target)
|
|
self.assertIs(alignment.sequences[1], alignment.query)
|
|
self.assertEqual(alignment.target.id, "chr1")
|
|
self.assertEqual(alignment.query.id, "name3")
|
|
self.assertTrue(
|
|
np.array_equal(alignment.coordinates, np.array([[200, 300], [0, 100]]))
|
|
)
|
|
counts = alignment.counts()
|
|
self.assertEqual(counts.left_insertions, 0)
|
|
self.assertEqual(counts.left_deletions, 0)
|
|
self.assertEqual(counts.right_insertions, 0)
|
|
self.assertEqual(counts.right_deletions, 0)
|
|
self.assertEqual(counts.internal_insertions, 0)
|
|
self.assertEqual(counts.internal_deletions, 0)
|
|
self.assertEqual(counts.left_gaps, 0)
|
|
self.assertEqual(counts.right_gaps, 0)
|
|
self.assertEqual(counts.internal_gaps, 0)
|
|
self.assertEqual(counts.insertions, 0)
|
|
self.assertEqual(counts.deletions, 0)
|
|
self.assertEqual(counts.gaps, 0)
|
|
self.assertEqual(counts.aligned, 100)
|
|
alignment = next(alignments)
|
|
self.assertEqual(alignment.score, 6)
|
|
self.assertEqual(alignment.shape, (2, 0))
|
|
self.assertEqual(len(alignment), 2)
|
|
self.assertIs(alignment.sequences[0], alignment.target)
|
|
self.assertIs(alignment.sequences[1], alignment.query)
|
|
self.assertEqual(alignment.target.id, "chr2")
|
|
self.assertEqual(alignment.query.id, "name4")
|
|
self.assertTrue(
|
|
np.array_equal(alignment.coordinates, np.array([[50, 50], [0, 0]]))
|
|
)
|
|
counts = alignment.counts()
|
|
self.assertEqual(counts.left_insertions, 0)
|
|
self.assertEqual(counts.left_deletions, 0)
|
|
self.assertEqual(counts.right_insertions, 0)
|
|
self.assertEqual(counts.right_deletions, 0)
|
|
self.assertEqual(counts.internal_insertions, 0)
|
|
self.assertEqual(counts.internal_deletions, 0)
|
|
self.assertEqual(counts.left_gaps, 0)
|
|
self.assertEqual(counts.right_gaps, 0)
|
|
self.assertEqual(counts.internal_gaps, 0)
|
|
self.assertEqual(counts.insertions, 0)
|
|
self.assertEqual(counts.deletions, 0)
|
|
self.assertEqual(counts.gaps, 0)
|
|
self.assertEqual(counts.aligned, 0)
|
|
self.assertEqual(counts.identities, 0)
|
|
self.assertEqual(counts.mismatches, 0)
|
|
alignment = next(alignments)
|
|
self.assertEqual(alignment.score, 4)
|
|
self.assertEqual(alignment.shape, (2, 10))
|
|
self.assertEqual(len(alignment), 2)
|
|
self.assertIs(alignment.sequences[0], alignment.target)
|
|
self.assertIs(alignment.sequences[1], alignment.query)
|
|
self.assertEqual(alignment.target.id, "chr2")
|
|
self.assertEqual(alignment.query.id, "name5")
|
|
self.assertTrue(
|
|
np.array_equal(alignment.coordinates, np.array([[100, 110], [0, 10]]))
|
|
)
|
|
counts = alignment.counts()
|
|
self.assertEqual(counts.left_insertions, 0)
|
|
self.assertEqual(counts.left_deletions, 0)
|
|
self.assertEqual(counts.right_insertions, 0)
|
|
self.assertEqual(counts.right_deletions, 0)
|
|
self.assertEqual(counts.internal_insertions, 0)
|
|
self.assertEqual(counts.internal_deletions, 0)
|
|
self.assertEqual(counts.left_gaps, 0)
|
|
self.assertEqual(counts.right_gaps, 0)
|
|
self.assertEqual(counts.internal_gaps, 0)
|
|
self.assertEqual(counts.insertions, 0)
|
|
self.assertEqual(counts.deletions, 0)
|
|
self.assertEqual(counts.gaps, 0)
|
|
self.assertEqual(counts.aligned, 10)
|
|
alignment = next(alignments)
|
|
self.assertEqual(alignment.score, 5)
|
|
self.assertEqual(alignment.shape, (2, 10))
|
|
self.assertEqual(len(alignment), 2)
|
|
self.assertIs(alignment.sequences[0], alignment.target)
|
|
self.assertIs(alignment.sequences[1], alignment.query)
|
|
self.assertEqual(alignment.target.id, "chr2")
|
|
self.assertEqual(alignment.query.id, "name6")
|
|
self.assertTrue(
|
|
np.array_equal(alignment.coordinates, np.array([[200, 210], [0, 10]]))
|
|
)
|
|
counts = alignment.counts()
|
|
self.assertEqual(counts.left_insertions, 0)
|
|
self.assertEqual(counts.left_deletions, 0)
|
|
self.assertEqual(counts.right_insertions, 0)
|
|
self.assertEqual(counts.right_deletions, 0)
|
|
self.assertEqual(counts.internal_insertions, 0)
|
|
self.assertEqual(counts.internal_deletions, 0)
|
|
self.assertEqual(counts.left_gaps, 0)
|
|
self.assertEqual(counts.right_gaps, 0)
|
|
self.assertEqual(counts.internal_gaps, 0)
|
|
self.assertEqual(counts.insertions, 0)
|
|
self.assertEqual(counts.deletions, 0)
|
|
self.assertEqual(counts.gaps, 0)
|
|
self.assertEqual(counts.aligned, 10)
|
|
alignment = next(alignments)
|
|
self.assertEqual(alignment.score, 6)
|
|
self.assertEqual(alignment.shape, (2, 0))
|
|
self.assertEqual(len(alignment), 2)
|
|
self.assertIs(alignment.sequences[0], alignment.target)
|
|
self.assertIs(alignment.sequences[1], alignment.query)
|
|
self.assertEqual(alignment.target.id, "chr2")
|
|
self.assertEqual(alignment.query.id, "name7")
|
|
self.assertTrue(
|
|
np.array_equal(alignment.coordinates, np.array([[220, 220], [0, 0]]))
|
|
)
|
|
counts = alignment.counts()
|
|
self.assertEqual(counts.left_insertions, 0)
|
|
self.assertEqual(counts.left_deletions, 0)
|
|
self.assertEqual(counts.right_insertions, 0)
|
|
self.assertEqual(counts.right_deletions, 0)
|
|
self.assertEqual(counts.internal_insertions, 0)
|
|
self.assertEqual(counts.internal_deletions, 0)
|
|
self.assertEqual(counts.left_gaps, 0)
|
|
self.assertEqual(counts.right_gaps, 0)
|
|
self.assertEqual(counts.internal_gaps, 0)
|
|
self.assertEqual(counts.insertions, 0)
|
|
self.assertEqual(counts.deletions, 0)
|
|
self.assertEqual(counts.gaps, 0)
|
|
self.assertEqual(counts.aligned, 0)
|
|
self.assertEqual(counts.identities, 0)
|
|
self.assertEqual(counts.mismatches, 0)
|
|
alignment = next(alignments)
|
|
self.assertEqual(alignment.score, 7)
|
|
self.assertEqual(alignment.shape, (2, 0))
|
|
self.assertEqual(len(alignment), 2)
|
|
self.assertIs(alignment.sequences[0], alignment.target)
|
|
self.assertIs(alignment.sequences[1], alignment.query)
|
|
self.assertEqual(alignment.target.id, "chr3")
|
|
self.assertEqual(alignment.query.id, "name8")
|
|
self.assertTrue(
|
|
np.array_equal(alignment.coordinates, np.array([[0, 0], [0, 0]]))
|
|
)
|
|
counts = alignment.counts()
|
|
self.assertEqual(counts.left_insertions, 0)
|
|
self.assertEqual(counts.left_deletions, 0)
|
|
self.assertEqual(counts.right_insertions, 0)
|
|
self.assertEqual(counts.right_deletions, 0)
|
|
self.assertEqual(counts.internal_insertions, 0)
|
|
self.assertEqual(counts.internal_deletions, 0)
|
|
self.assertEqual(counts.left_gaps, 0)
|
|
self.assertEqual(counts.right_gaps, 0)
|
|
self.assertEqual(counts.internal_gaps, 0)
|
|
self.assertEqual(counts.insertions, 0)
|
|
self.assertEqual(counts.deletions, 0)
|
|
self.assertEqual(counts.gaps, 0)
|
|
self.assertEqual(counts.aligned, 0)
|
|
self.assertEqual(counts.identities, 0)
|
|
self.assertEqual(counts.mismatches, 0)
|
|
|
|
def test_reading(self):
|
|
"""Test reading bigbedtest.bed."""
|
|
alignments = Align.parse(self.path, "bed")
|
|
self.check_alignments(alignments)
|
|
|
|
def test_writing(self):
|
|
"""Test writing bigbedtest.bed."""
|
|
alignments = Align.parse(self.path, "bed")
|
|
with tempfile.TemporaryFile("w+t") as output:
|
|
Align.write(alignments, output, "bed", bedN=6)
|
|
output.seek(0)
|
|
alignments = Align.parse(output, "bed")
|
|
self.check_alignments(alignments)
|
|
|
|
|
|
if __name__ == "__main__":
|
|
runner = unittest.TextTestRunner(verbosity=2)
|
|
unittest.main(testRunner=runner)
|