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test_Align_chain.py
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7281 lines (6934 loc) · 284 KB
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# Copyright 2023 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.chain module."""
import unittest
from io import StringIO
from tempfile import NamedTemporaryFile
from Bio import Align
from Bio import SeqIO
from Bio.Align import Alignment
from Bio.Seq import reverse_complement
from Bio.Seq import Seq
from Bio.SeqFeature import CompoundLocation
from Bio.SeqFeature import ExactPosition
from Bio.SeqFeature import SimpleLocation
from Bio.SeqRecord import SeqRecord
try:
import numpy as np
except ImportError:
from Bio import MissingPythonDependencyError
raise MissingPythonDependencyError(
"Install numpy if you want to use Bio.Align.chain."
) from None
class TestAlign_dna_rna(unittest.TestCase):
# The chain file dna_rna.chain was generated from the PSL file using:
# pslToChain dna_rna.psl dna_rna.chain
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 = data
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.shape, (2, 1711))
self.assertEqual(len(alignment), 2)
self.assertEqual(alignment.score, 176)
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.assertEqual(len(alignment.target.seq), 198295559)
self.assertEqual(len(alignment.query.seq), 181)
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
)
)
dna = Seq(self.dna, length=len(alignment.target))
alignment.target.seq = 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.],
])
# fmt: on
)
)
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, "chain"),
"""\
chain 176 chr3 198295559 + 42530895 42532606 NR_046654.1 181 - 0 181 1
63 1062 0
75 468 0
43
""",
)
counts = alignment.counts()
self.assertEqual(
repr(counts),
"<AlignmentCounts object (181 aligned letters; 175 identities; 6 mismatches; 1530 gaps) at 0x%x>"
% id(counts),
)
self.assertEqual(
str(counts),
"""\
AlignmentCounts object with
aligned = 181:
identities = 175,
mismatches = 6.
gaps = 1530:
left_gaps = 0:
left_insertions = 0:
open_left_insertions = 0,
extend_left_insertions = 0;
left_deletions = 0:
open_left_deletions = 0,
extend_left_deletions = 0;
internal_gaps = 1530:
internal_insertions = 0:
open_internal_insertions = 0,
extend_internal_insertions = 0;
internal_deletions = 1530:
open_internal_deletions = 2,
extend_internal_deletions = 1528;
right_gaps = 0:
right_insertions = 0:
open_right_insertions = 0,
extend_right_insertions = 0;
right_deletions = 0:
open_right_deletions = 0,
extend_right_deletions = 0.
""",
)
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.shape, (2, 1714))
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.assertEqual(len(alignment.target.seq), 198295559)
self.assertEqual(len(alignment.query.seq), 190)
self.assertTrue(
np.array_equal(
alignment.coordinates,
# fmt: off
np.array([[42530895, 42530922, 42530922, 42530958, 42532020,
42532037, 42532039, 42532095, 42532563, 42532606],
[ 185, 158, 155, 119, 119,
102, 102, 46, 46, 3],
])
# fmt: on
)
)
dna = Seq(self.dna, length=len(alignment.target))
alignment.target.seq = dna
alignment.query.seq = self.rna[alignment.query.id]
self.assertTrue(
np.array_equal(
alignment.substitutions,
# fmt: off
np.array([[34., 0., 0., 1., 0., 0., 0., 0.],
[ 0., 40., 0., 0., 0., 0., 0., 0.],
[ 0., 0., 57., 0., 0., 0., 0., 0.],
[ 0., 0., 0., 41., 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.],
]),
# fmt: on
)
)
self.assertEqual(alignment.substitutions.alphabet, "ACGTacgt")
self.assertEqual(
str(alignment),
"""\
chr3 42530895 CGGAAGTACTTCTGGGGGTACATACTC---ATCGGCTGGGGTATGGTACCAGGGAGGGCT
0 |||||||||||||||||||||||||||---||||||||||||||||||||||||||||||
NR_046654 185 CGGAAGTACTTCTGGGGGTACATACTCCCCATCGGCTGGGGTATGGTACCAGGGAGGGCT
chr3 42530952 TCCAGGCTGGGGACAGAGGGGGCAAGGCCTGGAGAACTCCCTAGGGGGAGGGTGCCAACC
60 ||||||------------------------------------------------------
NR_046654 125 TCCAGG------------------------------------------------------
chr3 42531012 CAGCTTGCAGTCCTACGTCTTGCTTAGCTGCAGGTCCTGCCTGCAAGGATATCAGCCAAG
120 ------------------------------------------------------------
NR_046654 119 ------------------------------------------------------------
chr3 42531072 GGTCAAGAAAGTCCTCAAAATGTCTGATCCCAGGACAAGTCCCTCAGGTTGCAGCTGCAC
180 ------------------------------------------------------------
NR_046654 119 ------------------------------------------------------------
chr3 42531132 CTAGGGCTGACCTGTGGGACAGATTTTGTGAACATCTTTCCATTTCCCTTTAGTTCCCGA
240 ------------------------------------------------------------
NR_046654 119 ------------------------------------------------------------
chr3 42531192 AATACAcagggccactgctaatctataaagggcctctgtcacaattagaaagagaatgtc
300 ------------------------------------------------------------
NR_046654 119 ------------------------------------------------------------
chr3 42531252 cgtctaggtagacacagcccttcaggcatacagcttCACCCCCTCAGTGGAGCATCCCTC
360 ------------------------------------------------------------
NR_046654 119 ------------------------------------------------------------
chr3 42531312 CGTGGTGAACAACCTATGCAACCAAAGACAGCAGACTGACAACCCACCCTTTtctctctc
420 ------------------------------------------------------------
NR_046654 119 ------------------------------------------------------------
chr3 42531372 cctccctctccctgcttttctccaaaatctctccctcatgccctctacccctgcttcctg
480 ------------------------------------------------------------
NR_046654 119 ------------------------------------------------------------
chr3 42531432 tgccctctctgctctttcactctccctGGGCCTGACAGGGGTACCCAGCACATTCACCAT
540 ------------------------------------------------------------
NR_046654 119 ------------------------------------------------------------
chr3 42531492 GGTGTGGACCATCGCCAGGATCCATTTTGAGGATTATGGGTGAGCTGCTGCCCCACACAC
600 ------------------------------------------------------------
NR_046654 119 ------------------------------------------------------------
chr3 42531552 TCCCCCGGCCGCCATCACTTGGGCAGGCCCCCTGGGTGGGATGATAATGCCATCTGGCCT
660 ------------------------------------------------------------
NR_046654 119 ------------------------------------------------------------
chr3 42531612 TGGTGAGTGGACAAAAACCACAGCTCTCGGGCCAGAGGGGAGGCTGGAGGAGGACCTGGG
720 ------------------------------------------------------------
NR_046654 119 ------------------------------------------------------------
chr3 42531672 GAGCAACAGACTCTGGGCCCGGGGTTGCTAAAGTGCTCAGGAGCAGAGCTGGGGACAACT
780 ------------------------------------------------------------
NR_046654 119 ------------------------------------------------------------
chr3 42531732 GGGGGAGGTGCTGCTGAGTCTCTCTCTGGCTGAGGACAATCCCTCTCATTCCTCCCCACG
840 ------------------------------------------------------------
NR_046654 119 ------------------------------------------------------------
chr3 42531792 GTCTGCTCAGGTGCTGGGACACCATCAACTCCTCACTGTGGTGGATCATAAAGGGCCCCA
900 ------------------------------------------------------------
NR_046654 119 ------------------------------------------------------------
chr3 42531852 TCCTCACCTCCATCTTGGTAAGATaccctcccaccacctagagatggggaaacaggccca
960 ------------------------------------------------------------
NR_046654 119 ------------------------------------------------------------
chr3 42531912 aagggcaggcaacttagcccaaggtcacatgggaaattagtatctaggtcagaactgaaa
1020 ------------------------------------------------------------
NR_046654 119 ------------------------------------------------------------
chr3 42531972 cgtagcttcctaatgcccaatgcaggatcatccccacccctgtcctaccagTTCTTCCTT
1080 ------------------------------------------------...|||||||||
NR_046654 119 ------------------------------------------------CAGTTCTTCCTT
chr3 42532032 GAGCGTAAGCGGATTGGGAGCACAGTCCTTAGGGATTTGAAGGAGGTAGAGTTCCCGGAT
1140 |||||--|||||||||||.|||||||||||||||||||||||||||||||||||||||||
NR_046654 107 GAGCG--AGCGGATTGGGTGCACAGTCCTTAGGGATTTGAAGGAGGTAGAGTTCCCGGAT
chr3 42532092 GACCTGCCCAAAGGGGAAATGCCAGAGGAGAGGTAAGATAGAGAGAGGGGCAGCAGGACC
1200 |||---------------------------------------------------------
NR_046654 49 GAC---------------------------------------------------------
chr3 42532152 CTGGGAAAGAAGACAGGCCAGCAGTCAAGGGGCCTGAACACCTCAGCCTTCCCGCTCTGA
1260 ------------------------------------------------------------
NR_046654 46 ------------------------------------------------------------
chr3 42532212 CTGCCCGAACTCGGGTCCCCACCCACTAGGTAAACTTCATCCTGTTTATTTGCATCATCC
1320 ------------------------------------------------------------
NR_046654 46 ------------------------------------------------------------
chr3 42532272 GAATCCTGCTTCAGAAACTGCGGCCCCCAGATATCAGGAAGAGTGACAGCAGTCCATACT
1380 ------------------------------------------------------------
NR_046654 46 ------------------------------------------------------------
chr3 42532332 CGTGAGTGTGGGCCTAGTGCCTCAGCCCCCAGTACCTCCATCCCCAGTCCTCAAATCATC
1440 ------------------------------------------------------------
NR_046654 46 ------------------------------------------------------------
chr3 42532392 CCACATCTCCTTGAAGTCCTCCCACCCCAAACATCCAGAGTCACCAAAGAGCCACATTGT
1500 ------------------------------------------------------------
NR_046654 46 ------------------------------------------------------------
chr3 42532452 TCTTTCCCACCTCCACCATGGCCTGGCTcagcccaccaccatcccctgctccagccccac
1560 ------------------------------------------------------------
NR_046654 46 ------------------------------------------------------------
chr3 42532512 cctcaCCAGGCTGCACTCAGAGCCCTGCATGCTTCTCCTGCCCACACTCACCTAGCATCC
1620 ---------------------------------------------------|||||||||
NR_046654 46 ---------------------------------------------------CTAGCATCC
chr3 42532572 TTCCCAGGTATGCATCTGCTGCCAAGCCAGGgag 42532606
1680 |||||||||||||||||||||||||||||||... 1714
NR_046654 37 TTCCCAGGTATGCATCTGCTGCCAAGCCAGGGAG 3
""",
)
self.assertEqual(
format(alignment, "chain"),
"""\
chain 170 chr3 198295559 + 42530895 42532606 NR_046654.1_modified 190 - 5 187 2
27 0 3
36 1062 0
17 2 0
56 468 0
43
""",
)
counts = alignment.counts()
self.assertEqual(
repr(counts),
"<AlignmentCounts object (179 aligned letters; 172 identities; 7 mismatches; 1535 gaps) at 0x%x>"
% id(counts),
)
self.assertEqual(
str(counts),
"""\
AlignmentCounts object with
aligned = 179:
identities = 172,
mismatches = 7.
gaps = 1535:
left_gaps = 0:
left_insertions = 0:
open_left_insertions = 0,
extend_left_insertions = 0;
left_deletions = 0:
open_left_deletions = 0,
extend_left_deletions = 0;
internal_gaps = 1535:
internal_insertions = 3:
open_internal_insertions = 1,
extend_internal_insertions = 2;
internal_deletions = 1532:
open_internal_deletions = 3,
extend_internal_deletions = 1529;
right_gaps = 0:
right_insertions = 0:
open_right_insertions = 0,
extend_right_insertions = 0;
right_deletions = 0:
open_right_deletions = 0,
extend_right_deletions = 0.
""",
)
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, 3)
self.assertEqual(counts.internal_deletions, 1532)
self.assertEqual(counts.left_gaps, 0)
self.assertEqual(counts.right_gaps, 0)
self.assertEqual(counts.internal_gaps, 1535)
self.assertEqual(counts.insertions, 3)
self.assertEqual(counts.deletions, 1532)
self.assertEqual(counts.gaps, 1535)
self.assertEqual(counts.aligned, 179)
self.assertEqual(counts.identities, 172)
self.assertEqual(counts.mismatches, 7)
alignment = next(alignments)
self.assertEqual(alignment.shape, (2, 5407))
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.assertEqual(len(alignment.target.seq), 198295559)
self.assertEqual(len(alignment.query.seq), 216)
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
)
)
dna = Seq(self.dna, length=len(alignment.target.seq))
alignment.target.seq = 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.],
])
# fmt: on
)
)
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, "chain"),
"""\
chain 182 chr3 198295559 + 48663767 48669174 NR_111921.1 216 + 0 204 3
46 1827 0
82 3376 0
76
""",
)
counts = alignment.counts()
self.assertEqual(
repr(counts),
"<AlignmentCounts object (204 aligned letters; 165 identities; 39 mismatches; 5203 gaps) at 0x%x>"
% id(counts),
)
self.assertEqual(
str(counts),
"""\
AlignmentCounts object with
aligned = 204:
identities = 165,
mismatches = 39.
gaps = 5203:
left_gaps = 0:
left_insertions = 0:
open_left_insertions = 0,
extend_left_insertions = 0;
left_deletions = 0:
open_left_deletions = 0,
extend_left_deletions = 0;
internal_gaps = 5203:
internal_insertions = 0:
open_internal_insertions = 0,
extend_internal_insertions = 0;
internal_deletions = 5203:
open_internal_deletions = 2,
extend_internal_deletions = 5201;
right_gaps = 0:
right_insertions = 0:
open_right_insertions = 0,
extend_right_insertions = 0;
right_deletions = 0:
open_right_deletions = 0,
extend_right_deletions = 0.
""",
)
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.shape, (2, 5409))
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.assertEqual(len(alignment.target.seq), 198295559)
self.assertEqual(len(alignment.query.seq), 220)
self.assertTrue(
np.array_equal(
alignment.coordinates,
# fmt: off
np.array([[48663767, 48663795, 48663796, 48663813, 48665640,
48665716, 48665716, 48665722, 48669098, 48669174],
[ 3, 31, 31, 48, 48,
124, 126, 132, 132, 208]
])
# fmt: on
)
)
dna = Seq(self.dna, length=len(alignment.target))
alignment.target.seq = 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., 34., 0., 0., 0., 0., 0., 0.],
[ 0., 2., 48., 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.],