def test_blat_contigs(self):
ev = GenomeEvidence(
Breakpoint('reference3', 1114, orient=ORIENT.RIGHT),
Breakpoint('reference3', 2187, orient=ORIENT.RIGHT),
opposing_strands=True,
bam_cache=BAM_CACHE,
reference_genome=REFERENCE_GENOME,
read_length=40,
stdev_fragment_size=25,
median_fragment_size=100,
stdev_count_abnormal=2,
min_splits_reads_resolution=1,
min_flanking_pairs_resolution=1
)
ev.contigs = [
Contig(
'CTGAGCATGAAAGCCCTGTAAACACAGAATTTGGATTCTTTCCTGTTTGGTTCCTGGTCGTGAGTGGCAGGTGCCATCATGTTTCATTCTGCCTGAGAGCAG'
'TCTACCTAAATATATAGCTCTGCTCACAGTTTCCCTGCAATGCATAATTAAAATAGCACTATGCAGTTGCTTACACTTCAGATAATGGCTTCCTACATATTG'
'TTGGTTATGAAATTTCAGGGTTTTCATTTCTGTATGTTAAT', 0)
]
print(ev.contigs[0].seq)
seq = align.align_sequences({'seq': ev.contigs[0].seq}, BAM_CACHE, REFERENCE_GENOME, aligner_reference=get_data('mock_reference_genome.2bit'), aligner='blat')
print(seq)
align.select_contig_alignments(ev, seq)
print(ev.contigs[0].alignments)
alignment = list(ev.contigs[0].alignments)[0]
self.assertEqual(1, alignment.read1.reference_id)
self.assertEqual(1, alignment.read2.reference_id)
self.assertEqual(Interval(125, 244), align.query_coverage_interval(alignment.read1))
self.assertEqual(Interval(117, 244), align.query_coverage_interval(alignment.read2))
self.assertEqual(1114, alignment.read1.reference_start)
self.assertEqual(2187, alignment.read2.reference_start)
self.assertEqual([(CIGAR.S, 125), (CIGAR.EQ, 120)], alignment.read1.cigar)
self.assertEqual([(CIGAR.S, 117), (CIGAR.EQ, 128)], alignment.read2.cigar)
def test_bwa_contigs(self):
ev = GenomeEvidence(
Breakpoint('reference3', 1114, orient=ORIENT.RIGHT),
Breakpoint('reference3', 2187, orient=ORIENT.RIGHT),
opposing_strands=True,
bam_cache=BAM_CACHE,
reference_genome=REFERENCE_GENOME,
read_length=40,
stdev_fragment_size=25,
median_fragment_size=100,
config={
'validate.stdev_count_abnormal': 2,
'validate.min_splits_reads_resolution': 1,
'validate.min_flanking_pairs_resolution': 1,
},
)
ev.contigs = [
Contig(
'CTGAGCATGAAAGCCCTGTAAACACAGAATTTGGATTCTTTCCTGTTTGGTTCCTGGTCGTGAGTGGCAGGTGCCATCATGTTTCATTCTGCCTGAGAGCAG'
'TCTACCTAAATATATAGCTCTGCTCACAGTTTCCCTGCAATGCATAATTAAAATAGCACTATGCAGTTGCTTACACTTCAGATAATGGCTTCCTACATATTG'
'TTGGTTATGAAATTTCAGGGTTTTCATTTCTGTATGTTAAT',
0,
)
]
print(ev.contigs[0].seq)
seq = align.align_sequences(
{'seq': ev.contigs[0].seq},
BAM_CACHE,
REFERENCE_GENOME,
aligner_reference=get_data('mock_reference_genome.fa'),
aligner='bwa mem',
aligner_output_file='mem.out',
aligner_fa_input_file='mem.in.fa',
)
align.select_contig_alignments(ev, seq)
print(ev.contigs[0].alignments)
alignment = list(ev.contigs[0].alignments)[0]
assert alignment.read2.query_sequence == reverse_complement(alignment.read1.query_sequence)
assert alignment.read1.reference_name == 'reference3'
assert alignment.read2.reference_name == 'reference3'
assert alignment.read1.reference_id == 1
assert alignment.read2.reference_id == 1
assert align.query_coverage_interval(alignment.read1) == Interval(125, 244)
assert align.query_coverage_interval(alignment.read2) == Interval(117, 244)
assert alignment.read1.reference_start == 1114
assert alignment.read2.reference_start == 2187
assert alignment.read1.cigar == [(CIGAR.S, 125), (CIGAR.EQ, 120)]
assert alignment.read2.cigar == [(CIGAR.S, 117), (CIGAR.EQ, 128)]
def test_pslx_row_to_pysam_single_block(self):
pslx_row = {
'score':
20,
'tseqs': ['AATACCAAATACATGATATA'],
'tstarts': [3432307],
'tstart':
3432307,
'block_sizes': [20],
'qname':
'seq1',
'tname':
'Y',
'qstarts': [93],
'strand':
'+',
'qseqs': ['AATACCATACATGATATA'],
'percent_ident':
100.0,
'qseq_full':
'AGCCTCCCAAGTAGCTGGGACTACAGGCGCCCGCCACTACGCCCGGCTAATTTTTTGTATTTTTAGTAGAGACGGGGTTTCACCGTTTT'
'AGCCAGGATGGTCTCGATCTCCTGACCTCATGATCCGCCCGCCTCGGC',
}
read = Blat.pslx_row_to_pysam(pslx_row, self.cache, None)
self.assertEqual(23, read.reference_id)
self.assertEqual(Interval(93, 112), query_coverage_interval(read))
def test_pslx_row_to_pysam_duplication(self):
reference = {
'14':
MockObject(seq=MockLongString(
'TTCTTCCATGCCCCCTAATCATGGCCACATTGTATCAGCCTGAGCATGAGCAACAGCACCATGGCCACATACGGGAATGGGCCTCATTGGTGTAATATTTGGCAGATTCTCTCCACACCCCCCGTGGCGGTCTGGCTTACTGTTAAGAAGGGTAACCTTAAAAAATACATTTCCCACTCCAGAAAATACTCATATGTGGCCTGTTAGCAGCACAAGAAGGGTGAAAGCAATGCCCATTCCTGCCTCCCTCCCCCTGCTCACCTCCACGTCCCTGTTTGCCCCTTTGTAGGTGAAGTGAGTATATTCAGCGTCTTCATGGCAGGGGAGAGGGTGTATTAATCCGTCTATGTCCGCTGGAAAGGCAGTCTCTGAGCGGGCCACAAGGGTTCAGCCATGGCCCATCCAATAACCTTTTTGATGACTTGGATGAAGAGACAAACATTCCAACCACATTCAAAGATCCAGACCTCCAAAGTGTGGCTCATTTGGTAGATAATGGAATTATATTTGGAAAGCATTTCCCGCAGCTGGGATGATGGGTCAAAAACAGATAGCATTTTACCAGATCATATTTGTGTGTGTGTGTGTGCGCGCGTGTGTGTGTGTGTGTGTGTGTGTTTTAAATTCAGTTTCCCAACTACAGGATG',
offset=73014463,
))
}
pslx_row = {
'block_count': 2,
'tstarts': [73014606, 73014747],
'block_sizes': [141, 30],
'qname': '',
'tname': '14',
'qstarts': [0, 239],
'strand': '+',
'qseq_full':
'AAGAAGGGTAACCTTAAAAAATACATTTCCCACTCCAGAAAATACTCATATGTGGCCTGTTAGCAGCACAAGAAGGGTGAAAGCAATGCCCATTCCTGCCTCCCTCCCCCTGCTCACCTCCACGTCCCTGTTTGCCCCTTTACTCATATGTGGCCTGTTAGCAGCACAAGAAGGGTGAAAGCAATGCCCATTCCTGCCTCCCTCCCCCTGCTCACCTCCACGTCCCTGTTTGCCCCTTTGTAGGTGAAGTGAGTATATTCAGCGTCTTC',
'score': 1,
}
read2 = Blat.pslx_row_to_pysam(pslx_row, self.cache, reference)
self.assertEqual(13, read2.reference_id)
self.assertEqual(73014606, read2.reference_start)
self.assertEqual([(CIGAR.M, 141), (CIGAR.I, 98), (CIGAR.M, 30)],
_cigar.convert_for_igv(read2.cigar))
self.assertEqual(Interval(0,
len(pslx_row['qseq_full']) - 1),
query_coverage_interval(read2))
def test_pslx_row_to_pysam_gapped_alignment_with_reference(self):
pslx_row = {
'block_count':
1,
'tstarts': [950, 7233],
'block_sizes': [47, 100],
'qname':
'seq1',
'tname':
'fake',
'qstarts': [0, 47],
'strand':
'+',
'qseq_full':
'ATCTAATAACTTGATCAATA'
'TCTGTGATTATATTTTCATT'
'GCCTTCC'
'AATTTTGCAGATTATAAGAT'
'CAATAGATATTTATTGTAAA'
'ATGCACAAATAGTGCAACAT'
'TTCTTAAAGTAGACCGTGAA'
'ATACTTCATGTTGCCATGTT',
'score':
1,
}
read = Blat.pslx_row_to_pysam(pslx_row, self.cache, REFERENCE_GENOME)
self.assertEqual(0, read.reference_id)
self.assertEqual(Interval(0, 146), query_coverage_interval(read))
self.assertEqual(950, read.reference_start)
self.assertEqual([(CIGAR.EQ, 53), (CIGAR.D, 6236), (CIGAR.EQ, 94)],
read.cigar)
def test_blat_contigs_deletion_revcomp(self):
ev = GenomeEvidence(Breakpoint('fake', 1714, orient=ORIENT.LEFT),
Breakpoint('fake', 2968, orient=ORIENT.RIGHT),
opposing_strands=False,
bam_cache=BAM_CACHE,
reference_genome=REFERENCE_GENOME,
read_length=40,
stdev_fragment_size=25,
median_fragment_size=100)
seq = 'GGTATATATTTCTCAGATAAAAGATATTTTCCCTTTTATCTTTCCCTAAGCTCACACTACATATATTGCATTTATCTTATATCTGCTTTAAAACCTATTTAT' \
'TATGTCATTTAAATATCTAGAAAAGTTATGACTTCACCAGGTATGAAAAATATAAAAAGAACTCTGTCAAGAAT'
ev.contigs = [Contig(reverse_complement(seq), 0)]
align.select_contig_alignments(
ev,
align.align_sequences({'seq': ev.contigs[0].seq},
BAM_CACHE,
REFERENCE_GENOME,
aligner_reference=REFERENCE_GENOME_FILE_2BIT,
aligner='blat'))
print('alignments:', ev.contigs[0].alignments)
alignment = list(ev.contigs[0].alignments)[0]
print(alignment)
self.assertTrue(alignment.read2 is None)
self.assertEqual(0, alignment.read1.reference_id)
self.assertTrue(alignment.read1.is_reverse)
self.assertEqual(seq, alignment.read1.query_sequence)
self.assertEqual(Interval(0, 175),
align.query_coverage_interval(alignment.read1))
self.assertEqual(1612, alignment.read1.reference_start)
self.assertEqual([(CIGAR.EQ, 102), (CIGAR.D, 1253), (CIGAR.EQ, 74)],
alignment.read1.cigar)
def test_blat_contigs_deletion(self):
ev = GenomeEvidence(
Breakpoint('fake', 1714, orient=ORIENT.LEFT),
Breakpoint('fake', 2968, orient=ORIENT.RIGHT),
opposing_strands=False,
bam_cache=BAM_CACHE,
reference_genome=REFERENCE_GENOME,
read_length=40,
stdev_fragment_size=25,
median_fragment_size=100
)
ev.contigs = [
Contig(
'GGTATATATTTCTCAGATAAAAGATATTTTCCCTTTTATCTTTCCCTAAGCTCACACTACATATATTGCATTTATCTTATATCTGCTTTAAAACCTATTTAT'
'TATGTCATTTAAATATCTAGAAAAGTTATGACTTCACCAGGTATGAAAAATATAAAAAGAACTCTGTCAAGAAT', 0)
]
seq = align.align_sequences({'seq': ev.contigs[0].seq}, BAM_CACHE, REFERENCE_GENOME, aligner_reference=get_data('mock_reference_genome.2bit'), aligner='blat')
for query, reads in seq.items():
print('>>>', query)
for read in reads:
print(repr(read))
align.select_contig_alignments(ev, seq)
alignments = list(ev.contigs[0].alignments)
print('alignments:')
for aln in alignments:
print(aln, repr(aln.read1), repr(aln.read2))
self.assertEqual(1, len(alignments))
alignment = alignments[0]
self.assertTrue(alignment.read2 is None)
self.assertEqual(0, alignment.read1.reference_id)
self.assertTrue(not alignment.read1.is_reverse)
self.assertEqual(Interval(0, 175), align.query_coverage_interval(alignment.read1))
self.assertEqual(1612, alignment.read1.reference_start)
self.assertEqual([(CIGAR.EQ, 102), (CIGAR.D, 1253), (CIGAR.EQ, 74)], alignment.read1.cigar)
def test_pslx_row_to_pysam_revcomp_deletion(self, cache):
pslx_row = {
'block_count':
2,
'tstarts': [2205, 2281],
'block_sizes': [50, 34],
'qname':
'seq1',
'tname':
'reference3',
'qstarts': [0, 50],
'strand':
'-',
'qseq_full':
'CTGAGCATGAAAGCCCTGTAAACACAGAATTTGGTGAGTGGCAGGTGCCATCATGTTTCATTCTGCCTGAGAGCAGTCTACCTA',
'score':
1,
'qseqs': [
'TAGGTAGACTGCTCTCAGGCAGAATGAAACATGATGGCACCTGCCACTCA',
'CCAAATTCTGTGTTTACAGGGCTTTCATGCTCAG',
],
'tseqs': [
'TAGGTAGACTGCTCTCAGGCAGAATGAAACATGATGGCACCTGCCACTCA',
'CCAAATTCTGTGTTTACAGGGCTTTCATGCTCAG',
],
}
read = Blat.pslx_row_to_pysam(pslx_row, cache, REFERENCE_GENOME)
assert read.reference_id == 3
assert query_coverage_interval(read) == Interval(0, 83)
assert read.reference_start == 2205
assert read.cigar == [(CIGAR.EQ, 51), (CIGAR.D, 26), (CIGAR.EQ, 33)]
assert read.query_sequence[
0:50] == 'TAGGTAGACTGCTCTCAGGCAGAATGAAACATGATGGCACCTGCCACTCA'
assert read.query_sequence[50:] == 'CCAAATTCTGTGTTTACAGGGCTTTCATGCTCAG'
def test_pslx_row_to_pysam_gapped_alignment(self, cache):
pslx_row = {
'block_count':
1,
'tstarts': [950, 7233],
'block_sizes': [47, 100],
'qname':
'seq1',
'tname':
'fake',
'qstarts': [0, 47],
'strand':
'+',
'qseq_full':
'ATCTAATAACTTGATCAATA'
'TCTGTGATTATATTTTCATT'
'GCCTTCC'
'AATTTTGCAGATTATAAGAT'
'CAATAGATATTTATTGTAAA'
'ATGCACAAATAGTGCAACAT'
'TTCTTAAAGTAGACCGTGAA'
'ATACTTCATGTTGCCATGTT',
'score':
1,
}
read = Blat.pslx_row_to_pysam(pslx_row, cache, None)
assert read.reference_id == 0
assert query_coverage_interval(read) == Interval(0, 146)
assert read.reference_start == 950
assert read.cigar == [(CIGAR.M, 47), (CIGAR.D, 6236), (CIGAR.M, 100)]
def test_pslx_row_to_pysam_full_reverse(self):
pslx_row = {
'match':
128,
'mismatch':
0,
'repmatch':
0,
'ncount':
0,
'qgap_count':
0,
'qgap_bases':
0,
'tgap_count':
0,
'tgap_bases':
0,
'strand':
'-',
'qname':
'seq1',
'tname':
'reference3',
'tsize':
3711,
'block_sizes': [128],
'qstarts': [117],
'tstarts': [2187],
'qseqs': [
'TGAGCAGAGCTATATATTTAGGTAGACTGCTCTCAGGCAGAATGAAACATGATGGCACCTGCCACTCACGACCAGGAACCAAACAGGAAAGAATCCAAATTCTGTGTTTACAGGGCTTTCATGCTCAG'
],
'tseqs': [
'TGAGCAGAGCTATATATTTAGGTAGACTGCTCTCAGGCAGAATGAAACATGATGGCACCTGCCACTCACGACCAGGAACCAAACAGGAAAGAATCCAAATTCTGTGTTTACAGGGCTTTCATGCTCAG'
],
'_index':
1,
'score':
128,
'percent_ident':
100.0,
'qseq_full':
'CTGAGCATGAAAGCCCTGTAAACACAGAATTTGGATTCTTTCCTGTTTGGTTCCTGGTCGTGAGTGGCAGGTGCCATCATGTTTCATTCTGCCTGAGAGCAGTCTACCTAAATATATAGCTCTGCTCACAGTTTCCCTGCAATGCATAATTAAAATAGCACTATGCAGTTGCTTACACTTCAGATAATGGCTTCCTACATATTGTTGGTTATGAAATTTCAGGGTTTTCATTTCTGTATGTTAAT',
}
read = Blat.pslx_row_to_pysam(pslx_row, self.cache, None)
self.assertEqual(3, read.reference_id)
self.assertEqual([(CIGAR.S, 117), (CIGAR.M, 128)], read.cigar)
self.assertEqual(2187, read.reference_start)
self.assertEqual(Interval(117, 244), query_coverage_interval(read))
def test_pslx_row_to_pysam_simple_with_reference(self):
pslx_row = {
'tstarts': [950],
'block_sizes': [53],
'qname':
'seq1',
'tname':
'fake',
'qstarts': [0],
'strand':
'+',
'score':
0,
'qseq_full':
'ATCTAATAACTTGATCAATA'
'TCTGTGATTATATTTTCATT'
'GCCTTCCAATTTT',
}
read = Blat.pslx_row_to_pysam(pslx_row, self.cache, REFERENCE_GENOME)
self.assertEqual(0, read.reference_id)
self.assertEqual(Interval(0, 52), query_coverage_interval(read))
self.assertEqual(950, read.reference_start)
self.assertEqual(1003, read.reference_end)
self.assertEqual([(CIGAR.EQ, 53)], read.cigar)
def test_pslx_row_to_pysam_simple_with_reference(self, cache):
pslx_row = {
'tstarts': [950],
'block_sizes': [53],
'qname':
'seq1',
'tname':
'fake',
'qstarts': [0],
'strand':
'+',
'score':
0,
'qseq_full':
'ATCTAATAACTTGATCAATA'
'TCTGTGATTATATTTTCATT'
'GCCTTCCAATTTT',
}
read = Blat.pslx_row_to_pysam(pslx_row, cache, REFERENCE_GENOME)
assert read.reference_id == 0
assert query_coverage_interval(read) == Interval(0, 52)
assert read.reference_start == 950
assert read.reference_end == 1003
assert read.cigar == [(CIGAR.EQ, 53)]
def test_pslx_row_to_pysam_revcomp_deletion(self):
pslx_row = {
'block_count':
2,
'tstarts': [2205, 2281],
'block_sizes': [50, 34],
'qname':
'seq1',
'tname':
'reference3',
'qstarts': [0, 50],
'strand':
'-',
'qseq_full':
'CTGAGCATGAAAGCCCTGTAAACACAGAATTTGGTGAGTGGCAGGTGCCATCATGTTTCATTCTGCCTGAGAGCAGTCTACCTA',
'score':
1,
'qseqs': [
'TAGGTAGACTGCTCTCAGGCAGAATGAAACATGATGGCACCTGCCACTCA',
'CCAAATTCTGTGTTTACAGGGCTTTCATGCTCAG'
],
'tseqs': [
'TAGGTAGACTGCTCTCAGGCAGAATGAAACATGATGGCACCTGCCACTCA',
'CCAAATTCTGTGTTTACAGGGCTTTCATGCTCAG'
]
}
read = Blat.pslx_row_to_pysam(pslx_row, self.cache, REFERENCE_GENOME)
self.assertEqual(3, read.reference_id)
self.assertEqual(Interval(0, 83), query_coverage_interval(read))
self.assertEqual(2205, read.reference_start)
self.assertEqual([(CIGAR.EQ, 51), (CIGAR.D, 26), (CIGAR.EQ, 33)],
read.cigar)
self.assertEqual('TAGGTAGACTGCTCTCAGGCAGAATGAAACATGATGGCACCTGCCACTCA',
read.query_sequence[0:50])
self.assertEqual('CCAAATTCTGTGTTTACAGGGCTTTCATGCTCAG',
read.query_sequence[50:])
def test_blat_contigs_deletion_revcomp(self):
ev = GenomeEvidence(
Breakpoint('fake', 1714, orient=ORIENT.LEFT),
Breakpoint('fake', 2968, orient=ORIENT.RIGHT),
opposing_strands=False,
bam_cache=BAM_CACHE,
reference_genome=REFERENCE_GENOME,
read_length=40,
stdev_fragment_size=25,
median_fragment_size=100,
)
seq = (
'GGTATATATTTCTCAGATAAAAGATATTTTCCCTTTTATCTTTCCCTAAGCTCACACTACATATATTGCATTTATCTTATATCTGCTTTAAAACCTATTTAT'
'TATGTCATTTAAATATCTAGAAAAGTTATGACTTCACCAGGTATGAAAAATATAAAAAGAACTCTGTCAAGAAT'
)
ev.contigs = [Contig(reverse_complement(seq), 0)]
align.select_contig_alignments(
ev,
align.align_sequences(
{'seq': ev.contigs[0].seq},
BAM_CACHE,
REFERENCE_GENOME,
aligner_reference=get_data('mock_reference_genome.2bit'),
aligner='blat',
),
)
print('alignments:', ev.contigs[0].alignments)
alignment = list(ev.contigs[0].alignments)[0]
print(alignment)
assert alignment.read2 is None
assert alignment.read1.reference_id == 0
assert alignment.read1.is_reverse
assert alignment.read1.query_sequence == seq
assert align.query_coverage_interval(alignment.read1) == Interval(0, 175)
assert alignment.read1.reference_start == 1612
assert alignment.read1.cigar == [(CIGAR.EQ, 102), (CIGAR.D, 1253), (CIGAR.EQ, 74)]
def test_pslx_row_to_pysam_inversion(self):
s = 'CTGAGCATGAAAGCCCTGTAAACACAGAATTTGGATTCTTTCCTGTTTGGTTCCTGGTCGTGAGTGGCAGGTGCCATCATGTTTCATTCTGCCTGAGAGCAGTCTACCTAAATATATAGCTCTGCTCACAGTTTCCCTGCAATGCATAATTAAAATAGCACTATGCAGTTGCTTACACTTCAGATAATGGCTTCCTACATATTGTTGGTTATGAAATTTCAGGGTTTTCATTTCTGTATGTTAAT'
# first part of the inversion
pslx_row = {
'block_count':
1,
'tstarts': [1114],
'block_sizes': [120],
'qname':
'seq1',
'tname':
'reference3',
'qstarts': [125],
'strand':
'+',
'qseq_full':
s,
'score':
1,
'qseqs': [
'TCACAGTTTCCCTGCAATGCATAATTAAAATAGCACTATGCAGTTGCTTACACTTCAGATAATGGCTTCCTACATATTGTTGGTTATGAAATTTCAGGG'
'TTTTCATTTCTGTATGTTAAT'
],
'tseqs': [
'TCACAGTTTCCCTGCAATGCATAATTAAAATAGCACTATGCAGTTGCTTACACTTCAGATAATGGCTTCCTACATATTGTTGGTTATGAAATTTCAGGG'
'TTTTCATTTCTGTATGTTAAT'
],
}
read1 = Blat.pslx_row_to_pysam(pslx_row, self.cache, REFERENCE_GENOME)
self.assertEqual(3, read1.reference_id)
self.assertEqual(Interval(125, 244), query_coverage_interval(read1))
self.assertEqual(1114, read1.reference_start)
self.assertEqual([(CIGAR.S, 125), (CIGAR.EQ, 120)], read1.cigar)
# second part of the inversion
pslx_row = {
'block_count':
1,
'tstarts': [2187],
'block_sizes': [128],
'qname':
'seq1',
'tname':
'reference3',
'qstarts': [117],
'strand':
'-',
'qseq_full':
s,
'score':
1,
'qseqs': [
'TGAGCAGAGCTATATATTTAGGTAGACTGCTCTCAGGCAGAATGAAACATGATGGCACCTGCCACTCACGACCAGGAACCAAACAGGAAAGAATCCAAAT'
'TCTGTGTTTACAGGGCTTTCATGCTCAG'
],
'tseqs': [
'TGAGCAGAGCTATATATTTAGGTAGACTGCTCTCAGGCAGAATGAAACATGATGGCACCTGCCACTCACGACCAGGAACCAAACAGGAAAGAATCCAAAT'
'TCTGTGTTTACAGGGCTTTCATGCTCAG'
],
}
read2 = Blat.pslx_row_to_pysam(pslx_row, self.cache, REFERENCE_GENOME)
self.assertEqual(3, read2.reference_id)
self.assertEqual(2187, read2.reference_start)
self.assertEqual([(CIGAR.S, 117), (CIGAR.EQ, 128)], read2.cigar)
self.assertEqual(Interval(117, 244), query_coverage_interval(read2))
self.assertEqual(read1.query_sequence,
reverse_complement(read2.query_sequence))
def query_coverage_interval(self):
return query_coverage_interval(self)
