def test___contains__(self):
self.assertTrue(Interval(1, 2) in Interval(1, 7))
self.assertFalse(Interval(1, 7) in Interval(1, 2))
self.assertTrue(Interval(1.0, 2) in Interval(1.0, 7))
self.assertFalse(Interval(1, 7) in Interval(1, 2))
self.assertTrue(1 in Interval(1, 7))
self.assertFalse(0 in Interval(1, 7))
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___contains__(self):
assert Interval(1, 2) in Interval(1, 7)
assert not Interval(1, 7) in Interval(1, 2)
assert Interval(1.0, 2) in Interval(1.0, 7)
assert not Interval(1, 7) in Interval(1, 2)
assert 1 in Interval(1, 7)
assert 0 not in Interval(1, 7)
def test_convert_pos_one_to_one(self):
mapping = {}
for x in range(0, 10):
s = x * 10 + 1
mapping[Interval(s, s + 9)] = Interval(s, s + 9)
for pos in range(1, 101):
assert Interval.convert_pos(mapping, pos) == pos
def test_net_zero(self):
bpp = BreakpointPair(Breakpoint('1', 1099, orient=ORIENT.LEFT),
Breakpoint('1', 1302, orient=ORIENT.RIGHT),
untemplated_seq='TT')
dist = partial(TranscriptomeEvidence.distance, self.trans_evidence)
self.assertEqual(Interval(-200), bpp.net_size())
self.assertEqual(Interval(0), bpp.net_size(dist))
def test_inversion_and_deletion(self):
s = 'CTGAGCATGAAAGCCCTGTAAACACAGAATTTGGATTCTTTCCTGTTTGGTTCCTGGTCGTGAGTGGCAGGTGCCATCATGTTTCATTCTGCCTGAGAGCAGTCTACCTAAATATATAGCTCTGCTCACAGTTTCCCTGCAATGCATAATTAAAATAGCACTATGCAGTTGCTTACACTTCAGATAATGGCTTCCTACATATTGTTGGTTATGAAATTTCAGGGTTTTCATTTCTGTATGTTAAT'
evidence = MockObject(
interchromosomal=False,
opposing_strands=True,
break1=MockObject(orient=ORIENT.RIGHT, chr='3'),
break2=MockObject(orient=ORIENT.RIGHT, chr='3'),
contigs=[MockObject(seq=s, alignments=set())],
standardize_read=lambda x: x,
contig_aln_max_event_size=DEFAULTS.contig_aln_max_event_size,
contig_aln_merge_inner_anchor=5,
contig_aln_merge_outer_anchor=DEFAULTS.contig_aln_merge_outer_anchor,
contig_aln_min_query_consumption=0.9,
contig_aln_min_extend_overlap=DEFAULTS.contig_aln_min_extend_overlap,
contig_aln_min_anchor_size=DEFAULTS.contig_aln_min_anchor_size,
contig_aln_min_score=DEFAULTS.contig_aln_min_score,
outer_window1=Interval(1000, 1200),
outer_window2=Interval(2000, 2200),
reference_genome=None,
bam_cache=mock.Mock(stranded=False)
)
read1 = SamRead(
reference_id=3, reference_start=1114, cigar=[(CIGAR.S, 125), (CIGAR.EQ, 120)], query_sequence=s,
is_reverse=False, reference_name='3', alignment_rank=0
)
read2 = SamRead(
reference_id=3, reference_start=2187, cigar=[(CIGAR.S, 117), (CIGAR.EQ, 8), (CIGAR.D, 1), (CIGAR.EQ, 120)],
query_sequence=reverse_complement(s), is_reverse=True, reference_name='3', alignment_rank=1
)
raw_alignments = {s: [read1, read2]}
align.select_contig_alignments(evidence, raw_alignments)
alignments = list(evidence.contigs[0].alignments)
self.assertEqual(2, len(alignments))
def test_net_zero(self):
transcript = PreTranscript([(1001, 1100), (1301, 1400), (1701, 1800)], strand=STRAND.POS)
for patt in transcript.generate_splicing_patterns():
transcript.transcripts.append(Transcript(transcript, patt))
trans_evidence = MockObject(
annotations={},
read_length=100,
max_expected_fragment_size=550,
call_error=11,
overlapping_transcripts={transcript},
)
setattr(
trans_evidence,
'_select_transcripts',
lambda *pos: trans_evidence.overlapping_transcripts,
)
setattr(
trans_evidence,
'distance',
partial(TranscriptomeEvidence.distance, trans_evidence),
)
bpp = BreakpointPair(
Breakpoint('1', 1099, orient=ORIENT.LEFT),
Breakpoint('1', 1302, orient=ORIENT.RIGHT),
untemplated_seq='TT',
)
dist = partial(TranscriptomeEvidence.distance, trans_evidence)
assert bpp.net_size() == Interval(-200)
assert bpp.net_size(dist) == Interval(0)
def test_intersection(self):
interval_list = [Interval(1, 10), Interval(5, 7), Interval(7)]
self.assertEqual(Interval(7), Interval.intersection(*interval_list))
interval_list.append(Interval(11))
self.assertEqual(None, Interval.intersection(*interval_list))
with self.assertRaises(AttributeError):
Interval.intersection()
def test_merge_large_length(self):
i1 = Interval(1001, 5003)
result = merge_integer_intervals(i1, i1, weight_adjustment=25)
self.assertEqual(i1, result)
i1 = Interval(12856838, 12897006)
result = merge_integer_intervals(i1, i1, weight_adjustment=25)
self.assertEqual(i1, result)
def test_intersection(self):
interval_list = [Interval(1, 10), Interval(5, 7), Interval(7)]
assert Interval.intersection(*interval_list) == Interval(7)
interval_list.append(Interval(11))
assert Interval.intersection(*interval_list) is None
with pytest.raises(AttributeError):
Interval.intersection()
def test_convert_pos_one_to_one(self):
mapping = {}
for x in range(0, 10):
s = x * 10 + 1
mapping[Interval(s, s + 9)] = Interval(s, s + 9)
mapping = IntervalMapping(mapping)
for pos in range(1, 101):
self.assertEqual(pos, mapping.convert_pos(pos))
def test_reverse_reads(self, genomic_evidence, trans_evidence):
read, mate = mock_read_pair(
MockRead('name', '1', 1001, 1100, is_reverse=False),
MockRead('name', '1', 2201, 2301, is_reverse=True),
)
assert genomic_evidence.compute_fragment_size(read, mate) == Interval(1300)
assert genomic_evidence.compute_fragment_size(mate, read) == Interval(1300)
assert trans_evidence.compute_fragment_size(read, mate) == Interval(1300)
assert trans_evidence.compute_fragment_size(mate, read) == Interval(1300)
def test_deletion_in_exon(self):
bpp = BreakpointPair(Breakpoint('7', 55238890, orient=ORIENT.LEFT),
Breakpoint('7', 55238899, orient=ORIENT.RIGHT),
untemplated_seq='')
self.assertEqual(Interval(-8), bpp.net_size(self.egfr_distance))
bpp = BreakpointPair(Breakpoint('7', 55238890, orient=ORIENT.LEFT),
Breakpoint('7', 55238899, orient=ORIENT.RIGHT),
untemplated_seq='GTAC')
self.assertEqual(Interval(-4), bpp.net_size(self.egfr_distance))
def test_insertion(self):
bpp = BreakpointPair(Breakpoint('1', 11, orient=ORIENT.RIGHT),
Breakpoint('1', 10, orient=ORIENT.LEFT),
untemplated_seq='T')
self.assertEqual(Interval(1), bpp.net_size())
bpp = BreakpointPair(Breakpoint('1', 11, orient=ORIENT.RIGHT),
Breakpoint('1', 10, orient=ORIENT.LEFT),
untemplated_seq='TT')
self.assertEqual(Interval(2), bpp.net_size())
def test_dist(self):
x = Interval(1, 4)
y = Interval(-1, 0)
z = Interval(0, 3)
assert Interval.dist(x, y) == 1
assert Interval.dist(y, x) == -1
assert Interval.dist(x, z) == 0
assert Interval.dist(z, x) == 0
assert Interval.dist(y, z) == 0
assert Interval.dist(z, y) == 0
assert Interval.dist((1, 4), (10, 12)) == -6
def test_dist(self):
x = Interval(1, 4)
y = Interval(-1, 0)
z = Interval(0, 3)
self.assertEqual(1, Interval.dist(x, y))
self.assertEqual(-1, Interval.dist(y, x))
self.assertEqual(0, Interval.dist(x, z))
self.assertEqual(0, Interval.dist(z, x))
self.assertEqual(0, Interval.dist(y, z))
self.assertEqual(0, Interval.dist(z, y))
self.assertEqual(-6, Interval.dist((1, 4), (10, 12)))
def test_deletion_across_intron(self):
# 55240539_55240621 55323947_55324313
bpp = BreakpointPair(Breakpoint('7', 55240610, orient=ORIENT.LEFT),
Breakpoint('7', 55323950, orient=ORIENT.RIGHT),
untemplated_seq='GTAC')
self.assertEqual(Interval(-10), bpp.net_size(self.egfr_distance))
# 55210998_55211181 55218987_55219055
bpp = BreakpointPair(Breakpoint('7', 55211180, orient=ORIENT.LEFT),
Breakpoint('7', 55218990, orient=ORIENT.RIGHT),
untemplated_seq='')
self.assertEqual(Interval(-4 + -135, -4),
bpp.net_size(self.egfr_distance))
def test_reverse_reads(self):
read, mate = mock_read_pair(
MockRead('name', '1', 1001, 1100, is_reverse=False),
MockRead('name', '1', 2201, 2301, is_reverse=True))
self.assertEqual(Interval(1300),
self.genomic_ev.compute_fragment_size(read, mate))
self.assertEqual(Interval(1300),
self.genomic_ev.compute_fragment_size(mate, read))
self.assertEqual(Interval(1300),
self.trans_ev.compute_fragment_size(read, mate))
self.assertEqual(Interval(1300),
self.trans_ev.compute_fragment_size(mate, read))
def test_convert_pos_ratioed_intervals(self):
mapping = {
(1.0, 100): (1, 20.0),
(101.0, 500): (21.0, 30),
(501.0, 600): (31.0, 51),
(601.0, 900): (52, 57.0),
(901.0, 1100): (58.0, 100)
}
self.assertEqual(Interval(1), Interval.convert_ratioed_pos(mapping, 1))
self.assertEqual(Interval(20),
Interval.convert_ratioed_pos(mapping, 100))
self.assertEqual(Interval(100, 100),
Interval.convert_ratioed_pos(mapping, 1100))
mapping = {(1, 100): (1, 1), (101, 500): (21, 30)}
self.assertEqual(Interval(1, 1),
Interval.convert_ratioed_pos(mapping, 1))
self.assertEqual(Interval(1, 1),
Interval.convert_ratioed_pos(mapping, 100))
mapping = {(1, 100.0): (20.0, 30), (100.1, 500): (1.0, 1.0)}
self.assertEqual(Interval(1, 1),
Interval.convert_ratioed_pos(mapping, 101))
self.assertEqual(Interval(1, 1),
Interval.convert_ratioed_pos(mapping, 500))
self.assertEqual(Interval(25, 25),
Interval.convert_ratioed_pos(mapping, 50))
def test_generate_gene_mapping_err(self):
# _generate_interval_mapping [genomic.IntergenicRegion(11:77361962_77361962+)] 1181.39453125 5 30 None 77356962 77366962)
ir = genomic.IntergenicRegion('11', 5000, 5000, STRAND.POS)
tgt_width = 1000
d = DiagramSettings()
d.gene_min_buffer = 10
# (self, canvas, gene, width, height, fill, label='', reference_genome=None)
draw_genes(d, self.canvas, [ir], tgt_width, [])
# _generate_interval_mapping ['Interval(29684391, 29684391)', 'Interval(29663998, 29696515)'] 1181.39453125 5 60 None 29662998 29697515
# def generate_interval_mapping(cls, input_intervals, target_width, ratio, min_width, buffer_length=None, start=None, end=None, min_inter_width=None)
itvls = [Interval(29684391, 29684391), Interval(29663998, 29696515)]
generate_interval_mapping(itvls, 1181.39, 5, 60, None, 29662998,
29697515)
def test_split_overlapping_no_weight(self):
input_intervals = [Interval(1, 10), Interval(2, 11), Interval(4, 5), Interval(4, 8)]
exp = [
Interval(1, 1),
Interval(2, 3),
Interval(4, 4),
Interval(5, 7),
Interval(8, 9),
Interval(10, 11),
]
print('expected', exp)
result = Interval.split_overlap(*input_intervals)
result = sorted(result)
print('found', result)
self.assertEqual(exp, result)
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_deletion_in_exon(self, egfr_evidence):
bpp = BreakpointPair(
Breakpoint('7', 55238890, orient=ORIENT.LEFT),
Breakpoint('7', 55238899, orient=ORIENT.RIGHT),
untemplated_seq='',
)
assert bpp.net_size(lambda p1, p2: TranscriptomeEvidence.distance(
egfr_evidence, p1, p2)) == Interval(-8)
bpp = BreakpointPair(
Breakpoint('7', 55238890, orient=ORIENT.LEFT),
Breakpoint('7', 55238899, orient=ORIENT.RIGHT),
untemplated_seq='GTAC',
)
assert bpp.net_size(lambda p1, p2: TranscriptomeEvidence.distance(
egfr_evidence, p1, p2)) == Interval(-4)
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_single_bp_dup(self):
transcript = fusion.FusionTranscript()
transcript.position = Interval(1, 500)
transcript.exons = [
genomic.Exon(1, 7, transcript=transcript, intact_end_splice=False),
genomic.Exon(8,
8,
transcript=transcript,
intact_start_splice=False,
intact_end_splice=False),
genomic.Exon(9,
100,
transcript=transcript,
intact_start_splice=False),
genomic.Exon(200, 500, transcript=transcript),
]
cfg = DiagramSettings(width=1500)
canvas = Drawing(size=(cfg.width, 1000))
drawing_width = cfg.width - cfg.label_left_margin - cfg.left_margin - cfg.right_margin
canvas.add(
draw_ustranscript(cfg,
canvas,
transcript,
target_width=drawing_width))
if OUTPUT_SVG:
canvas.saveas('test_single_bp_dup.svg')
def test_single_bp_ins_exon(self):
transcript = fusion.FusionTranscript()
transcript.position = Interval(401258, 408265)
transcript.exons = [
genomic.Exon(401258, 401461, transcript=transcript),
genomic.Exon(404799,
405254,
intact_end_splice=False,
transcript=transcript),
genomic.Exon(
405255,
405255,
intact_start_splice=False,
intact_end_splice=False,
transcript=transcript,
),
genomic.Exon(405256,
408265,
intact_start_splice=False,
transcript=transcript),
]
cfg = DiagramSettings(width=1500)
canvas = Drawing(size=(cfg.width, 1000))
drawing_width = cfg.width - cfg.label_left_margin - cfg.left_margin - cfg.right_margin
canvas.add(
draw_ustranscript(cfg,
canvas,
transcript,
target_width=drawing_width))
if OUTPUT_SVG:
canvas.saveas('test_single_bp_ins_exon.svg')
