def test_no_id(self, vcf_translocation):
bpp_list = _convert_tool_row(
_parse_vcf_record(vcf_translocation)[0], SUPPORTED_TOOL.VCF, False
)
assert len(bpp_list) == 1
bpp = bpp_list[0]
assert bpp.data[COLUMNS.tracking_id]
def test_non_trans_bnd_from_mate(self):
row = Mock(
chrom='chr1',
pos=234912188,
id='MantaBND:207:0:1:0:0:0:1',
info=dict(
SVTYPE='BND',
MATEID='MantaBND:207:0:1:0:0:0:0',
SVINSLEN=7,
SVINSSEQ='ATGGGGC',
BND_DEPTH=5,
MATE_BND_DEPTH=4,
),
ref='A',
alts=['[chr1:17051724[ATGGGGCA'],
)
vcf_list = _parse_vcf_record(row)
bpp_list = _convert_tool_row(vcf_list[0], SUPPORTED_TOOL.MANTA, False)
assert len(bpp_list) == 1
bpp = bpp_list[0]
assert bpp.break1.chr == '1'
assert bpp.break2.chr == '1'
assert bpp.break1.start == 17051724
assert bpp.break2.start == 234912188
assert bpp.break1.orient == 'R'
assert bpp.break2.orient == 'R'
assert bpp.data['tracking_id'] == 'manta-MantaBND:207:0:1:0:0:0:1'
assert len(bpp_list) == 1
def test_id_given(self, vcf_translocation):
vcf_translocation.id = 'thing-1'
bpp_list = _convert_tool_row(
_parse_vcf_record(vcf_translocation)[0], SUPPORTED_TOOL.VCF, False
)
assert len(bpp_list) == 1
bpp = bpp_list[0]
assert bpp.data[COLUMNS.tracking_id] == 'vcf-thing-1'
def test_no_ci(self, vcf_translocation):
bpp_list = _convert_tool_row(
_parse_vcf_record(vcf_translocation)[0], SUPPORTED_TOOL.VCF, False
)
assert len(bpp_list) == 1
bpp = bpp_list[0]
assert bpp.break1.start == 21673582
assert bpp.break1.end == 21673582
assert bpp.break2.start == 58921502
assert bpp.break2.end == 58921502
def test_precise_flag_ignores_ci(self, vcf_translocation):
vcf_translocation.info.update({'CIEND': [-700, 700], 'CIPOS': [-700, 700], 'PRECISE': True})
bpp_list = _convert_tool_row(
_parse_vcf_record(vcf_translocation)[0], SUPPORTED_TOOL.VCF, False
)
assert len(bpp_list) == 1
bpp = bpp_list[0]
assert bpp.break1.start == 21673582
assert bpp.break1.end == 21673582
assert bpp.break2.start == 58921502
assert bpp.break2.end == 58921502
def test_ci(self, vcf_translocation):
vcf_translocation.info.update({'CIEND': [-700, 700], 'CIPOS': [-700, 700]})
bpp_list = _convert_tool_row(
_parse_vcf_record(vcf_translocation)[0], SUPPORTED_TOOL.VCF, False
)
assert len(bpp_list) == 1
bpp = bpp_list[0]
print(bpp)
assert bpp.break1.start == 21673582 - 700
assert bpp.break1.end == 21673582 + 700
assert bpp.break2.start == 58921502 - 700
assert bpp.break2.end == 58921502 + 700
def testMalformated(self):
event = Mock(
chrom='1',
pos=53678660,
id=None,
info={'SVTYPE': 'BND'},
ref='C',
alts=('CTTTTAAATGTAACATGACATAATATATTTCCTAAATAATTTAAAATAATC.',),
stop=53678660,
)
with pytest.raises(NotImplementedError):
_convert_tool_row(_parse_vcf_record(event)[0], SUPPORTED_TOOL.STRELKA, False)
def testInsertion(self):
event = Mock(
chrom='1', pos=724986, id=None, info={}, ref='G', stop=724986, alts=('GGAATT',)
)
bpp_list = _convert_tool_row(_parse_vcf_record(event)[0], SUPPORTED_TOOL.STRELKA, False)
assert len(bpp_list) == 1
bpp = bpp_list[0]
assert bpp.break1.start == 724986
assert bpp.break1.end == 724986
assert bpp.break2.start == 724986
assert bpp.break2.end == 724986
assert bpp.event_type == SVTYPE.INS
def test_convert_insertion(self):
row = Mock(
chrom='1',
pos=247760043,
id='1DEL00000330',
info={
'SVTYPE': 'INS',
'CT': 'NtoN',
'CHR2': '1',
'CIEND': [-10, 10],
'CIPOS': [-10, 10],
},
stop=247760044,
alts=[],
)
bpp_list = _convert_tool_row(_parse_vcf_record(row)[0], SUPPORTED_TOOL.DELLY, False)
assert len(bpp_list) == 1
bpp = bpp_list[0]
assert bpp.break1.chr == '1'
assert bpp.break1.start == 247760043 - 10
assert bpp.break1.end == 247760043 + 10
assert bpp.break1.orient == ORIENT.LEFT
assert bpp.break1.strand == STRAND.NS
assert bpp.break2.start == 247760044 - 10
assert bpp.break2.end == 247760044 + 10
assert bpp.break2.orient == ORIENT.RIGHT
assert bpp.break2.strand == STRAND.NS
assert bpp.break2.chr == '1'
assert bpp.event_type == SVTYPE.INS
assert bpp.untemplated_seq is None
bpp_list = _convert_tool_row(
_parse_vcf_record(row)[0], SUPPORTED_TOOL.DELLY, False, assume_no_untemplated=True
)
assert len(bpp_list) == 1
bpp = bpp_list[0]
assert bpp.untemplated_seq is None
assert bpp.untemplated_seq != ''
def test_convert_convert_translocation(self):
row = Mock(
chrom='7',
pos=21673582,
id='TRA00016056',
info={
'SVTYPE': 'TRA',
'CT': '5to5',
'CIEND': [-700, 700],
'CIPOS': [-700, 700],
'CHR2': '2',
},
stop=58921502,
alts=[],
)
bpp_list = _convert_tool_row(_parse_vcf_record(row)[0], SUPPORTED_TOOL.DELLY, False)
for b in bpp_list:
print(b)
assert len(bpp_list) == 1
row.info['CT'] = 'NtoN'
bpp_list = _convert_tool_row(_parse_vcf_record(row)[0], SUPPORTED_TOOL.DELLY, False)
for b in bpp_list:
print(b)
assert len(bpp_list) == 4
def test_convert_duplication(self):
row = Mock(
chrom='1',
pos=224646602,
id='MantaDUP:TANDEM:22477:0:1:0:9:0',
info={'SVTYPE': 'DUP', 'SVINSSEQ': 'CAAAACTTACTATAGCAGTTCTGTGAGCTGCTCTAGC'},
stop=224800120,
alts=[],
)
bpp_list = _convert_tool_row(_parse_vcf_record(row)[0], SUPPORTED_TOOL.MANTA, False)
assert len(bpp_list) == 1
bpp = bpp_list[0]
assert bpp.break1.chr == '1'
assert bpp.break2.chr == '1'
assert bpp.data['tracking_id'] == 'manta-MantaDUP:TANDEM:22477:0:1:0:9:0'
def testDeletion(self):
event = Mock(
chrom='1',
pos=1265353,
id=None,
info={},
ref='GCGTGTGCCATGCA',
stop=1265366,
alts=('G',),
)
bpp_list = _convert_tool_row(_parse_vcf_record(event)[0], SUPPORTED_TOOL.STRELKA, False)
assert len(bpp_list) == 1
bpp = bpp_list[0]
assert bpp.break1.start == 1265353
assert bpp.break1.end == 1265353
assert bpp.break2.start == 1265366
assert bpp.break2.end == 1265366
assert bpp.event_type == SVTYPE.DEL
def test_convert_inversion(self):
row = Mock(chrom='21', pos=9412306, info={'SVTYPE': 'INV'}, stop=9412400, id=None, alts=[])
bpp_list = _convert_tool_row(_parse_vcf_record(row)[0], SUPPORTED_TOOL.PINDEL, False)
assert len(bpp_list) == 2
bpp = sorted(bpp_list, key=lambda x: x.break1)[0]
assert bpp.break1.chr == '21'
assert bpp.break2.chr == '21'
assert bpp.event_type == SVTYPE.INV
assert bpp.break1.start == row.pos
assert bpp.break1.end == row.pos
assert bpp.break2.start == row.stop
assert bpp.break2.end == row.stop
assert bpp.break1.orient == ORIENT.LEFT
assert bpp.break1.strand == STRAND.NS
assert bpp.break2.orient == ORIENT.LEFT
assert bpp.break2.strand == STRAND.NS
assert bpp.stranded is False
assert bpp.opposing_strands is True
def test_convert_deletion(self):
row = Mock(chrom='21', pos=9412306, info={'SVTYPE': 'DEL'}, stop=9412400, id=None, alts=[])
bpp_list = _convert_tool_row(_parse_vcf_record(row)[0], SUPPORTED_TOOL.PINDEL, False)
assert len(bpp_list) == 1
bpp = bpp_list[0]
assert bpp.break1.chr == '21'
assert bpp.break2.chr == '21'
assert bpp.event_type == SVTYPE.DEL
assert bpp.break1.start == row.pos
assert bpp.break1.end == row.pos
assert bpp.break2.start == row.stop
assert bpp.break2.end == row.stop
assert bpp.break1.orient == ORIENT.LEFT
assert bpp.break1.strand == STRAND.NS
assert bpp.break2.orient == ORIENT.RIGHT
assert bpp.break2.strand == STRAND.NS
assert bpp.stranded is False
assert bpp.opposing_strands is False
def test_convert_deletion(self):
row = Mock(
chrom='21',
pos=9412306,
id='MantaDEL:20644:0:2:0:0:0',
info={'SVTYPE': 'DEL', 'CIPOS': [0, 4], 'CIEND': [0, 4]},
stop=9412400,
alts=[],
)
bpp_list = _convert_tool_row(_parse_vcf_record(row)[0], SUPPORTED_TOOL.MANTA, False)
assert len(bpp_list) == 1
bpp = bpp_list[0]
assert bpp.break1.chr == '21'
assert bpp.break1.start == 9412306
assert bpp.break1.end == 9412310
assert bpp.break2.start == 9412400
assert bpp.break2.end == 9412404
assert bpp.break2.chr == '21'
print(bpp, bpp.data['tracking_id'])
assert bpp.data['tracking_id'] == 'manta-MantaDEL:20644:0:2:0:0:0'
