def test_N_id(self):
self.tra.id = 'N'
bpp_list = _convert_tool_row(_parse_vcf_record(self.tra)[0], SUPPORTED_TOOL.VCF, False)
self.assertEqual(1, len(bpp_list))
bpp = bpp_list[0]
self.assertTrue(bpp.data[COLUMNS.tracking_id])
self.assertNotEqual('N', 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)
self.assertEqual(1, len(bpp_list))
bpp = bpp_list[0]
self.assertEqual('1', bpp.break1.chr)
self.assertEqual('1', bpp.break2.chr)
self.assertEqual(17051724, bpp.break1.start)
self.assertEqual(234912188, bpp.break2.start)
self.assertEqual('R', bpp.break1.orient)
self.assertEqual('R', bpp.break2.orient)
self.assertEqual('manta-MantaBND:207:0:1:0:0:0:1', bpp.tracking_id)
self.assertEqual(1, len(bpp_list))
def test_no_ci(self):
bpp_list = _convert_tool_row(_parse_vcf_record(self.tra)[0], SUPPORTED_TOOL.VCF, False)
self.assertEqual(1, len(bpp_list))
bpp = bpp_list[0]
self.assertEqual(21673582, bpp.break1.start)
self.assertEqual(21673582, bpp.break1.end)
self.assertEqual(58921502, bpp.break2.start)
self.assertEqual(58921502, bpp.break2.end)
def test_precise_flag_ignores_ci(self):
self.tra.info.update({'CIEND': [-700, 700], 'CIPOS': [-700, 700], 'PRECISE': True})
bpp_list = _convert_tool_row(_parse_vcf_record(self.tra)[0], SUPPORTED_TOOL.VCF, False)
self.assertEqual(1, len(bpp_list))
bpp = bpp_list[0]
self.assertEqual(21673582, bpp.break1.start)
self.assertEqual(21673582, bpp.break1.end)
self.assertEqual(58921502, bpp.break2.start)
self.assertEqual(58921502, bpp.break2.end)
def test_ci(self):
self.tra.info.update({'CIEND': [-700, 700], 'CIPOS': [-700, 700]})
bpp_list = _convert_tool_row(_parse_vcf_record(self.tra)[0], SUPPORTED_TOOL.VCF, False)
self.assertEqual(1, len(bpp_list))
bpp = bpp_list[0]
print(bpp)
self.assertEqual(21673582 - 700, bpp.break1.start)
self.assertEqual(21673582 + 700, bpp.break1.end)
self.assertEqual(58921502 - 700, bpp.break2.start)
self.assertEqual(58921502 + 700, bpp.break2.end)
def testMalformated(self):
event = Mock(
chrom='1',
pos=53678660,
id=None,
info={'SVTYPE': 'BND'},
ref='C',
alts=('CTTTTAAATGTAACATGACATAATATATTTCCTAAATAATTTAAAATAATC.',),
stop=53678660,
)
with self.assertRaises(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)
self.assertEqual(1, len(bpp_list))
bpp = bpp_list[0]
self.assertEqual(724986, bpp.break1.start)
self.assertEqual(724986, bpp.break1.end)
self.assertEqual(724986, bpp.break2.start)
self.assertEqual(724986, bpp.break2.end)
self.assertEqual(SVTYPE.INS, bpp.event_type)
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)
self.assertEqual(1, len(bpp_list))
bpp = bpp_list[0]
self.assertEqual('1', bpp.break1.chr)
self.assertEqual(247760043 - 10, bpp.break1.start)
self.assertEqual(247760043 + 10, bpp.break1.end)
self.assertEqual(ORIENT.LEFT, bpp.break1.orient)
self.assertEqual(STRAND.NS, bpp.break1.strand)
self.assertEqual(247760044 - 10, bpp.break2.start)
self.assertEqual(247760044 + 10, bpp.break2.end)
self.assertEqual(ORIENT.RIGHT, bpp.break2.orient)
self.assertEqual(STRAND.NS, bpp.break2.strand)
self.assertEqual('1', bpp.break2.chr)
self.assertEqual(SVTYPE.INS, bpp.event_type)
self.assertEqual(None, bpp.untemplated_seq)
bpp_list = _convert_tool_row(
_parse_vcf_record(row)[0], SUPPORTED_TOOL.DELLY, False, assume_no_untemplated=True
)
self.assertEqual(1, len(bpp_list))
bpp = bpp_list[0]
self.assertEqual(None, bpp.untemplated_seq)
self.assertNotEqual('', 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)
self.assertEqual(1, len(bpp_list))
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)
self.assertEqual(4, len(bpp_list))
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)
self.assertEqual(1, len(bpp_list))
bpp = bpp_list[0]
self.assertEqual('1', bpp.break1.chr)
self.assertEqual('1', bpp.break2.chr)
self.assertEqual('manta-MantaDUP:TANDEM:22477:0:1:0:9:0', bpp.tracking_id)
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)
self.assertEqual(1, len(bpp_list))
bpp = bpp_list[0]
self.assertEqual(1265353, bpp.break1.start)
self.assertEqual(1265353, bpp.break1.end)
self.assertEqual(1265366, bpp.break2.start)
self.assertEqual(1265366, bpp.break2.end)
self.assertEqual(SVTYPE.DEL, bpp.event_type)
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)
self.assertEqual(2, len(bpp_list))
bpp = sorted(bpp_list, key=lambda x: x.break1)[0]
self.assertEqual('21', bpp.break1.chr)
self.assertEqual('21', bpp.break2.chr)
self.assertEqual(SVTYPE.INV, bpp.event_type)
self.assertEqual(row.pos, bpp.break1.start)
self.assertEqual(row.pos, bpp.break1.end)
self.assertEqual(row.stop, bpp.break2.start)
self.assertEqual(row.stop, bpp.break2.end)
self.assertEqual(ORIENT.LEFT, bpp.break1.orient)
self.assertEqual(STRAND.NS, bpp.break1.strand)
self.assertEqual(ORIENT.LEFT, bpp.break2.orient)
self.assertEqual(STRAND.NS, bpp.break2.strand)
self.assertEqual(False, bpp.stranded)
self.assertEqual(True, bpp.opposing_strands)
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)
self.assertEqual(1, len(bpp_list))
bpp = bpp_list[0]
self.assertEqual('21', bpp.break1.chr)
self.assertEqual('21', bpp.break2.chr)
self.assertEqual(SVTYPE.DEL, bpp.event_type)
self.assertEqual(row.pos, bpp.break1.start)
self.assertEqual(row.pos, bpp.break1.end)
self.assertEqual(row.stop, bpp.break2.start)
self.assertEqual(row.stop, bpp.break2.end)
self.assertEqual(ORIENT.LEFT, bpp.break1.orient)
self.assertEqual(STRAND.NS, bpp.break1.strand)
self.assertEqual(ORIENT.RIGHT, bpp.break2.orient)
self.assertEqual(STRAND.NS, bpp.break2.strand)
self.assertEqual(False, bpp.stranded)
self.assertEqual(False, bpp.opposing_strands)
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)
self.assertEqual(1, len(bpp_list))
bpp = bpp_list[0]
self.assertEqual('21', bpp.break1.chr)
self.assertEqual(9412306, bpp.break1.start)
self.assertEqual(9412310, bpp.break1.end)
self.assertEqual(9412400, bpp.break2.start)
self.assertEqual(9412404, bpp.break2.end)
self.assertEqual('21', bpp.break2.chr)
print(bpp, bpp.tracking_id)
self.assertEqual('manta-MantaDEL:20644:0:2:0:0:0', bpp.tracking_id)
def test_id_given(self):
self.tra.id = 'thing-1'
bpp_list = _convert_tool_row(_parse_vcf_record(self.tra)[0], SUPPORTED_TOOL.VCF, False)
self.assertEqual(1, len(bpp_list))
bpp = bpp_list[0]
self.assertEqual('vcf-thing-1', bpp.data[COLUMNS.tracking_id])
