def test_malformed(self):
row = {
'FusionName': 'BCAS4--BCAS3',
'LeftBreakpoint': '',
'RightBreakpoint': None
}
with self.assertRaises(AssertionError):
_convert_tool_row(row, SUPPORTED_TOOL.STARFUSION, False)
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 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])
def test_inversion(self):
row = {
'Chr1': '1',
'Pos1': '13143396',
'Orientation1': '18+4-',
'Chr2': '1',
'Pos2': '13218683',
'Orientation2': '10+10-',
'Type': 'INV',
'Size': '74618',
'Score': '31',
'num_Reads': '2'
}
bpps = _convert_tool_row(row, SUPPORTED_TOOL.BREAKDANCER, False, True)
self.assertEqual(2, len(bpps))
self.assertEqual(SVTYPE.INV, bpps[0].event_type)
self.assertEqual(13143396, bpps[0].break1.start)
self.assertEqual(13143396, bpps[0].break1.end)
self.assertEqual(ORIENT.LEFT, bpps[0].break1.orient)
self.assertEqual(13218683, bpps[0].break2.start)
self.assertEqual(13218683, bpps[0].break2.end)
self.assertEqual(ORIENT.LEFT, bpps[0].break2.orient)
self.assertEqual(True, bpps[0].opposing_strands)
self.assertEqual(SVTYPE.INV, bpps[1].event_type)
self.assertEqual(13143396, bpps[1].break1.start)
self.assertEqual(13143396, bpps[1].break1.end)
self.assertEqual(ORIENT.RIGHT, bpps[1].break1.orient)
self.assertEqual(13218683, bpps[1].break2.start)
self.assertEqual(13218683, bpps[1].break2.end)
self.assertEqual(ORIENT.RIGHT, bpps[1].break2.orient)
self.assertEqual(True, bpps[1].opposing_strands)
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 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_stranded_translocation(self):
row = {
'strands': '+,-',
'rearrangement': 'translocation',
'breakpoint': '17:16342728|17:39766281',
'orientations': 'L,L',
'type': 'sense_fusion',
'_index': 5261,
'id': 1
}
bpp_list = _convert_tool_row(row, SUPPORTED_TOOL.TA, True)
self.assertEqual(2, len(bpp_list))
def test_convert_duplication(self):
row = {'event_type': 'duplication', 'coordinates': '1:1-10000'}
bpp_list = _convert_tool_row(row, SUPPORTED_TOOL.CNVNATOR, False)
self.assertEqual(1, len(bpp_list))
bpp = bpp_list[0]
self.assertEqual(1, bpp.break1.start)
self.assertEqual(1, bpp.break1.end)
self.assertEqual(10000, bpp.break2.start)
self.assertEqual(10000, bpp.break2.start)
self.assertEqual(SVTYPE.DUP, bpp.event_type)
self.assertEqual('1', bpp.break1.chr)
self.assertEqual('1', bpp.break2.chr)
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 test_convert_standard_event(self):
row = {
'FusionName': 'GAS6--RASA3',
'LeftBreakpoint': 'chr13:114529969:-',
'RightBreakpoint': 'chr13:114751269:-'
}
bpp_list = _convert_tool_row(row, SUPPORTED_TOOL.STARFUSION, True)
self.assertEqual(2, len(bpp_list))
bpp = bpp_list[0]
self.assertEqual('chr13', bpp.break1.chr)
self.assertEqual('chr13', bpp.break2.chr)
self.assertEqual(114529969, bpp.break1.start)
self.assertEqual(114751269, bpp.break2.start)
self.assertEqual(False, bpp.opposing_strands)
self.assertEqual(True, bpp.stranded)
def test_convert_translocation(self):
row = {
'FusionName': 'BCAS4--BCAS3',
'LeftBreakpoint': 'chr20:49411710:+',
'RightBreakpoint': 'chr17:59445688:+'
}
bpp_list = _convert_tool_row(row, SUPPORTED_TOOL.STARFUSION, True)
self.assertEqual(2, len(bpp_list))
bpp = bpp_list[0]
self.assertEqual('chr17', bpp.break1.chr)
self.assertEqual('chr20', bpp.break2.chr)
self.assertEqual(59445688, bpp.break1.start)
self.assertEqual(49411710, bpp.break2.start)
self.assertEqual(False, bpp.opposing_strands)
self.assertEqual(True, bpp.stranded)
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_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_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_indel_deletion(self):
row = {
'id': '1177',
'type': 'del',
'chr': 'X',
'chr_start': '153523769',
'chr_end': '153523790',
'alt': 'na',
'ctg_strand': '+',
'_index': 9
}
bpp_list = _convert_tool_row(row, SUPPORTED_TOOL.TA, True)
print('after call')
print(_convert_tool_row)
for bpp in bpp_list:
print(bpp)
self.assertEqual(2, len(bpp_list))
bpp = bpp_list[0]
self.assertEqual('', bpp.untemplated_seq)
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_convert_stranded_indel_insertion(self):
row = {
'chr': '1',
'chr_start': '10015',
'chr_end': '10015',
'ctg_strand': '-',
'type': 'ins',
'alt': 'aat',
'id': 1
}
bpp_list = _convert_tool_row(row, SUPPORTED_TOOL.TA, True)
self.assertEqual(2, len(bpp_list))
bpp = bpp_list[0]
self.assertEqual('1', bpp.break1.chr)
self.assertEqual('1', bpp.break2.chr)
self.assertEqual(10015, bpp.break1.start)
self.assertEqual(10016, bpp.break2.start)
self.assertEqual(SVTYPE.INS, bpp.event_type)
self.assertEqual(False, bpp.opposing_strands)
self.assertEqual(True, bpp.stranded)
self.assertEqual('AAT', bpp.untemplated_seq)
def test_convert_indel_unstranded_insertion(self):
row = {
'id': '1',
'type': 'ins',
'chr': '1',
'chr_start': '8877520',
'chr_end': '8877520',
'alt': 'tt',
'ctg_strand': '+',
'_index': 1
}
bpp_list = _convert_tool_row(row, SUPPORTED_TOOL.TA, False)
print([str(b) for b in bpp_list])
self.assertEqual(1, len(bpp_list))
bpp = bpp_list[0]
self.assertEqual(SVTYPE.INS, bpp.event_type)
self.assertEqual(STRAND.NS, bpp.break1.strand)
self.assertEqual(STRAND.NS, bpp.break2.strand)
self.assertEqual(False, bpp.stranded)
self.assertEqual(False, bpp.opposing_strands)
self.assertEqual('TT', bpp.untemplated_seq)
def test_convert_indel_duplication(self):
row = {
'id': '1185',
'type': 'dup',
'chr': 'GL000211.1',
'chr_start': '108677',
'chr_end': '108683',
'alt': 'aaaaaaa',
'ctg_strand': '+',
'_index': 15
}
bpp_list = _convert_tool_row(row, SUPPORTED_TOOL.TA, False)
print([str(b) for b in bpp_list])
self.assertEqual(1, len(bpp_list))
bpp = bpp_list[0]
self.assertEqual(SVTYPE.DUP, bpp.event_type)
self.assertEqual(STRAND.NS, bpp.break1.strand)
self.assertEqual(STRAND.NS, bpp.break2.strand)
self.assertEqual(False, bpp.stranded)
self.assertEqual(False, bpp.opposing_strands)
self.assertEqual('', bpp.untemplated_seq)
def test_convert_indel(self):
row = {
'gene_chromosome1': '1',
'gene_chromosome2': '1',
'genomic_break_pos1': '151732089',
'genomic_break_pos2': '1663681',
'genomic_strand1': '-',
'genomic_strand2': '+',
'cluster_id': 1
}
bpp_list = _convert_tool_row(row, SUPPORTED_TOOL.DEFUSE, 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(1663681, bpp.break1.start)
self.assertEqual(151732089, bpp.break2.start)
self.assertEqual(None, bpp.event_type)
self.assertEqual(False, bpp.opposing_strands)
self.assertEqual(ORIENT.LEFT, bpp.break1.orient)
self.assertEqual(ORIENT.RIGHT, bpp.break2.orient)
self.assertEqual(False, bpp.stranded)
self.assertEqual('defuse-1', bpp.tracking_id)
def test_convert_inversion(self):
row = {
'gene_chromosome1': '1',
'gene_chromosome2': '1',
'genomic_break_pos1': '235294748',
'genomic_break_pos2': '144898348',
'genomic_strand1': '+',
'genomic_strand2': '+',
'cluster_id': 1
}
bpp_list = _convert_tool_row(row, SUPPORTED_TOOL.DEFUSE, 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(144898348, bpp.break1.start)
self.assertEqual(235294748, bpp.break2.start)
self.assertEqual(None, bpp.event_type)
self.assertEqual(True, bpp.opposing_strands)
self.assertEqual(ORIENT.LEFT, bpp.break1.orient)
self.assertEqual(ORIENT.LEFT, bpp.break2.orient)
self.assertEqual(False, bpp.stranded)
self.assertEqual('defuse-1', bpp.tracking_id)
def test_insertion(self):
row = {
'Chr1': '1',
'Pos1': '20216146',
'Orientation1': '23+26-',
'Chr2': '1',
'Pos2': '20218060',
'Orientation2': '23+26-',
'Type': 'INS',
'Size': '-421',
'Score': '99',
'num_Reads': '3'
}
bpps = _convert_tool_row(row, SUPPORTED_TOOL.BREAKDANCER, False, True)
self.assertEqual(1, len(bpps))
self.assertEqual(SVTYPE.INS, bpps[0].event_type)
self.assertEqual(20216146, bpps[0].break1.start)
self.assertEqual(20216146, bpps[0].break1.end)
self.assertEqual(ORIENT.LEFT, bpps[0].break1.orient)
self.assertEqual(20218060, bpps[0].break2.start)
self.assertEqual(20218060, bpps[0].break2.end)
self.assertEqual(ORIENT.RIGHT, bpps[0].break2.orient)
self.assertEqual(False, bpps[0].opposing_strands)
def test_itx(self):
row = {
'Chr1': '1',
'Pos1': '10001',
'Orientation1': '83+126-',
'Chr2': '1',
'Pos2': '10546',
'Orientation2': '83+126-',
'Type': 'ITX',
'Size': '-352',
'Score': '99',
'num_Reads': '43'
}
bpps = _convert_tool_row(row, SUPPORTED_TOOL.BREAKDANCER, False, True)
self.assertEqual(1, len(bpps))
self.assertEqual(SVTYPE.DUP, bpps[0].event_type)
self.assertEqual(10001, bpps[0].break1.start)
self.assertEqual(10001, bpps[0].break1.end)
self.assertEqual(ORIENT.RIGHT, bpps[0].break1.orient)
self.assertEqual(10546, bpps[0].break2.start)
self.assertEqual(10546, bpps[0].break2.end)
self.assertEqual(ORIENT.LEFT, bpps[0].break2.orient)
self.assertEqual(False, bpps[0].opposing_strands)
def test_deletion(self):
row = {
'Chr1': '1',
'Pos1': '869445',
'Orientation1': '89+21-',
'Chr2': '1',
'Pos2': '870225',
'Orientation2': '5+93-',
'Type': 'DEL',
'Size': '892',
'Score': '99',
'num_Reads': '67'
}
bpps = _convert_tool_row(row, SUPPORTED_TOOL.BREAKDANCER, False, True)
self.assertEqual(1, len(bpps))
self.assertEqual(SVTYPE.DEL, bpps[0].event_type)
self.assertEqual(869445, bpps[0].break1.start)
self.assertEqual(869445, bpps[0].break1.end)
self.assertEqual(ORIENT.LEFT, bpps[0].break1.orient)
self.assertEqual(870225, bpps[0].break2.start)
self.assertEqual(870225, bpps[0].break2.end)
self.assertEqual(ORIENT.RIGHT, bpps[0].break2.orient)
self.assertEqual(False, bpps[0].opposing_strands)
