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 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)
assert len(bpps) == 2
assert bpps[0].event_type == SVTYPE.INV
assert bpps[0].break1.start == 13143396
assert bpps[0].break1.end == 13143396
assert bpps[0].break1.orient == ORIENT.LEFT
assert bpps[0].break2.start == 13218683
assert bpps[0].break2.end == 13218683
assert bpps[0].break2.orient == ORIENT.LEFT
assert bpps[0].opposing_strands is True
assert bpps[1].event_type == SVTYPE.INV
assert bpps[1].break1.start == 13143396
assert bpps[1].break1.end == 13143396
assert bpps[1].break1.orient == ORIENT.RIGHT
assert bpps[1].break2.start == 13218683
assert bpps[1].break2.end == 13218683
assert bpps[1].break2.orient == ORIENT.RIGHT
assert bpps[1].opposing_strands is True
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 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_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)
assert len(bpp_list) == 2
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 test_convert_duplication(self):
row = {'event_type': 'duplication', 'coordinates': '1:1-10000'}
bpp_list = _convert_tool_row(row, SUPPORTED_TOOL.CNVNATOR, False)
assert len(bpp_list) == 1
bpp = bpp_list[0]
assert bpp.break1.start == 1
assert bpp.break1.end == 1
assert bpp.break2.start == 10000
assert bpp.break2.start == 10000
assert bpp.event_type == SVTYPE.DUP
assert bpp.break1.chr == '1'
assert bpp.break2.chr == '1'
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 test_convert_translocation(self):
row = {
'FusionName': 'BCAS4--BCAS3',
'LeftBreakpoint': 'chr20:49411710:+',
'RightBreakpoint': 'chr17:59445688:+',
}
bpp_list = _convert_tool_row(row, SUPPORTED_TOOL.STARFUSION, True)
assert len(bpp_list) == 2
bpp = bpp_list[0]
assert bpp.break1.chr == 'chr17'
assert bpp.break2.chr == 'chr20'
assert bpp.break1.start == 59445688
assert bpp.break2.start == 49411710
assert bpp.opposing_strands is False
assert bpp.stranded is True
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)
assert len(bpp_list) == 2
bpp = bpp_list[0]
assert bpp.break1.chr == 'chr13'
assert bpp.break2.chr == 'chr13'
assert bpp.break1.start == 114529969
assert bpp.break2.start == 114751269
assert bpp.opposing_strands is False
assert bpp.stranded 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_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 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_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)
assert len(bpp_list) == 2
bpp = bpp_list[0]
assert 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)
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'
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)
assert len(bpp_list) == 2
bpp = bpp_list[0]
assert bpp.break1.chr == '1'
assert bpp.break2.chr == '1'
assert bpp.break1.start == 10015
assert bpp.break2.start == 10016
assert bpp.event_type == SVTYPE.INS
assert bpp.opposing_strands is False
assert bpp.stranded is True
assert bpp.untemplated_seq == 'AAT'
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])
assert len(bpp_list) == 1
bpp = bpp_list[0]
assert bpp.event_type == SVTYPE.INS
assert bpp.break1.strand == STRAND.NS
assert bpp.break2.strand == STRAND.NS
assert bpp.stranded is False
assert bpp.opposing_strands is False
assert bpp.untemplated_seq == 'TT'
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])
assert len(bpp_list) == 1
bpp = bpp_list[0]
assert bpp.event_type == SVTYPE.DUP
assert bpp.break1.strand == STRAND.NS
assert bpp.break2.strand == STRAND.NS
assert bpp.stranded is False
assert bpp.opposing_strands is False
assert bpp.untemplated_seq == ''
def test_convert_translocation(self):
row = {
'gene_chromosome1': 'X',
'gene_chromosome2': '3',
'genomic_break_pos1': '153063989',
'genomic_break_pos2': '50294136',
'genomic_strand1': '+',
'genomic_strand2': '+',
'cluster_id': 1,
}
bpp_list = _convert_tool_row(row, SUPPORTED_TOOL.DEFUSE, False)
assert len(bpp_list) == 1
bpp = bpp_list[0]
assert bpp.break1.chr == '3'
assert bpp.break2.chr == 'X'
assert bpp.break1.start == 50294136
assert bpp.break2.start == 153063989
assert bpp.event_type is None
assert bpp.opposing_strands is True
assert bpp.break1.orient == ORIENT.LEFT
assert bpp.break2.orient == ORIENT.LEFT
assert bpp.stranded is False
assert bpp.data['tracking_id'] == 'defuse-1'
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)
assert len(bpp_list) == 1
bpp = bpp_list[0]
assert bpp.break1.chr == '1'
assert bpp.break2.chr == '1'
assert bpp.break1.start == 1663681
assert bpp.break2.start == 151732089
assert bpp.event_type is None
assert bpp.opposing_strands is False
assert bpp.break1.orient == ORIENT.LEFT
assert bpp.break2.orient == ORIENT.RIGHT
assert bpp.stranded is False
assert bpp.data['tracking_id'] == 'defuse-1'
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)
assert len(bpps) == 1
assert bpps[0].event_type == SVTYPE.INS
assert bpps[0].break1.start == 20216146
assert bpps[0].break1.end == 20216146
assert bpps[0].break1.orient == ORIENT.LEFT
assert bpps[0].break2.start == 20218060
assert bpps[0].break2.end == 20218060
assert bpps[0].break2.orient == ORIENT.RIGHT
assert bpps[0].opposing_strands is False
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)
assert len(bpp_list) == 1
bpp = bpp_list[0]
assert bpp.break1.chr == '1'
assert bpp.break2.chr == '1'
assert bpp.break1.start == 144898348
assert bpp.break2.start == 235294748
assert bpp.event_type is None
assert bpp.opposing_strands is True
assert bpp.break1.orient == ORIENT.LEFT
assert bpp.break2.orient == ORIENT.LEFT
assert bpp.stranded is False
assert bpp.data['tracking_id'] == 'defuse-1'
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)
assert len(bpps) == 1
assert bpps[0].event_type == SVTYPE.DEL
assert bpps[0].break1.start == 869445
assert bpps[0].break1.end == 869445
assert bpps[0].break1.orient == ORIENT.LEFT
assert bpps[0].break2.start == 870225
assert bpps[0].break2.end == 870225
assert bpps[0].break2.orient == ORIENT.RIGHT
assert bpps[0].opposing_strands is False
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)
assert len(bpps) == 1
assert bpps[0].event_type == SVTYPE.DUP
assert bpps[0].break1.start == 10001
assert bpps[0].break1.end == 10001
assert bpps[0].break1.orient == ORIENT.RIGHT
assert bpps[0].break2.start == 10546
assert bpps[0].break2.end == 10546
assert bpps[0].break2.orient == ORIENT.LEFT
assert bpps[0].opposing_strands is False
