def test_merge3():
manta = viola.read_vcf(StringIO(DATA1), variant_caller='manta')
delly = viola.read_vcf(StringIO(DATA2), variant_caller='delly')
result = viola.merge([delly, manta],
mode='confidence_intervals',
integration=True)
assert result.sv_count == 4
assert result.get_ids() == {
'manta_M1', 'delly_MD1', 'delly_MDL1', 'delly_D1'
}
def test_merge():
merged_all = viola.merge(ls_inputs=[delly, gridss, lumpy, manta],
integration=True)
print(merged_all.table_list)
info_lst = [
"positions", "mergedid", 'supportingid', 'supportingcaller',
'supportingidcount', 'supportingcallercount'
]
for i in info_lst:
print(merged_all.get_table(i))
print(merged_all.get_table(i).dtypes)
print()
def test_merge2():
gridss = viola.read_vcf(StringIO(DATA1), variant_caller='gridss').breakend2breakpoint()
manta = viola.read_vcf(StringIO(DATA2), variant_caller='manta').breakend2breakpoint()
result = viola.merge([manta, gridss], mode='confidence_intervals', integration=True)
result = result.filter('supportingcallercount > 1')
assert result.sv_count == 5
assert result.get_ids() == {
'manta_MantaDUP:TANDEM:88695:0:1:0:0:0',
'manta_viola_breakpoint:0',
'manta_MantaDUP:TANDEM:93040:0:1:0:0:0',
'manta_viola_breakpoint:1',
'manta_viola_breakpoint:2'
}
def test_merge1():
gridss = viola.read_vcf(StringIO(DATA1), variant_caller='gridss').breakend2breakpoint()
manta = viola.read_vcf(StringIO(DATA2), variant_caller='manta').breakend2breakpoint()
result = viola.merge([gridss, manta], mode='confidence_intervals', integration=True)
result = result.filter('supportingcallercount > 1')
assert result.sv_count == 5
assert result.get_ids() == {
'gridss_viola_breakpoint:0',
'gridss_viola_breakpoint:1',
'gridss_viola_breakpoint:6',
'gridss_viola_breakpoint:7',
'gridss_viola_breakpoint:8',
}
def test_merge():
manta = viola.read_vcf(os.path.join(HERE, 'data/test.merge.manta.vcf'),
variant_caller='manta')
delly = viola.read_vcf(os.path.join(HERE, 'data/test.merge.delly.vcf'),
variant_caller='delly')
lumpy = viola.read_vcf(os.path.join(HERE, 'data/test.merge.lumpy.vcf'),
variant_caller='lumpy')
gridss = viola.read_vcf(os.path.join(HERE, 'data/test.merge.gridss.vcf'),
variant_caller='gridss')
result = manta._generate_distance_matrix_by_confidence_intervals(
viola.TmpVcfForMerge([manta, delly, gridss, lumpy],
['manta', 'delly', 'gridss', 'lumpy']))
result = viola.merge([manta, delly, lumpy, gridss],
mode='confidence_intervals')
assert result.get_ids() == {
'manta_M1', 'manta_MD1', 'manta_ML1', 'manta_MG1', 'manta_MDL1',
'manta_MDG1', 'manta_MLG1', 'manta_MDLG1o', 'delly_D1', 'delly_DL1',
'delly_DG1', 'delly_DLG1', 'lumpy_L1', 'lumpy_LG1', 'gridss_G1o'
}
def test_merge_to_vcf_like():
merged = viola.merge([manta, gridss, delly, lumpy], integration=True)
merged = merged.filter('supportingcallercount > 1')
merged.to_vcf(os.path.join(HERE, 'data/output_merged.vcf'))
def test_merge_to_vcf_like():
merged = viola.merge([manta, gridss, delly, lumpy], integration=True)
print(merged)
merged_integrated = merged.filter('supportingcallercount > 1')
print(merged_integrated)