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)