def test_parse_main_cols_strelka(strelka): p = vcf_snv_parser.SNV_vcf(strelka) record = next(p.reader) main_cols = p.parse_main_cols(record)["main_cols"] assert main_cols["chrom"] == record.CHROM assert main_cols["pos"] == record.POS assert main_cols["ref"] == record.REF assert main_cols["alt"] == record.ALT[0] assert main_cols["qual"] == record.QUAL assert main_cols["filter"] == record.FILTER
def test_read_sample_names_museq_germline(museq_germline): p = vcf_snv_parser.SNV_vcf(museq_germline) n, t = p._read_sample_names(museq_germline) assert t == None assert n == "SA220N"
def test_read_sample_names_strelka(strelka): p = vcf_snv_parser.SNV_vcf(strelka) n, t = p._read_sample_names(strelka) assert t == "SA224" assert n == "SA224N"
def test_read_sample_names_mutect(mutect): p = vcf_snv_parser.SNV_vcf(mutect) n, t = p._read_sample_names(mutect) assert t == "SA225" assert n == "SA225N"
def test_read_sample_names_samtools(samtools): p = vcf_snv_parser.SNV_vcf(samtools) n, t = p._read_sample_names(samtools) assert t == None assert n == "SA219N"
def test_read_sample_names_rtg(rtg): p = vcf_snv_parser.SNV_vcf(rtg) n, t = p._read_sample_names(rtg) assert t == None assert n == "SA219N"
def test_read_sample_names_freebayes(freebayes): p = vcf_snv_parser.SNV_vcf(freebayes) n, t = p._read_sample_names(freebayes) assert t == None assert n == "SA219N"
def test_read_sample_names_museq_somatic(museq_somatic): p = vcf_snv_parser.SNV_vcf(museq_somatic) n, t = p._read_sample_names(museq_somatic) assert t == "SA224" assert n == "SA224N"
def test_parse_main_cols_museq_germline(museq_germline): p = vcf_snv_parser.SNV_vcf(museq_germline) record = next(p.reader) main_cols = p.parse_main_cols(record)["main_cols"] assert main_cols["chrom"] == record.CHROM assert main_cols["pos"] == record.POS assert main_cols["ref"] == record.REF assert main_cols["alt"] == record.ALT[0] assert main_cols["qual"] == record.QUAL assert main_cols["filter"] == record.FILTER # import os # ls # test_data_dir = "/juno/work/shah/abramsd/CODE/testdata" # svaba = "/juno/work/shah/abramsd/CODE/testdata/out.svaba.germline.sv.vcf.gz" # lumpy = "/juno/work/shah/abramsd/CODE/testdata/SA1256PP_lumpy.vcf" # gridss = "/juno/work/shah/abramsd/CODE/testdata/gridss.vcf.gz" # freebayes = "/juno/work/shah/isabl_data_lake/analyses/74/87/7487/results/germline/SA219N/SA219N_freebayes_germline.vcf.gz" # rtg = "/juno/work/shah/isabl_data_lake/analyses/74/87/7487/results/germline/SA219N/SA219N_rtg_germline.vcf.gz" # samtools = "/juno/work/shah/isabl_data_lake/analyses/74/87/7487/results/germline/SA219N/SA219N_samtools_germline.vcf.gz" # museq = "/juno/work/shah/isabl_data_lake/analyses/74/86/7486/results/germline/SA220N/SA220N_museq_single_annotated.vcf.gz" # mutect = "/juno/work/shah/isabl_data_lake/analyses/77/97/7797/results/somatic/SA225/SA225_mutect.vcf.gz" # strelka = "/juno/work/shah/isabl_data_lake/analyses/77/96/7796/results/somatic/SA224/SA224_strelka_snv_annotated.vcf.gz" # museq_somatic = "/juno/work/shah/isabl_data_lake/analyses/77/96/7796/results/somatic/SA224/SA224_museq_paired_annotated.vcf.gz" # # testoutput_dir = "/juno/work/shah/abramsd/CODE/vcfutils/vcfutils/tests/test_outs" # # parser = vcf_sv_parser.Lumpy_vcf(lumpy) # # parser.parse() # # parser.to_ # # (os.path.join(testoutput_dir, "lumpy_csv.csv")) # # parser = vcf_sv_parser.Gridss_vcf(gridss) # # parser.parse() # # parser.to_csv(os.path.join(testoutput_dir, "gridss_csv.csv")) # # parser = vcf_sv_parser.Svaba_vcf(svaba) # # parser.parse() # # parser.to_csv(os.path.join(testoutput_dir, "svaba_csv.csv")) # filter_out = [] # filter_out.append(('LOW_MAPPABILITY', 'eq', True)) # chromosomes = list((map(str,list(range(1, 23))))) + ["X"] # filter_out.append(('CHROM', 'notin', chromosomes)) # filter_out.append(('PR', 'lt', 0)) # # p = vcf_snv_parser.Freebayes_vcf(freebayes, filter_out) # # p.parse() # # p.to_csv("/juno/work/shah/abramsd/CODE/test_outs/freebayes.csv.gz") # # p = vcf_snv_parser.Rtg_vcf(rtg, filter_out) # # p.parse() # # p.to_csv("/juno/work/shah/abramsd/CODE/test_outs/rtg.csv.gz") # # p = vcf_snv_parser.Samtools_vcf(samtools, filter_out) # # p.parse() # # p.to_csv("/juno/work/shah/abramsd/CODE/test_outs/samtools.csv.gz") # # p = vcf_snv_parser.Museq_vcf(museq, filter_out) # # p.parse() # # p.to_csv("/juno/work/shah/abramsd/CODE/test_outs/museq_germline.csv.gz") # # p = vcf_snv_parser.Mutect_vcf(mutect, filter_out) # # p.parse() # # p.to_csv("/juno/work/shah/abramsd/CODE/test_outs/mutect.csv.gz") # # p = vcf_snv_parser.Strelka_vcf(strelka, filter_out) # # p.parse() # # p.to_csv("/juno/work/shah/abramsd/CODE/test_outs/strelka.csv.gz") # p = vcf_snv_parser.Museq_vcf(museq_somatic) # p.parse() # print(p.to_csv("/juno/work/shah/abramsd/CODE/test_outs/museq_csv.csv.gz"))