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"))
