def initialize0(results_path, cancer_dir_path):
try:
vcf_path = bamhelp.GetVCF()
exons_path = bamhelp.GetExons()
reference_path = bamhelp.GetRef()
bedtools_path = bamhelp.GetBedtoolsPath()
vpath, vcf = os.path.split(vcf_path)
if (params.GetPhase()):
phasedvcf = "/".join(
[results_path,
sub('.vcf$', '_phased.vcf.gz', vcf)])
vcftobed = "/".join([results_path, sub('.vcf$', '.bed', vcf)])
hap1vcf = "/".join([results_path, "hap1_het.vcf"])
hap2vcf = "/".join([results_path, "hap2_het.vcf"])
hap1vcffiltered = "/".join([results_path, "hap1_het_filtered"])
hap2vcffiltered = "/".join([results_path, "hap2_het_filtered"])
hap1vcffilteredtobed = "/".join(
[results_path, "hap1_het_filtered.bed"])
hap2vcffilteredtobed = "/".join(
[results_path, "hap2_het_filtered.bed"])
phased_bed = "/".join([results_path, "PHASED.BED"])
phaseVCF(vcf_path, phasedvcf)
getVCFHaplotypes(phasedvcf, hap1vcf, hap2vcf)
thinVCF(hap1vcf, hap1vcffiltered)
thinVCF(hap2vcf, hap2vcffiltered)
convertvcftobed(hap1vcffiltered + ".recode.vcf",
hap1vcffilteredtobed)
convertvcftobed(hap2vcffiltered + ".recode.vcf",
hap2vcffilteredtobed)
cmd1 = """sed -i 's/$/\thap1/' """ + hap1vcffilteredtobed
cmd2 = """sed -i 's/$/\thap2/' """ + hap2vcffilteredtobed
cmd3 = "cat " + hap1vcffilteredtobed + " " + hap2vcffilteredtobed + " > " + 'tmp.bed'
cmd4 = "sort -V -k1,1 -k2,2 tmp.bed > " + phased_bed
runCommand(cmd1)
runCommand(cmd2)
runCommand(cmd3)
runCommand(cmd4)
os.remove('tmp.bed')
except:
raise
return
def initialize0(results_path, cancer_dir_path):
try:
vcf_path = bamhelp.GetVCF()
exons_path = bamhelp.GetExons()
reference_path = bamhelp.GetRef()
bedtools_path = bamhelp.GetBedtoolsPath()
vpath, vcf = os.path.split(vcf_path)
if params.GetPhase():
phasedvcf = "/".join(
[results_path,
sub('.vcf$', '_phased.vcf.gz', vcf)])
vcftobed = "/".join([results_path, sub('.vcf$', '.bed', vcf)])
hap1vcf = "/".join([results_path, "hap1_het.vcf"])
hap2vcf = "/".join([results_path, "hap2_het.vcf"])
hap1vcffiltered = "/".join([results_path, "hap1_het_filtered"])
hap2vcffiltered = "/".join([results_path, "hap2_het_filtered"])
hap1vcffilteredtobed = "/".join(
[results_path, "hap1_het_filtered.bed"])
hap2vcffilteredtobed = "/".join(
[results_path, "hap2_het_filtered.bed"])
phased_bed = "/".join([results_path, "PHASED.BED"])
phaseVCF(vcf_path, phasedvcf)
getVCFHaplotypes(phasedvcf, hap1vcf, hap2vcf)
thinVCF(hap1vcf, hap1vcffiltered)
thinVCF(hap2vcf, hap2vcffiltered)
convertvcftobed(hap1vcffiltered + ".recode.vcf",
hap1vcffilteredtobed)
convertvcftobed(hap2vcffiltered + ".recode.vcf",
hap2vcffilteredtobed)
generatePhasedBed(hap1vcffilteredtobed, hap2vcffilteredtobed,
phased_bed)
except:
logger.exception("Initialization error !")
raise
return
def initialize0(results_path, cancer_dir_path):
"""
Initialize paths for files provided by user.
Phasing is also performed if requested by user.
"""
try:
vcf_path = params.GetVCFPath()
exons_path = params.GetExonsPath()
#reference_path = bamhelp.GetRef()
bedtools_path = bamhelp.GetBedtoolsPath()
vpath, vcf = os.path.split(vcf_path)
phasedvcf = "/".join([results_path, sub('.vcf$', '_phased.vcf.gz', vcf)])
vcftobed = "/".join([results_path, sub('.vcf$', '.bed', vcf)])
hap1vcf = "/".join([results_path, "hap1_het.vcf"])
hap2vcf = "/".join([results_path, "hap2_het.vcf"])
hap1vcffiltered = "/".join([results_path, "hap1_het_filtered"])
hap2vcffiltered = "/".join([results_path, "hap2_het_filtered"])
hap1vcffilteredtobed = "/".join([results_path, "hap1_het_filtered.bed"])
hap2vcffilteredtobed = "/".join([results_path, "hap2_het_filtered.bed"])
phased_bed = "/".join([results_path, "PHASED.BED"])
if params.GetPhase():
phaseVCF(vcf_path, phasedvcf)
getVCFHaplotypes(phasedvcf, hap1vcf, hap2vcf)
else:
getVCFHaplotypes(vcf_path, hap1vcf, hap2vcf)
convertvcftobed(hap1vcf, hap1vcffilteredtobed)
convertvcftobed(hap2vcf, hap2vcffilteredtobed)
generatePhasedBed(hap1vcffilteredtobed, hap2vcffilteredtobed, phased_bed)
except:
logger.exception("Initialization error!")
raise
return