def main(): args = usage() conf = config(args.reference) soft = conf['software'] ref = conf['reference'][args.reference] # pprint.pprint(conf) #Test for qualityQcontol multiprocessing.Process(target=qualityQcontol.run, args=(args.pe1,args.pe2,args.indir,args.out,soft['IllQC'],args.nthreads)).start() #Test mapping sam,mappingOut=mappingAndDedup.mapping(args.pe1,args.pe2,args.indir,args.out,ref['genomeBuild'],soft=soft['bwa'],t=args.nthreads) dedup = mappingAndDedup.dedup(sam, mappingOut, sortsam = soft['sortsam'], mark = soft['mark']) #Test recalibrate recal = recalibrate.realignAndrecal(dedup,mappingOut,mappingOut,index=ref['genomeBuild'],soft = soft['gatk'],t = args.nthreads,mill = ref['mill'], kg = ref['kg'],dbsnp=ref['dbsnp']) #Test Call SV cmd="bash %s/bin/callSV.sh -b %s -i %s -o %s -r %s &" %(root,recal,mappingOut,args.out,args.reference) os.system(cmd) #Test call CNV cmd = "bash %s/bin/callCNV.sh -b %s -i %s -o %s -r %s &" %(root,recal,mappingOut,args.out,args.reference) os.system(cmd) #Test variant calling vcf,variantout = callVariants.gatkCall(recal,mappingOut,args.out,index=ref['genomeBuild'],soft = soft['gatk'],t = args.nthreads,mill = ref['mill'], kg = ref['kg'],dbsnp=ref['dbsnp'],omni=ref['omni'],hapmap=ref['hapmap']) #Test annotation annotateWithAnnovar.annotate(vcf,variantout,args.out,hd=ref['humandb'],con=soft['convert2annovar'],tb=soft['table_annovar'])
def main(): args = usage() conf = config(args.reference) soft = conf['software'] ref = conf['reference'][args.reference] script = conf['script'] # pprint.pprint(conf) #Test for qualityQcontol multiprocessing.Process(target=qualityQcontol.run, args=(args.pe1,args.pe2,args.indir,args.out,soft['IllQC'],args.nthreads)).start() #Test mapping sam,mappingOut=mappingAndDedup.mapping(args.pe1,args.pe2,args.indir,args.out,ref['genomeBuild'],soft=soft['bwa'],t=args.nthreads) dedup = mappingAndDedup.dedup(sam, mappingOut, sortsam = soft['sortsam'], mark = soft['mark']) #Test mappingRate bam = sam + '.bam' #mappingRate.mappingRate(bam,mappingOut,args.out,index = ref['genomeBuild'],cap = ref[args.capture],soft = soft['ngscat'],t=args.nthreads) #In multiprocessing method multiprocessing.Process(target=mappingRate.mappingRate,args=(bam,mappingOut,args.out,ref['genomeBuild'],ref[args.capture],soft['ngscat'],args.nthreads)).start() #Test recalibrate recal = recalibrate.realignAndrecal(dedup,mappingOut,mappingOut,index=ref['genomeBuild'],soft = soft['gatk'],t = args.nthreads,mill = ref['mill'], kg = ref['kg'],dbsnp=ref['dbsnp']) #Test variant calling vcf,variantout = callVariants.gatkCall(recal,mappingOut,args.out,index=ref['genomeBuild'],soft = soft['gatk'],t = args.nthreads,mill = ref['mill'], kg = ref['kg'],dbsnp=ref['dbsnp'],omni=ref['omni'],hapmap=ref['hapmap']) #Test annotation annotateWithAnnovar.annotate(vcf,variantout,args.out,hd=ref['humandb'],con=soft['convert2annovar'],tb=soft['table_annovar'])
def main():
args = usage()
conf = config(args.reference)
soft = conf['software']
ref = conf['reference'][args.reference]
# pprint.pprint(conf)
#Test for qualityQcontol
multiprocessing.Process(target=qualityQcontol.run,
args=(args.pe1, args.pe2, args.indir, args.out,
soft['IllQC'], args.nthreads)).start()
#Test mapping
sam, mappingOut = mappingAndDedup.mapping(args.pe1,
args.pe2,
args.indir,
args.out,
ref['genomeBuild'],
soft=soft['bwa'],
t=args.nthreads)
dedup = mappingAndDedup.dedup(sam,
mappingOut,
sortsam=soft['sortsam'],
mark=soft['mark'])
#Test recalibrate
recal = recalibrate.realignAndrecal(dedup,
mappingOut,
mappingOut,
index=ref['genomeBuild'],
soft=soft['gatk'],
t=args.nthreads,
mill=ref['mill'],
kg=ref['kg'],
dbsnp=ref['dbsnp'])
#Test Call SV
cmd = "bash %s/bin/callSV.sh -b %s -i %s -o %s -r %s &" % (
root, recal, mappingOut, args.out, args.reference)
os.system(cmd)
#Test call CNV
cmd = "bash %s/bin/callCNV.sh -b %s -i %s -o %s -r %s &" % (
root, recal, mappingOut, args.out, args.reference)
os.system(cmd)
#Test variant calling
vcf, variantout = callVariants.gatkCall(recal,
mappingOut,
args.out,
index=ref['genomeBuild'],
soft=soft['gatk'],
t=args.nthreads,
mill=ref['mill'],
kg=ref['kg'],
dbsnp=ref['dbsnp'],
omni=ref['omni'],
hapmap=ref['hapmap'])
#Test annotation
annotateWithAnnovar.annotate(vcf,
variantout,
args.out,
hd=ref['humandb'],
con=soft['convert2annovar'],
tb=soft['table_annovar'])
