locus = int(r[snvheaders[1]].strip()) ref = r[snvheaders[2]].strip() alt = r[snvheaders[3]].strip() if r.get('INFO:INDEL'): continue if len(ref) != 1: continue if not re.search(r'^[ACGT](,[ACGT])*$', alt): continue # for h in r: # if r.get(h): # usedsnvheaders.add(h) snvkey = (filename, chr, locus, ref, alt) if snvkey not in snvdata: snvdata[snvkey] = r progress.update() progress.done() chrreg = ChromLabelRegistry() for snvfile in snvchroms: chrreg.add_labels(snvfile, snvchroms[snvfile]) snvdata1 = {} for (sf, chr, locus, ref, alt), r in snvdata.iteritems(): chrom = chrreg.label2chrom(sf, chr) assert (chrom) snvkey = (chrom, locus, ref, alt) if snvkey not in snvdata1: snvdata1[snvkey] = (chrom, locus, ref, alt, r)
ref = r[snvheaders[2]].strip() alt = r[snvheaders[3]].strip() if r.get('INFO:INDEL'): continue if len(ref) != 1: continue if not re.search(r'^[ACGT](,[ACGT])*$', alt): continue # for h in r: # if r.get(h): # usedsnvheaders.add(h) snvkey = (filename, chr, locus, ref, alt) if snvkey not in snvdata: snvdata[snvkey] = r progress.update() progress.done() chrreg = ChromLabelRegistry() for snvfile in snvchroms: chrreg.add_labels(snvfile,snvchroms[snvfile]) snvdata1 = {} for (sf, chr, locus, ref, alt), r in snvdata.iteritems(): chrom = chrreg.label2chrom(sf,chr) assert(chrom) snvkey = (chrom,locus,ref,alt) if snvkey not in snvdata1: snvdata1[snvkey] = (chrom,locus,ref,alt,r)