comparison vcf_gff.py @ 5:b321e0517be3 draft

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4:be070a68521e

        rec = rec[1:]
    else:
        record_type = "SNP"
    for entry in rec:
        detail = entry.split("=")
        INFO[detail[0]] = detail[1]
    if INFO.has_key("DP"):
        reads = INFO.get("DP")
    else:
        reads = "NA"

                gen = "HOM_mut"
            if genotypes == "0/1":
                gen = "HET"
            if genotypes == "0/0":
                gen = "HOM_ref"
        else:
            gen = "NA"
        geno = ("%s:%s " % (reads, gen))
        genos += geno
        sample_dict = {}
    return genos

            end = start + len(reference)
        else:
            end = start 
        gen = get_gen(info[8:], reference)
        out_gff_file.write(
            ("%s\t%s\t%s\t%d\t%d\t%s\t%s\t%s\tID=%s:%s:%d;Variant" +
             "_seq=%s;Reference_seq=%s;Total_reads=%s;Zygosity=%s\n") %
            ( seqid, source,record_type, start, end, score, strand, phase,seqid, 
              record_type, start, variant, reference, reads, gen))
    
out_gff_file.close()    

5:b321e0517be3

        rec = rec[1:]
    else:
        record_type = "SNP"
    for entry in rec:
        detail = entry.split("=")
        if len(detail) < 2:
            continue
        INFO[detail[0]] = detail[1]
    if INFO.has_key("DP"):
        reads = INFO.get("DP")
    else:
        reads = "NA"

                gen = "HOM_mut"
            if genotypes == "0/1":
                gen = "HET"
            if genotypes == "0/0":
                gen = "HOM_ref"
        try: # set gen to 'NA' if still unset
            gen
        except NameError:
            gen = "NA"
        geno = ("%s:%s " % (reads, gen))
        genos += geno
        sample_dict = {}
    return genos

            end = start + len(reference)
        else:
            end = start 
        gen = get_gen(info[8:], reference)
        out_gff_file.write(
            ("%s\t%s\t%s\t%d\t%d\t%s\t%s\t%s\tID=%s:%s:%s:%d;Variant" +
             "_seq=%s;Reference_seq=%s;Total_reads=%s;Zygosity=%s\n") %
            ( seqid, source,record_type, start, end, score, strand, phase,seqid, 
              source, record_type, start, variant, reference, reads, gen))

out_gff_file.close()