Mercurial > repos > john-mccallum > pcr_markers
diff vcf_gff.py @ 5:b321e0517be3 draft
Uploaded
author | ben-warren |
---|---|
date | Thu, 22 May 2014 20:30:19 -0400 |
parents | 402c3f0fe807 |
children |
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--- a/vcf_gff.py Thu Oct 18 19:47:07 2012 -0400 +++ b/vcf_gff.py Thu May 22 20:30:19 2014 -0400 @@ -46,6 +46,8 @@ 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") @@ -108,7 +110,9 @@ gen = "HET" if genotypes == "0/0": gen = "HOM_ref" - else: + try: # set gen to 'NA' if still unset + gen + except NameError: gen = "NA" geno = ("%s:%s " % (reads, gen)) genos += geno @@ -141,11 +145,11 @@ 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" + + ("%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, - record_type, start, variant, reference, reads, gen)) - + source, record_type, start, variant, reference, reads, gen)) + out_gff_file.close()