Mercurial > repos > john-mccallum > pcr_markers
changeset 3:402c3f0fe807 draft
Uploaded revised vcf_gff.py from Github to fix bug
| author | john-mccallum |
|---|---|
| date | Thu, 18 Oct 2012 17:54:38 -0400 |
| parents | ea2117a7b363 |
| children | be070a68521e |
| files | vcf_gff.py |
| diffstat | 1 files changed, 3 insertions(+), 2 deletions(-) [+] |
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--- a/vcf_gff.py Sun Sep 09 23:16:56 2012 -0400 +++ b/vcf_gff.py Thu Oct 18 17:54:38 2012 -0400 @@ -110,7 +110,7 @@ gen = "HOM_ref" else: gen = "NA" - geno = ("%s:%s;" % (reads, gen)) + geno = ("%s:%s " % (reads, gen)) genos += geno sample_dict = {} return genos @@ -120,6 +120,7 @@ Get relevant info from vcf file and put to proper gff columns """ +out_gff_file.write("#gff-version 3\n") for line in in_vcf_file: if line.startswith("#") == False: info = line.split() @@ -141,7 +142,7 @@ 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") % + "_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))