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Make annotated VCF not be broken 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2906 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
andrewk 2010-03-01 23:22:41 +00:00
parent af6e476df5
commit 9298e13201
1 changed files with 3 additions and 1 deletions
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4
python/AnnotateVCFwithMAF.py
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@ -53,6 +53,8 @@ if not header_fields.startswith("#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\t
sys.exit()
vcf_out_file.write("##source=AnnotateVCFwithMAF\n")
for header_field in headers:
vcf_out_file.write("##INFO="+header_field+",1,String,"+header_field+"\n")
vcf_out_file.write(header_fields)
for vcf_line, locus_and_info in zip(vcf_file.readlines(), loci_and_info):
@ -64,6 +66,6 @@ for vcf_line, locus_and_info in zip(vcf_file.readlines(), loci_and_info):
print "ERROR: VCF and MAF loci did not match"
sys.exit()
vcf_line_fields[7] = vcf_line_fields[7]+","+maf_info
vcf_line_fields[7] = vcf_line_fields[7]+";"+maf_info
new_vcf_line = "\t".join(vcf_line_fields)
vcf_out_file.write(new_vcf_line)