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Added a header crediting the python script as a source. Looping over an arbitrary number of headers. 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2804 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
kshakir 2010-02-07 03:38:30 +00:00
parent 3b1ab86d11
commit 57a168c0db
1 changed files with 10 additions and 15 deletions
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25
python/AnnotateVCFwithMAF.py
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@ -39,16 +39,22 @@ if vcf_format_line != "##fileformat=VCFv3.3\n":
print ("VCF not v 3.3")
sys.exit()
for i in range(33):
vcf_out_file.write(vcf_file.readline())
header = vcf_file.readline()
while header != "" and header.startswith("#"):
if header.startswith("#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\tFORMAT"):
break
vcf_out_file.write(header)
header = vcf_file.readline()
header_fields = vcf_file.readline()
vcf_out_file.write(header_fields)
header_fields = header
if not header_fields.startswith("#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\tFORMAT"):
print ("VCF header fields not in expected order")
print header_fields
sys.exit()
vcf_out_file.write("##source=AnnotateVCFwithMAF\n")
vcf_out_file.write(header_fields)
for vcf_line, locus_and_info in zip(vcf_file.readlines(), loci_and_info):
vcf_line_fields = vcf_line.split("\t")
vcf_locus = vcf_line_fields[0]+":"+vcf_line_fields[1]
@ -61,14 +67,3 @@ for vcf_line, locus_and_info in zip(vcf_file.readlines(), loci_and_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)