zzh
/
gatk-3.8
1
0
Fork 0
Code Issues Pull Requests Packages Projects Releases Wiki Activity

Outputing annotated VCF to the current directory instead of attempting to write in the directory next to the original vcf. 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2869 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
kshakir 2010-02-22 21:31:24 +00:00
parent 8b555ff17c
commit 5f9c3f3884
1 changed files with 1 additions and 1 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

2
python/AnnotateVCFwithMAF.py
View File

@ -32,7 +32,7 @@ for record in maf_gen:
#vcf_gen = FlatFileTable.record_generator(vcf_file, "\t", 34)
vcf_file = open(vcf_filename)
vcf_out_file = open(os.path.splitext(vcf_filename)[0]+".maf_annotated.vcf", "w")
vcf_out_file = open(os.path.splitext(os.path.basename(vcf_filename))[0]+".maf_annotated.vcf", "w")
vcf_format_line = vcf_file.readline()
vcf_out_file.write(vcf_format_line)
if vcf_format_line != "##fileformat=VCFv3.3\n":