From 5f9c3f38845c4aa543f39d86627f742bc9a41c8b Mon Sep 17 00:00:00 2001 From: kshakir Date: Mon, 22 Feb 2010 21:31:24 +0000 Subject: [PATCH] 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 --- python/AnnotateVCFwithMAF.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/python/AnnotateVCFwithMAF.py b/python/AnnotateVCFwithMAF.py index 486c3682f..73ed2d52d 100755 --- a/python/AnnotateVCFwithMAF.py +++ b/python/AnnotateVCFwithMAF.py @@ -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":