From 19a5830186969d0911001e867cbd7295cdfdd3dd Mon Sep 17 00:00:00 2001 From: chartl Date: Tue, 13 Jul 2010 17:33:15 +0000 Subject: [PATCH] Restore "type" annotation (but not genomechange or cDNA change, which are already encoded in the VCF) git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3784 348d0f76-0448-11de-a6fe-93d51630548a --- python/AnnotateVCFwithMAF.py | 3 +++ 1 file changed, 3 insertions(+) diff --git a/python/AnnotateVCFwithMAF.py b/python/AnnotateVCFwithMAF.py index 3aed3a326..07378a0c9 100755 --- a/python/AnnotateVCFwithMAF.py +++ b/python/AnnotateVCFwithMAF.py @@ -77,6 +77,9 @@ def addFormat(infoString): last = val[len(val)-1] num = val.split(".")[1][1:len(val.split(".")[1])-1] newItems.append("proteinchange="+first+">"+last+";proteinoffset="+num) + if key == "type" : + newItems.append(item) + return ";".join(newItems) for vcf_line, locus_and_info in zip(vcf_file.readlines(), loci_and_info):