From 27fb6f7594778f82923718f995a1c5715a2083bd Mon Sep 17 00:00:00 2001 From: chartl Date: Sat, 3 Apr 2010 20:01:21 +0000 Subject: [PATCH] Make sure to convert non-integer chromosomes (M,X,Y) back from their corresponding integer representations (0,23,24) when writing in .bed format git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3119 348d0f76-0448-11de-a6fe-93d51630548a --- python/RefseqLibrary.py | 12 +++++++++++- 1 file changed, 11 insertions(+), 1 deletion(-) diff --git a/python/RefseqLibrary.py b/python/RefseqLibrary.py index e88ef3a96..bd3ce7c2f 100755 --- a/python/RefseqLibrary.py +++ b/python/RefseqLibrary.py @@ -1,4 +1,14 @@ import math +def chrFormat(chr): + if ( chr == "chr0"): + return "chrM" + if ( chr == "chr23" ): + return "chrX" + if ( chr == "chr24" ): + return "chrY" + else: + return chr + def chr2int(chr): try: chr = chr.split("chr")[1] @@ -123,7 +133,7 @@ class Exon: return self.interval.size() def getBedEntry(self): - return "\t".join([self.interval.chromosome,str(self.interval.start),str(self.interval.stop),self.gene,self.id,str(self.getCoverageProportion())]) + return "\t".join([chrFormat(self.interval.chromosome),str(self.interval.start),str(self.interval.stop),self.gene,self.id,str(self.getCoverageProportion())]) def getCoverageProportion(self): if ( self.size() > 0 ):