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

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
This commit is contained in:
chartl 2010-04-03 20:01:21 +00:00
parent 705b28e90d
commit 27fb6f7594
1 changed files with 11 additions and 1 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

12
python/RefseqLibrary.py
View File

@ -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 ):