https://github.com/kpalin/EEL
Tip revision: c0cd936bedca30564088c8aeb8f43ebe4e05421f authored by Kimmo Palin on 07 November 2012, 13:23:26 UTC
Fixed a variable format clash which sometimes caused core dumps.
Fixed a variable format clash which sometimes caused core dumps.
Tip revision: c0cd936
SyntenyToEnsembl.py
import re,fileinput,sys
# $Log$
Species={"HUMAN":"http://www.ensembl.org/Homo_sapiens/contigview?chr=%d&vc_start=%d&vc_end=%d",
"MOUSE":"http://www.ensembl.org/Mus_musculus/contigview?chr=%d&vc_start=%d&vc_end=%d"}
m=re.compile(r"(%s)\|(\d+)[.](\d+)-(\d+) "%("|".join(Species.keys())))
def SyntenyToEnsembl(string):
mat=m.search(string)
if not mat:
return None
else:
return Species[mat.group(1)]%(int(mat.group(2)),int(mat.group(3)),int(mat.group(4)))
def SyntenyLen(string):
mat=m.search(string)
if not mat:
return None
else:
return int(mat.group(4))-int(mat.group(3))
for line in fileinput.input():
link=SyntenyToEnsembl(line)
if not link:continue
print link
print >> sys.stderr, "%s:%d"%(fileinput.filename(),SyntenyLen(line))