danielecook
6/22/2015 - 7:45 PM

Get dictionary of wormbase IDs to genes

Get dictionary of wormbase IDs to genes

import urllib2
import StringIO
import gzip
URL = "ftp://ftp.wormbase.org/pub/wormbase/species/c_elegans/annotation/geneIDs/c_elegans.PRJNA13758.current.geneIDs.txt.gz"
response = urllib2.urlopen(URL)
compressedFile = StringIO.StringIO()
compressedFile.write(response.read())
compressedFile.seek(0)
decompressedFile = gzip.GzipFile(fileobj=compressedFile, mode='rb').read()
genes = dict([x.split(",")[1:3] for x in decompressedFile.splitlines()])