-import sys, optparse
+import sys
+import optparse
from cistematic.genomes import Genome
-from cistematic.core.geneinfo import geneinfoDB
+from commoncode import getGeneInfoDict, getConfigParser, getConfigOption, getConfigBoolOption
-print "%prog: version 3.1"
+print "getGOgenes: version 3.2"
def main(argv=None):
if not argv:
usage = "usage: python %s genome GOID1 [GOID2 ....] [--outfile outfilename] [--append] [--restrict genefile]"
- parser = optparse.OptionParser(usage=usage)
- parser.add_option("--outfile", dest="outfilename")
- parser.add_option("--append", action="store_true", dest="append")
- parser.add_option("--restrict", dest="restrictfilename")
- parser.set_defaults(outfilename=None, restrictfilename=None, append=False)
+ parser = makeParser(usage)
(options, args) = parser.parse_args(argv[1:])
if len(args) < 2:
getGOgenes(genome, GOIDlist, options.outfilename, options.restrictfilename, options.append)
+def makeParser(usage=""):
+ parser = optparse.OptionParser(usage=usage)
+ parser.add_option("--outfile", dest="outfilename")
+ parser.add_option("--append", action="store_true", dest="append")
+ parser.add_option("--restrict", dest="restrictfilename")
+
+ configParser = getConfigParser()
+ section = "getGOgenes"
+ outfilename = getConfigOption(configParser, section, "outfilename", None)
+ restrictfilename = getConfigOption(configParser, section, "restrictfilename", None)
+ append = getConfigBoolOption(configParser, section, "append", False)
+
+ parser.set_defaults(outfilename=outfilename, restrictfilename=restrictfilename, append=append)
+
+ return parser
+
+
def getGOgenes(genome, GOIDlist, outfilename=None, restrictfilename=None, append=False):
writeOut = False
if outfilename is not None:
restrict = True
hg = Genome(genome)
- idb = geneinfoDB()
print sys.argv
print GOIDlist
geneList = geneDict.keys()
print len(geneList)
- geneInfoList = idb.getallGeneInfo(genome)
+ geneInfoList = getGeneInfoDict(genome)
if writeOut:
if append: