except:
pass
-import sys, optparse
-from commoncode import readDataset
+import sys
+import optparse
+import ReadDataset
from cistematic.genomes import Genome
from cistematic.core import chooseDB, cacheGeneDB, uncacheGeneDB
+from commoncode import getConfigParser, getConfigOption, getConfigIntOption, getConfigBoolOption, getConfigFloatOption
-print "%prog: version 5.6"
+print "normalizeExpandedExonic: version 5.7"
def main(argv=None):
usage = "usage: python %s genome rdsfile uniqcountfile splicecountfile outfile [candidatefile acceptfile] [--gidField fieldID] [--maxLength kblength] [--cache]"
- parser = optparse.OptionParser(usage=usage)
- parser.add_option("--gidField", type="int", dest="fieldID")
- parser.add_option("--maxLength", type="float", dest="maxLength")
- parser.add_option("--cache", action="store_true", dest="doCache")
- parser.add_option("--models", dest="extendGenome")
- parser.add_option("--replacemodels", action="store_true", dest="replaceModels")
- parser.set_defaults(fieldID=0, maxLength=1000000000., doCache=False, extendGenome="",
- replaceModels=False)
-
+ parser = makeParser(usage)
(options, args) = parser.parse_args(argv[1:])
if len(sys.argv) < 6:
options.replaceModels)
+def makeParser(usage=""):
+ parser = optparse.OptionParser(usage=usage)
+ parser.add_option("--gidField", type="int", dest="fieldID")
+ parser.add_option("--maxLength", type="float", dest="maxLength")
+ parser.add_option("--cache", action="store_true", dest="doCache")
+ parser.add_option("--models", dest="extendGenome")
+ parser.add_option("--replacemodels", action="store_true", dest="replaceModels")
+
+ configParser = getConfigParser()
+ section = "normalizeExpandedExonic"
+ fieldID = getConfigIntOption(configParser, section, "fieldID", 0)
+ maxLength = getConfigFloatOption(configParser, section, "maxLength", 1000000000.)
+ doCache = getConfigBoolOption(configParser, section, "doCache", False)
+ extendGenome = getConfigOption(configParser, section, "extendGenome", "")
+ replaceModels = getConfigBoolOption(configParser, section, "replaceModels", False)
+
+ parser.set_defaults(fieldID=fieldID, maxLength=maxLength, doCache=doCache, extendGenome=extendGenome,
+ replaceModels=replaceModels)
+
+ return parser
+
+
def normalizeExpandedExonic(genome, hitfile, uniquecountfilename, splicecountfilename,
outfilename, candidateLines=[], acceptedfilename="",
fieldID=0, maxLength=1000000000., doCache=False,
if extendGenome != "":
hg.extendFeatures(extendGenome, replace=replaceModels)
- RDS = readDataset(hitfile, verbose = True, cache=doCache, reportCount=False)
+ RDS = ReadDataset.ReadDataset(hitfile, verbose = True, cache=doCache, reportCount=False)
uniqcount = RDS.getUniqsCount()
print "%d unique reads" % uniqcount