-"""
-Based on shell script provided by Ali.
-"""
-
import sys
import optparse
-from Erange import chksnp, getSNPs, getSNPGeneInfo, analyzego, getNovelSNPs, makeSNPtrack, rnaAToIFilter
-from Erange.commoncode import countDuplicatesInList
+from erange import chksnp, getSNPs, getSNPGeneInfo, analyzego, getNovelSNPs, makeSNPtrack, rnaAToIFilter
+from erange.commoncode import countDuplicatesInList, getConfigParser, getConfigOption
def main(argv=None):
usage = "usage: python %prog dbfile snpsfile genome rpkmfile [options]"
- parser = optparse.OptionParser(usage=usage)
- parser.add_option("--goprefix", dest="prefix")
- parser.add_option("--novelsnp", dest="novelsnpoutfilename")
- parser.add_option("--bedfile", dest="bedoutfilename")
- parser.add_option("--cache", type="int", dest="cachePages")
- parser.add_option("--snpDB", action="append", dest="snpDBList",
- help="additional snp db files to check will be searched in order given")
- parser.set_defaults(prefix=None, novelsnpoutfilename=None, bedoutfilename=None, cachePages=None, snpDBList=[])
+ parser = getParser(usage)
(options, args) = parser.parse_args(argv[1:])
if len(args) < 4:
genome = args[2]
rpkmfilename = args[3]
+ rnaEditing(dbfile, hitfile, genome, rpkmfilename, options)
+
+
+def getParser(usage):
+ parser = optparse.OptionParser(usage=usage)
+ parser.add_option("--goprefix", dest="prefix")
+ parser.add_option("--novelsnp", dest="novelsnpoutfilename")
+ parser.add_option("--bedfile", dest="bedoutfilename")
+ parser.add_option("--cache", type="int", dest="cachePages")
+ parser.add_option("--snpDB", action="append", dest="snpDBList",
+ help="additional snp db files to check will be searched in order given")
+
+ configParser = getConfigParser()
+ section = "rnaEditing"
+ prefix = getConfigOption(configParser, section, "prefix", None)
+ novelsnpoutfilename = getConfigOption(configParser, section, "novelsnpoutfilename", None)
+ bedoutfilename = getConfigOption(configParser, section, "bedoutfilename", None)
+ cachePages = getConfigOption(configParser, section, "cachePages", None)
+
+ parser.set_defaults(prefix=prefix, novelsnpoutfilename=novelsnpoutfilename, bedoutfilename=bedoutfilename,
+ cachePages=cachePages, snpDBList=[])
+
+ return parser
+
+
+def rnaEditing(dbfile, hitfile, genome, rpkmfilename, options):
if options.cachePages is not None:
doCache = True
else: