+def getParser(usage):
+ parser = optparse.OptionParser(usage=usage)
+ parser.add_option("--fastq", action="store_true", dest="fastq")
+ parser.add_option("--fromback", action="store_true", dest="fromBack")
+ parser.add_option("--paired", action="store_true", dest="paired")
+ parser.add_option("--flip", action="store_true", dest="flipseq")
+ parser.add_option("--filter", type="int", dest="maxN")
+
+ configParser = getConfigParser()
+ section = "trimreads"
+ fastq = getConfigBoolOption(configParser, section, "fastq", False)
+ fromBack = getConfigBoolOption(configParser, section, "fromBack", False)
+ paired = getConfigBoolOption(configParser, section, "paired", False)
+ flipseq = getConfigBoolOption(configParser, section, "flipseq", False)
+ maxN = getConfigOption(configParser, section, "maxN", None)
+
+ parser.set_defaults(fastq=fastq, fromBack=fromBack, paired=paired, flipseq=flipseq, maxN=maxN)
+
+ return parser
+
+