# Created by Ali Mortazavi on 8/12/08.
#
-import sys, optparse
+import sys
+import optparse
from cistematic.core import complement
+from commoncode import getConfigParser, getConfigBoolOption, getConfigOption
-print "%prog: version 2.1"
+print "trimreads: version 2.2"
def main(argv=None):
if not argv:
usage = "usage: python %prog length infile outfile [--fastq] [--fromback] [--paired] [--flip] [--filter maxN]"
- 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")
- parser.set_defaults(fastq=False, fromBack=False, paired=False, flipseq=False, maxN=None)
+ parser = getParser(usage)
(options, args) = parser.parse_args(argv[1:])
if len(args) < 3:
trimreads(length, infile, outfile, options.fastq, options.fromBack, options.paired, options.flipseq, options.maxN)
+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
+
+
def trimreads(length, inFileName, outFileName, fastq=False, fromBack=False, paired=False, flipseq=False, maxN=None):
infile = open(inFileName)
outfile = open(outFileName, "w")