except:
pass
-import sys, string, optparse
-from commoncode import readDataset, writeLog
+import sys
+import string
+import optparse
+from commoncode import writeLog, getConfigParser, getConfigOption, getConfigBoolOption, getConfigIntOption
+import ReadDataset
-verstring = "%prog: version 4.1"
+verstring = "makerdsfrombowtie: version 4.2"
print verstring
def main(argv=None):
usage = "usage: python %prog label infilename outrdsfile [propertyName::propertyValue] [options]"
- parser = optparse.OptionParser(usage=usage)
- parser.add_option("--RNA", dest="genedatafilename")
- parser.add_option("--append", action="store_false", dest="init")
- parser.add_option("--index", action="store_true", dest="doIndex")
- parser.add_option("--spacer", type="int", dest="spacer")
- parser.add_option("--rawreadID", action="store_false", dest="trimReadID")
- parser.add_option("--forcepair", type="int", dest="forceID")
- parser.add_option("--flip", action="store_true", dest="flip")
- parser.add_option("--verbose", action="store_true", dest="verbose")
- parser.add_option("--strip", action="store_true", dest="stripSpace")
- parser.add_option("--cache", type="int", dest="cachePages")
- parser.set_defaults(genedatafilename=None, init=True, doIndex=False, spacer=2,
- trimReadID=True, forceID=None, flip=False, verbose=False,
- stripSpace=False, cachePages=100000)
-
+ parser = getParser(usage)
(options, args) = parser.parse_args(argv[1:])
if len(args) < 3:
propertyList)
+def getParser(usage):
+ parser = optparse.OptionParser(usage=usage)
+ parser.add_option("--RNA", dest="genedatafilename")
+ parser.add_option("--append", action="store_false", dest="init")
+ parser.add_option("--index", action="store_true", dest="doIndex")
+ parser.add_option("--spacer", type="int", dest="spacer")
+ parser.add_option("--rawreadID", action="store_false", dest="trimReadID")
+ parser.add_option("--forcepair", type="int", dest="forceID")
+ parser.add_option("--flip", action="store_true", dest="flip")
+ parser.add_option("--verbose", action="store_true", dest="verbose")
+ parser.add_option("--strip", action="store_true", dest="stripSpace")
+ parser.add_option("--cache", type="int", dest="cachePages")
+
+ configParser = getConfigParser()
+ section = "makerdsfrom bowtie"
+ genedatafilename = getConfigOption(configParser, section, "genedatafilename", None)
+ init = getConfigBoolOption(configParser, section, "init", True)
+ doIndex = getConfigBoolOption(configParser, section, "doIndex", False)
+ spacer = getConfigIntOption(configParser, section, "spacer", 2)
+ trimReadID = getConfigBoolOption(configParser, section, "trimReadID", True)
+ forceID = getConfigOption(configParser, section, "forceID", None)
+ flip = getConfigBoolOption(configParser, section, "flip", False)
+ verbose = getConfigBoolOption(configParser, section, "verbose", False)
+ stripSpace = getConfigBoolOption(configParser, section, "stripSpace", False)
+ cachePages = getConfigIntOption(configParser, section, "cachePages", 100000)
+
+ parser.set_defaults(genedatafilename=genedatafilename, init=init, doIndex=doIndex, spacer=spacer,
+ trimReadID=trimReadID, forceID=forceID, flip=flip, verbose=verbose,
+ stripSpace=stripSpace, cachePages=cachePages)
+
+ return parser
+
+
def makerdsfrombowtie(label, filename, outdbname, genedatafilename=None, init=True,
doIndex=False, spacer=2, trimReadID=True, forceID=None,
flip=False, verbose=False, stripSpace=False, cachePages=100000,
genedatafile.close()
- rds = readDataset(outdbname, init, dataType, verbose=True)
+ rds = ReadDataset.ReadDataset(outdbname, init, dataType, verbose=True)
#check that our cacheSize is better than the dataset's default cache size
defaultCacheSize = rds.getDefaultCacheSize()