except:
pass
-import sys, string, optparse
-from commoncode import readDataset, writeLog
+import sys
+import string
+import optparse
+from commoncode import writeLog, getConfigParser, getConfigIntOption, getConfigBoolOption
+import ReadDataset
-verstring = "%prog: version 2.1" % sys.argv[0]
+verstring = "makerdsfrombed: version 2.2"
print verstring
usage = "usage: python %prog label bedfile outrdsfile [--append] [--index] [propertyName::propertyValue] [--cache numPages]"
- parser = optparse.OptionParser(usage=usage)
- parser.add_option("--append", action="store_false", dest="init")
- parser.add_option("--index", action="store_true", dest="doIndex")
- parser.add_option("--cache", type="int", dest="cachePages")
- parser.add_option("--RNA", action="store_true", dest="rnaDataType")
- parser.set_defaults(init=True, rnaDataType=False, doIndex=False, cachePages=100000)
+ parser = makeParser(usage)
(options, args) = parser.parse_args(argv[1:])
if len(args) < 3:
makerdsfrombed(label, filename, outdbname, options.init, dataType, options.doIndex, options.cachePages, propertyList)
+def makeParser(usage=""):
+ parser = optparse.OptionParser(usage=usage)
+ parser.add_option("--append", action="store_false", dest="init")
+ parser.add_option("--index", action="store_true", dest="doIndex")
+ parser.add_option("--cache", type="int", dest="cachePages")
+ parser.add_option("--RNA", action="store_true", dest="rnaDataType")
+
+ configParser = getConfigParser()
+ section = "makerdsfrombed"
+ init = getConfigBoolOption(configParser, section, "init", True)
+ rnaDataType = getConfigBoolOption(configParser, section, "RNA", False)
+ doIndex = getConfigBoolOption(configParser, section, "doIndex", False)
+ cachePages = getConfigIntOption(configParser, section, "cachePages", 100000)
+
+ parser.set_defaults(init=init, rnaDataType=rnaDataType, doIndex=doIndex, cachePages=cachePages)
+
+ return parser
+
+
def makerdsfrombed(label, filename, outdbname, init=True, dataType="DNA", doIndex=False, cachePages=100000, propertyList=[]):
readsize = 0
padsize = 0
infile = open(filename,"r")
- rds = readDataset(outdbname, init, dataType, verbose=True)
+ rds = ReadDataset.ReadDataset(outdbname, init, dataType, verbose=True)
if not init:
rds.dropIndex()