import sys
import optparse
-from commoncode import readDataset
+import ReadDataset
+from commoncode import getConfigParser, getConfigBoolOption, getConfigIntOption
-print "%prog: version 2.7"
+print "rdsmetadata: version 2.8"
def main(argv=None):
usage = "usage: python %prog rdsfile [propertyName1::propertyValue1] ... [propertyNameN::propertyValueN] [options]"
- parser = optparse.OptionParser(usage=usage)
- parser.add_option("--defaultcache", type="int", dest="cacheVal")
- parser.add_option("--index", action="store_true", dest="buildIndex")
- parser.add_option("--dropindex", action="store_true", dest="dropIndex")
- parser.add_option("--nocount", action="store_false", dest="doCount")
- parser.add_option("--complexity", action="store_true", dest="doComplexity")
- parser.add_option("--reset", action="store_true", dest="resetFlags")
- parser.add_option("--initrna", action="store_true", dest="rnaDataType")
- parser.add_option("--cache", type="int", dest="cachePages")
- parser.set_defaults(cacheVal=0, buildIndex=False, dropIndex=False, doCount=True,
- doComplexity=False, resetFlags=False, rnaDataType=False,
- cachePages=-1)
-
+ parser = makeParser(usage)
(options, args) = parser.parse_args(argv[1:])
if len(args) < 1:
options.resetFlags, options.rnaDataType, options.cachePages)
+def makeParser(usage=""):
+ parser = optparse.OptionParser(usage=usage)
+ parser.add_option("--defaultcache", type="int", dest="cacheVal")
+ parser.add_option("--index", action="store_true", dest="buildIndex")
+ parser.add_option("--dropindex", action="store_true", dest="dropIndex")
+ parser.add_option("--nocount", action="store_false", dest="doCount")
+ parser.add_option("--complexity", action="store_true", dest="doComplexity")
+ parser.add_option("--reset", action="store_true", dest="resetFlags")
+ parser.add_option("--initrna", action="store_true", dest="rnaDataType")
+ parser.add_option("--cache", type="int", dest="cachePages")
+
+ configParser = getConfigParser()
+ section = "rdsmetadata"
+ cacheVal = getConfigIntOption(configParser, section, "cacheVal", 0)
+ buildIndex = getConfigBoolOption(configParser, section, "buildIndex", False)
+ dropIndex = getConfigBoolOption(configParser, section, "dropIndex", False)
+ doCount = getConfigBoolOption(configParser, section, "doCount", True)
+ doComplexity = getConfigBoolOption(configParser, section, "doComplexity", False)
+ resetFlags = getConfigBoolOption(configParser, section, "resetFlags", False)
+ rnaDataType = getConfigBoolOption(configParser, section, "rnaDataType", False)
+ cachePages = getConfigIntOption(configParser, section, "cachePages", -1)
+
+ parser.set_defaults(cacheVal=cacheVal, buildIndex=buildIndex, dropIndex=dropIndex, doCount=doCount,
+ doComplexity=doComplexity, resetFlags=resetFlags, rnaDataType=rnaDataType,
+ cachePages=cachePages)
+
+ return parser
+
+
def rdsmetadata(datafile, propertyList=[], cacheVal=0, buildIndex=False,
dropIndex=False, doCount=True, doComplexity=False, resetFlags=False,
rnaDataType=False, cachePages=-1):
doCache = True
if rnaDataType:
- rds = readDataset(datafile, initialize=True, datasetType="RNA", verbose=True, cache=doCache)
+ rds = ReadDataset.ReadDataset(datafile, initialize=True, datasetType="RNA", verbose=True, cache=doCache)
else:
- rds = readDataset(datafile, verbose=True, reportCount=doCount, cache=doCache)
+ rds = ReadDataset.ReadDataset(datafile, verbose=True, reportCount=doCount, cache=doCache)
if cachePages > rds.getDefaultCacheSize():
rds.setDBcache(cachePages)