- (options, args) = parser.parse_args(argv[1:])
-
- if len(args) < 3:
- usage()
- sys.exit(2)
-
- factor = args[0]
- hitfile = args[1]
- outfilename = args[2]
-
- findall(factor, hitfile, outfilename, options.minHits, options.minRatio, options.maxSpacing, options.listPeak, options.shift,
- options.stringency, options.noshift, options.autoshift, options.reportshift,
- options.minPlusRatio, options.maxPlusRatio, options.leftPlusRatio, options.minPeak,
- options.normalize, options.logfilename, options.withFlag, options.doDirectionality,
- options.trimValue, options.doTrim, options.doAppend, options.rnaSettings,
- options.cachePages, options.ptype, options.mockfile, options.doRevBackground, options.noMulti,
- options.strandfilter, options.combine5p)
+ configParser = getConfigParser()
+ section = "findall"
+ minHits = getConfigFloatOption(configParser, section, "minHits", 4.0)
+ minRatio = getConfigFloatOption(configParser, section, "minRatio", 4.0)
+ maxSpacing = getConfigIntOption(configParser, section, "maxSpacing", 50)
+ listPeak = getConfigBoolOption(configParser, section, "listPeak", False)
+ shift = getConfigOption(configParser, section, "shift", None)
+ stringency = getConfigFloatOption(configParser, section, "stringency", 4.0)
+ noshift = getConfigBoolOption(configParser, section, "noshift", False)
+ autoshift = getConfigBoolOption(configParser, section, "autoshift", False)
+ reportshift = getConfigBoolOption(configParser, section, "reportshift", False)
+ minPlusRatio = getConfigFloatOption(configParser, section, "minPlusRatio", 0.25)
+ maxPlusRatio = getConfigFloatOption(configParser, section, "maxPlusRatio", 0.75)
+ leftPlusRatio = getConfigFloatOption(configParser, section, "leftPlusRatio", 0.3)
+ minPeak = getConfigFloatOption(configParser, section, "minPeak", 0.5)
+ normalize = getConfigBoolOption(configParser, section, "normalize", True)
+ logfilename = getConfigOption(configParser, section, "logfilename", "findall.log")
+ withFlag = getConfigOption(configParser, section, "withFlag", "")
+ doDirectionality = getConfigBoolOption(configParser, section, "doDirectionality", True)
+ trimValue = getConfigOption(configParser, section, "trimValue", None)
+ doTrim = getConfigBoolOption(configParser, section, "doTrim", True)
+ doAppend = getConfigBoolOption(configParser, section, "doAppend", False)
+ rnaSettings = getConfigBoolOption(configParser, section, "rnaSettings", False)
+ cachePages = getConfigOption(configParser, section, "cachePages", None)
+ ptype = getConfigOption(configParser, section, "ptype", None)
+ mockfile = getConfigOption(configParser, section, "mockfile", None)
+ doRevBackground = getConfigBoolOption(configParser, section, "doRevBackground", False)
+ noMulti = getConfigBoolOption(configParser, section, "noMulti", False)
+ strandfilter = getConfigOption(configParser, section, "strandfilter", None)
+ combine5p = getConfigBoolOption(configParser, section, "combine5p", False)
+
+ parser.set_defaults(minHits=minHits, minRatio=minRatio, maxSpacing=maxSpacing, listPeak=listPeak, shift=shift,
+ stringency=stringency, noshift=noshift, autoshift=autoshift, reportshift=reportshift,
+ minPlusRatio=minPlusRatio, maxPlusRatio=maxPlusRatio, leftPlusRatio=leftPlusRatio, minPeak=minPeak,
+ normalize=normalize, logfilename=logfilename, withFlag=withFlag, doDirectionality=doDirectionality,
+ trimValue=trimValue, doTrim=doTrim, doAppend=doAppend, rnaSettings=rnaSettings,
+ cachePages=cachePages, ptype=ptype, mockfile=mockfile, doRevBackground=doRevBackground, noMulti=noMulti,
+ strandfilter=strandfilter, combine5p=combine5p)
+
+ return parser