if args['avoidrefine'] == "False": abunHouseKeeper.abunGlobalAvoidrefine = False else: abunHouseKeeper.abunGlobalAvoidrefine = True if args['readsearch'] != None: abunHouseKeeper.abunGlobalReadSearchDepth = int(args['readsearch']) else: abunHouseKeeper.abunGlobalReadSearchDepth = 0 if args['replace'] != None: if args['replace'] == 'skip': print "skip copy" else: abunHouseKeeper.replaceFiles(newFolderName, args['replace']) else: abunHouseKeeper.replaceFiles(newFolderName, "mFixed.fasta") if args['RRDisable'] == "False": abunHouseKeeper.abunGlobalRRDisable = False else: abunHouseKeeper.abunGlobalRRDisable = True if args['pickup'] in ["map", "count", "split", "graph"]: abunHouseKeeper.abunGlobalRunPickUp = args['pickup'] if args['runemalgo'] == "True": abunHouseKeeper.abunGlobalRunEM = True else: abunHouseKeeper.abunGlobalRunEM = False
if args['avoidrefine'] == "True": abunHouseKeeper.abunGlobalAvoidrefine = True else: abunHouseKeeper.abunGlobalAvoidrefine = False if args['readsearch'] != None: abunHouseKeeper.abunGlobalReadSearchDepth = int(args['readsearch']) else: abunHouseKeeper.abunGlobalReadSearchDepth = 1 if args['replace'] != None : replacedName = args['replace'] abunHouseKeeper.replaceFiles( newFolderName, replacedName) if args['RRDisable'] == "True": abunHouseKeeper.abunGlobalRRDisable = True else: abunHouseKeeper.abunGlobalRRDisable = False if pathExists: abunSplitter.mainFlow(newFolderName, newMummerLink) else: print "Sorry. The above folders or files are missing. If you continue to have problems, please contact me(Ka-Kit Lam) at [email protected]" print "Time", time.time() - t0
if args['large'] == "True": houseKeeper.globalLarge = True else: houseKeeper.globalLarge = False if args['avoidrefine'] == "True": abunHouseKeeper.abunGlobalAvoidrefine = True else: abunHouseKeeper.abunGlobalAvoidrefine = False if args['readsearch'] != None: abunHouseKeeper.abunGlobalReadSearchDepth = int(args['readsearch']) else: abunHouseKeeper.abunGlobalReadSearchDepth = 1 if args['replace'] != None: replacedName = args['replace'] abunHouseKeeper.replaceFiles(newFolderName, replacedName) if args['RRDisable'] == "True": abunHouseKeeper.abunGlobalRRDisable = True else: abunHouseKeeper.abunGlobalRRDisable = False if pathExists: abunSplitter.mainFlow(newFolderName, newMummerLink) else: print "Sorry. The above folders or files are missing. If you continue to have problems, please contact me(Ka-Kit Lam) at [email protected]" print "Time", time.time() - t0
abunHouseKeeper.abunGlobalAvoidrefine = False else: abunHouseKeeper.abunGlobalAvoidrefine = True if args['readsearch'] != None: abunHouseKeeper.abunGlobalReadSearchDepth = int(args['readsearch']) else: abunHouseKeeper.abunGlobalReadSearchDepth = 0 if args['replace'] != None : if args['replace'] == 'skip': print "skip copy" else: abunHouseKeeper.replaceFiles( newFolderName, args['replace']) else: abunHouseKeeper.replaceFiles( newFolderName, "mFixed.fasta") if args['RRDisable'] == "False": abunHouseKeeper.abunGlobalRRDisable = False else: abunHouseKeeper.abunGlobalRRDisable = True if args['pickup'] in [ "map", "count", "split"] : abunHouseKeeper.abunGlobalRunPickUp = args['pickup'] if args['option'] != None: settingDataCombo = args['option'].split()