Python replaceFiles Examples

Example #1

    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

Example #2

File: aSplitter.py Project: Imoteph/finishingTool

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

Example #3

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

Example #4

File: aSplitter.py Project: sophy7074/MetaFinisherSC

    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()