Example #1
0
def mainFlow(folderName, mummerLink):

    contigFilename = "improved3"
    readsetFilename = "phasingSeedName"
    optTypeFileHeader = "phaseString"
    contigReadGraph = "phaseStringGraph1"
    repeatFilename = "phaseRepeat.txt"
    repeatSpec = "repeatSpecification.txt"
    optionToRun = "xphase"

    if False:
		associatedReadFinder.getAllAssociatedReads(folderName, mummerLink,readsetFilename)
   		readContigGraphFormer.formReadContigStringGraph(folderName, mummerLink,contigFilename, readsetFilename, optTypeFileHeader , contigReadGraph )
    	repeatFinder.identifyRepeat(folderName, mummerLink,contigFilename,contigReadGraph, repeatFilename, optionToRun )
    
    if False:
	    myCountDic = generateAbundanceGraph(folderName, mummerLink, contigFilename)
    
	if False:
    	splitter(folderName, mummerLink, contigReadGraph, contigFilename,readsetFilename )

        
	os.system("cp selected_raw.part-* "+ folderName )
	os.system("rm selected_raw.part-*")

#mainFlow()
def mainFlow(folderName, mummerLink):
    print "Hello world"

    contigFilename = "improved3"
    readsetFilename = "phasingSeedName"
    optTypeFileHeader = "phaseString"
    contigReadGraph = "phaseStringGraph1"
    repeatFilename = "phaseRepeat.txt"
    repeatSpec = "repeatSpecification.txt"
    optionToRun = "xphase"

    if True:
        associatedReadFinder.getAllAssociatedReads(folderName, mummerLink, readsetFilename)
        readContigGraphFormer.formReadContigStringGraph(
            folderName, mummerLink, contigFilename, readsetFilename, optTypeFileHeader, contigReadGraph
        )
        repeatFinder.identifyRepeat(
            folderName, mummerLink, contigFilename, contigReadGraph, repeatFilename, optionToRun
        )

    if True:
        myCountDic = generateAbundanceGraph(folderName, mummerLink)

    if True:
        splitter(folderName, mummerLink)

    os.system("cp selected_raw.part-* " + folderName)
    os.system("rm selected_raw.part-*")
def skeletonIdentification(
    folderName,
    mummerLink,
    contigFilename,
    readsetFilename,
    optTypeFileHeader,
    contigReadGraph,
    repeatFilename,
    repeatSpec,
    optionToRun,
):
    print "skeletonIdentification"
    associatedReadFinder.getAllAssociatedReads(folderName, mummerLink, readsetFilename)
    readContigGraphFormer.formReadContigStringGraph(
        folderName, mummerLink, contigFilename, readsetFilename, optTypeFileHeader, contigReadGraph
    )
    repeatFinder.identifyRepeat(folderName, mummerLink, contigFilename, contigReadGraph, repeatFilename, optionToRun)
    repeatFlankingDefiner.defineRepeatAndFlanking(
        folderName, mummerLink, contigFilename, contigReadGraph, repeatFilename, repeatSpec
    )
Example #4
0
def mainFlow(folderName="SampleTest2/", mummerLink="MUMmer3.23/"):
    print "Hello world"
    
    contigFilename = "improved3"
    readsetFilename = "phasingSeedName"
    optTypeFileHeader = "phaseString"
    contigReadGraph = "phaseStringGraph1"
    repeatFilename = "phaseRepeat.txt"
    repeatSpec = "repeatSpecification.txt"
    
    optionToRun = "xphase"
    
    if True:
        associatedReadFinder.getAllAssociatedReads(folderName, mummerLink,readsetFilename)
    
        readContigGraphFormer.formReadContigStringGraph(folderName, mummerLink,contigFilename, readsetFilename, optTypeFileHeader , contigReadGraph )
    
        repeatFinder.identifyRepeat(folderName, mummerLink,contigFilename,contigReadGraph, repeatFilename, optionToRun )
    
    repeatFlankingDefiner.defineRepeatAndFlanking(folderName, mummerLink,contigFilename,contigReadGraph,repeatFilename,repeatSpec )    
    
    performPhasing(folderName, mummerLink)
Example #5
0
def mainFlow(folderName, mummerLink):
    print "Hello world"

    contigFilename = "improved3"
    readsetFilename = "phasingSeedName"
    optTypeFileHeader = "phaseString"
    contigReadGraph = "phaseStringGraph1"
    repeatFilename = "phaseRepeat.txt"
    repeatSpec = "repeatSpecification.txt"
    optionToRun = "xphase"

    if abunHouseKeeper.abunGlobalRunPickUp == "map":
        associatedReadFinder.getAllAssociatedReads(folderName, mummerLink,
                                                   readsetFilename)
        readContigGraphFormer.formReadContigStringGraph(
            folderName, mummerLink, contigFilename, readsetFilename,
            optTypeFileHeader, contigReadGraph)
        repeatFinder.identifyRepeat(folderName, mummerLink, contigFilename,
                                    contigReadGraph, repeatFilename,
                                    optionToRun)

    if abunHouseKeeper.abunGlobalRunPickUp == "map" or abunHouseKeeper.abunGlobalRunPickUp == "count":
        myCountDic = generateAbundanceGraph(folderName, mummerLink,
                                            contigFilename)

    if abunHouseKeeper.abunGlobalRunPickUp == "map" or abunHouseKeeper.abunGlobalRunPickUp == "count" or abunHouseKeeper.abunGlobalRunPickUp == "split":
        splitter(folderName, mummerLink, contigReadGraph, contigFilename,
                 readsetFilename)

    if abunHouseKeeper.abunGlobalRunPickUp == "graph":
        print "Graph here"
        readContigGraphFormer.formReadContigStringGraph(
            folderName, mummerLink, contigFilename, readsetFilename,
            optTypeFileHeader, contigReadGraph, False)
        splitter(folderName, mummerLink, contigReadGraph, contigFilename,
                 readsetFilename)

    os.system("cp selected_raw.part-* " + folderName)
    os.system("rm selected_raw.part-*")
Example #6
0
def skeletonIdentification(folderName, mummerLink, contigFilename, readsetFilename, optTypeFileHeader, contigReadGraph , repeatFilename, repeatSpec, optionToRun):
    print "skeletonIdentification"
    associatedReadFinder.getAllAssociatedReads(folderName, mummerLink,readsetFilename)
    readContigGraphFormer.formReadContigStringGraph(folderName, mummerLink, contigFilename, readsetFilename, optTypeFileHeader , contigReadGraph)
    repeatFinder.identifyRepeat(folderName, mummerLink, contigFilename, contigReadGraph, repeatFilename, optionToRun)
    repeatFlankingDefiner.defineRepeatAndFlanking(folderName, mummerLink, contigFilename, contigReadGraph, repeatFilename, repeatSpec)