コード例 #1
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
    )
コード例 #2
0
ファイル: polyPhaser.py プロジェクト: Imoteph/finishingTool
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)
コード例 #3
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)