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 )
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)
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)