def mainFlow(folderName , mummerLink, pickupname, mapcontigsname):      
    print "Go Bears! ! !" 
    
    print "pickupname, mapcontigsname", pickupname, mapcontigsname
    
    
    if not pickupname in ["noEmbed.fasta", "improved.fasta", "improved2.fasta"]:
        print "NonRedundantResolver RemoveEmbedded"
        nonRedundantResolver.removeEmbedded(folderName , mummerLink)
     
    if not pickupname in ["improved.fasta", "improved2.fasta"]:
        print "OverlapResolver FetchSuccessor"
        overlapResolver.fetchSuccessor(folderName , mummerLink)
        print "OverlapResolver FormSeqGraph"
        overlapResolver.formSeqGraph(folderName , mummerLink)
    
    if not pickupname in ["improved2.fasta"]:
        print "GapFiller FillGap"
        gapFiller.fillGap(folderName , mummerLink)
    
    print "TwoRepeatOneBridgeSolver XPhased"
    twoRepeatOneBridgeSolver.xPhased(folderName , mummerLink)
    
    # ECReduction(folderName , mummerLink )
    # compareWithReference(folderName , mummerLink)
    
    if mapcontigsname != None:
        print "HouseKeeper PerformMapping"
        houseKeeper.performMapping(folderName, mummerLink, mapcontigsname)
        
    print "<3 Do cool things that matter <3"
示例#2
0
def mainFlow(folderName , mummerLink, pickupname, mapcontigsname):      
    print "Go Bears! ! !" 
    
    print "pickupname, mapcontigsname", pickupname, mapcontigsname
    
    if not pickupname in ["noEmbed.fasta", "improved.fasta", "improved2.fasta"]:
        nonRedundantResolver.removeEmbedded(folderName , mummerLink)
     
    if not pickupname in ["improved.fasta", "improved2.fasta"]:
        overlapResolver.fetchSuccessor(folderName , mummerLink)
        overlapResolver.formSeqGraph(folderName , mummerLink)
    
    if not pickupname in ["improved2.fasta"]:
        gapFiller.fillGap(folderName , mummerLink)
    
    twoRepeatOneBridgeSolver.xPhased(folderName , mummerLink)
    
    # ECReduction(folderName , mummerLink )
    # compareWithReference(folderName , mummerLink)
    
    IORobot.fillInMissed(folderName, mummerLink, houseKeeper.globalContigName, "noEmbedtmp.fasta", "noEmbed.fasta")
    IORobot.fillInMissed(folderName, mummerLink, houseKeeper.globalContigName, "improvedtmp.fasta", "improved.fasta")
    IORobot.fillInMissed(folderName, mummerLink, houseKeeper.globalContigName, "improved2tmp.fasta", "improved2.fasta")
    IORobot.fillInMissed(folderName, mummerLink, houseKeeper.globalContigName, "improved3tmp.fasta", "improved3.fasta")
    

    if mapcontigsname != None:
        houseKeeper.performMapping(folderName, mummerLink, mapcontigsname)
        
    print "<3 Do cool things that matter <3"