def contigWorker((contigsFilePath, minMatchLen)): #get contig map for the passed contigs refContigsNameLen, queryContigsNameLen, refAdjList, queryAdjList\ = contigsCoordsConv.parseContigFileNGetMapInfo(contigsFilePath,\ minMatchLen) #try to plot cross minimize ordering contigsCoordsConv.plotCrossMinimizedOrdering(refAdjList, queryAdjList,\ minMatchLen) return True
def main(): if len(sys.argv) >= 4: #contigMapFile contigMapFilePath = os.path.abspath(sys.argv[1]) #min match length minMatchLen = int(sys.argv[2]) #plot outputfile plotOutFilePath = os.path.abspath(sys.argv[3]) #get scaff map for the passed sequences contigMap = contigsCoordsConv.parseContigFileNGetMapInfo(contigMapFilePath) #generate plot for scaff map scaffMapPlotter.generatePlot(contigMap, minMatchLen, plotOutFilePath) else: print 'err: files missin'