active=chrlist.pop(0) while(True): tested=[] activeUnmodified=True while(len(chrlist)>0): totest=chrlist.pop(0) #if(comparecount%100000==0): # print "Finished {0} comparision; len chrlist {1}".format(comparecount,len(chrlist)) comparecount+=1 testdist,narrowdist=get_distance(active,totest) if(testdist < maxdist): active = mergeNucmer(active,totest,testdist) activeUnmodified=False else: tested.append(totest) chrlist=tested if activeUnmodified: break chrentries.append(active) print "Finished {0} with {1} fragments".format(chr,len(chrentries)) finallist.extend(chrentries) refgtf=get_refgtflist(finallist) querygtf=get_querygtflist(finallist) GTFWriter.write_all(options.outputref,refgtf) # (cls,file,gtfentries): GTFWriter.write_all(options.outputquery,querygtf) if(options.outputdist): print_distances(options.outputdist,finallist)
while (len(chrlist) > 0): active = chrlist.pop(0) while (True): tested = [] activeUnmodified = True while (len(chrlist) > 0): totest = chrlist.pop(0) #if(comparecount%100000==0): # print "Finished {0} comparision; len chrlist {1}".format(comparecount,len(chrlist)) comparecount += 1 testdist, narrowdist = get_distance(active, totest) if (testdist < maxdist): active = mergeNucmer(active, totest, testdist) activeUnmodified = False else: tested.append(totest) chrlist = tested if activeUnmodified: break chrentries.append(active) print "Finished {0} with {1} fragments".format(chr, len(chrentries)) finallist.extend(chrentries) refgtf = get_refgtflist(finallist) querygtf = get_querygtflist(finallist) GTFWriter.write_all(options.outputref, refgtf) # (cls,file,gtfentries): GTFWriter.write_all(options.outputquery, querygtf) if (options.outputdist): print_distances(options.outputdist, finallist)