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)
