def getDist(absPath,count=1000):
fastq = fastq2reads.getReads(absPath)
if count<=1 :count=1000
reads = fastq[1::4][:count]
dist=[]
for pos in xrange(1,len(reads)):
dist.append(edDistDp(reads[pos-1],reads[pos]))
return sorted(dist,reverse=True)
def getAssembly(absPath,count=2000000):
fastq=fastq2reads.getReads(absPath)
if count<=1 :count=1000
reads = [ read+'0' for read in fastq[1::4][:count]]
SA = dc.getSA(''.join(reads))
links = overlap.getOverlap(SA,reads)
links = layout.getLayout(links)
return getPartAssembly(fastq,links,0)
def getHamm(absPath,count=1000):
hamm=[]
fastq=fastq2reads.getReads(absPath)
if count<=1 :count=1000
reads = fastq[1::4][:count]
for pos in (xrange(1,len(reads))):
hamm.append(distance(reads[pos-1],reads[pos]))
return sorted(hamm,reverse=True)
