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)