def getSeeds(fafile,sense=True,start_at=2,stop_at=8): if sense: for fa in IO.BioReader(fafile,'fasta'): yield fa.id,fa.seq.seq[start_at-1:stop_at-1] else: for fa in IO.BioReader(fafile,'fasta'): yield fa.id,Utils.rc(fa.seq.seq)[start_at-1:stop_at-1]
def findSeeds(seq,sary): sary.fill(0) seq = Utils.rc(seq) for i in range(len(seq)-7): sary[twoBytesTable[seq[i:i+8]]] += 1