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
