def gwConvolve(genome, seq):
seq_hits = 0
for chrom in genome.seq_names:
if chrom == 'chrM': continue # ignore mitochondria
num = len(list(genome.nongeneIter(chrom)))
for bp_seq, record in genome.nongeneIter(chrom):
score_deque = deque()
max_score = convolveSubsequence(seq, bp_seq, score_deque)
while score_deque:
seq_hits += 1
pos,score = score_deque.pop()
return seq_hits, seq
def gwConvolveTrack(genome, seq):
seq_hits = 0
X = {}
Y = {}
P = {}
for chrom in genome.seq_names:
if chrom == 'chrM': continue # ignore mitochondria
X[chrom] = [0.0]
Y[chrom] = [0.0]
P[chrom] = []
num = len(list(genome.nongeneIter(chrom)))
for bp_seq, record in genome.nongeneIter(chrom):
score_deque = deque()
max_score = convolveSubsequence(seq, bp_seq, score_deque)
while score_deque:
seq_hits += 1
pos,score = score_deque.pop()
pos += record.start # locate on chromasome
X[chrom].extend((pos,pos,pos))
Y[chrom].extend((0.0,1.2,0.0))
P[chrom].append(pos)
return X,Y,P
