def calculate_average_ngram_presence(coordinates,genome,ngram):
ngram_presence=np.zeros(len(coordinates))
ngram_reversed=Sequence.reverse_complement(ngram)
for idx,c in enumerate(coordinates):
seq=genome.extract_sequence(c)
ngram_presence[idx]=(seq.count(ngram)+seq.count(ngram_reversed))/float(len(c))
return ngram_presence
def calculate_average_ngram_presence(coordinates, genome, ngram):
ngram_presence = np.zeros(len(coordinates))
ngram_reversed = Sequence.reverse_complement(ngram)
for idx, c in enumerate(coordinates):
seq = genome.extract_sequence(c)
ngram_presence[idx] = (seq.count(ngram) +
seq.count(ngram_reversed)) / float(len(c))
return ngram_presence