def kmer_kernel(seq, k, canonical=True):
kmer_counts = {}
if canonical:
seq_rc = dna.rc(seq)
for i in range(len(seq)-k+1):
kmer = seq[i:i+k]
if kmer.find('N') == -1:
kmer_counts[kmer] = kmer_counts.get(kmer,0) + 1
if canonical:
kmer_rc = seq_rc[i:i+k]
kmer_counts[kmer_rc] = kmer_counts.get(kmer_rc,0) + 1
if canonical:
kmer_counts = dna.canonical_kmers(kmer_counts)
# normalize
# kmer_sum = float(sum(kmer_counts.values()))
kmer_sum = float(sum(np.square(list(kmer_counts.values()))))
vec = {}
for kmer in kmer_counts:
vec[kmer] = kmer_counts[kmer] / kmer_sum
return vec
def kmer_kernel(seq, k, canonical=True):
kmer_counts = {}
if canonical:
seq_rc = dna.rc(seq)
for i in range(len(seq) - k + 1):
kmer = seq[i:i + k]
if kmer.find('N') == -1:
kmer_counts[kmer] = kmer_counts.get(kmer, 0) + 1
if canonical:
kmer_rc = seq_rc[i:i + k]
kmer_counts[kmer_rc] = kmer_counts.get(kmer_rc, 0) + 1
if canonical:
kmer_counts = dna.canonical_kmers(kmer_counts)
# normalize
# kmer_sum = float(sum(kmer_counts.values()))
kmer_sum = float(sum(np.square(list(kmer_counts.values()))))
vec = {}
for kmer in kmer_counts:
vec[kmer] = kmer_counts[kmer] / kmer_sum
return vec
def __init__(self, header, seq, k):
self.header = header
self.kmers = dna.canonical_kmers(dna.count_kmers(k, seq.upper(), True))
def __init__(self, header, seq, k):
self.header = header
self.kmers = dna.canonical_kmers(dna.count_kmers(k,seq.upper(),True))
