def test_four_kmers_all(self):
k = Kmers('AAAAATTTTTTTT', 4)
self.assertEqual(k.get_all_kmers_freq(max_kmer_count=5), {
'AAAA': 2,
'AAAT': 1,
'AATT': 1,
'ATTT': 1,
'TTTT': 4
})
def sequence_kmers_vals(self):
seq_counter = 0
kmer_to_sequences = {}
for record in SeqIO.parse(self.filename, "fasta"):
sequence_length = len(record.seq)
if self.divisible_by_3 and sequence_length % 3 != 0:
self.logger.warning(
"Excluding gene as it is not divisible by 3:" + record.id)
continue
kmers = Kmers(str(record.seq), self.k)
# We assume here that the sequence name is unique in the FASTA file
kmer_to_sequences[record.id] = kmers.get_all_kmers_freq(
max_kmer_count=self.max_kmers)
seq_counter += 1
return kmer_to_sequences