def encode_sequence(sequence: ReceptorSequence, params: EncoderParams):
"""
creates overlapping continuous k-mers from a sequence as features for use in KmerFrequencyEncoder
object of type EncoderParams, same object as passed into KmerFrequencyEncoder
:param sequence: ReceptorSequence
:param params: EncoderParams (where params["model"]["k"] is used)
:return: SequenceEncodingResult consisting of features and feature information names
"""
k = params.model["k"]
sequence_type = params.model.get('sequence_type', None)
length = len(sequence.get_sequence(sequence_type))
if length < k:
logging.warning(
'Sequence length is less than k. Ignoring sequence')
return None
kmers = KmerHelper.create_IMGT_kmers_from_sequence(
sequence=sequence, k=k, sequence_type=sequence_type)
kmers = [
Constants.FEATURE_DELIMITER.join([str(mer) for mer in kmer])
for kmer in kmers
]
return kmers
def test_create_IMGT_kmers_from_sequence(self):
kmers = KmerHelper.create_IMGT_kmers_from_sequence(ReceptorSequence("CASSRYUF"), 3, sequence_type=SequenceType.AMINO_ACID)
self.assertTrue(("CAS", 105) in kmers)
self.assertTrue(("ASS", 106) in kmers)
self.assertTrue(("SSR", 107) in kmers)
self.assertTrue(("SRY", 108) in kmers)
self.assertTrue(("RYU", 114) in kmers)
self.assertTrue(("YUF", 115) in kmers)