from immuneML.data_model.receptor.receptor_sequence.ReceptorSequence import ReceptorSequence
from immuneML.encodings.EncoderParams import EncoderParams
from immuneML.encodings.kmer_frequency.sequence_encoding.SequenceEncodingStrategy import SequenceEncodingStrategy
from immuneML.environment.Constants import Constants
from immuneML.environment.EnvironmentSettings import EnvironmentSettings
[docs]
class IdentitySequenceEncoder(SequenceEncodingStrategy):
[docs]
@staticmethod
def encode_sequence(sequence: ReceptorSequence, params: EncoderParams):
"""
Encodes a ReceptorSequence based on information from within the ReceptorSequence and SequenceMetadata
instances. This allows for looking at frequency for whole sequences, with flexible definition of what a unique
whole sequence is.
:param sequence: ReceptorSequence
:param params: EncoderParams (params["model"]["sequence"] and params["model"]["metadata_fields_to_include"] are
used)
:return: list with only single feature
"""
res = []
sequence_type = params.model.get('sequence_type', EnvironmentSettings.sequence_type)
if params.model.get("sequence", True):
res.append(sequence.get_sequence(sequence_type))
for field in params.model.get("metadata_fields_to_include", []):
if sequence.metadata is None:
res.append("unknown")
else:
res.append(getattr(sequence.metadata, field))
return [Constants.FEATURE_DELIMITER.join(res)]
[docs]
@staticmethod
def get_feature_names(params: EncoderParams):
res = []
if params.model.get("sequence", True):
res.append("sequence")
for field in params.model.get("metadata_fields_to_include", []):
res.append(field)
return res