# quality: gold
import json
from uuid import uuid4
import numpy as np
from immuneML.data_model.DatasetItem import DatasetItem
from immuneML.data_model.receptor.receptor_sequence.SequenceAnnotation import SequenceAnnotation
from immuneML.data_model.receptor.receptor_sequence.SequenceMetadata import SequenceMetadata
from immuneML.environment.EnvironmentSettings import EnvironmentSettings
from immuneML.environment.SequenceType import SequenceType
from immuneML.util.NumpyHelper import NumpyHelper
[docs]
class ReceptorSequence(DatasetItem):
FIELDS = {'amino_acid_sequence': str, 'nucleotide_sequence': str, 'identifier': str, 'metadata': dict, 'annotation': dict, 'version': str}
version = "1"
[docs]
@classmethod
def create_from_record(cls, record: np.void):
if 'version' in record.dtype.names and record['version'] == cls.version:
return ReceptorSequence(**{**{key: record[key] for key, val_type in ReceptorSequence.FIELDS.items()
if val_type == str and key != 'version'},
**{'metadata': SequenceMetadata(**json.loads(record['metadata'])) if record['metadata'] != '' else None,
'annotation': SequenceAnnotation(**json.loads(record['annotation'])) if record['annotation'] != ''
else None}})
else:
raise NotImplementedError
[docs]
@classmethod
def get_record_names(cls):
return [key for key in cls.FIELDS]
def __init__(self,
amino_acid_sequence: str = None,
nucleotide_sequence: str = None,
identifier: str = None,
annotation: SequenceAnnotation = None,
metadata: SequenceMetadata = None):
self.identifier = identifier if identifier is not None and identifier != "" else uuid4().hex
self.amino_acid_sequence = amino_acid_sequence
self.nucleotide_sequence = nucleotide_sequence
self.annotation = annotation
self.metadata = metadata if metadata is not None else SequenceMetadata()
def __repr__(self):
return f"ReceptorSequence(sequence_aa={self.amino_acid_sequence}, sequence={self.nucleotide_sequence}, " \
f"annotation={vars(self.annotation) if self.annotation is not None else '{}'}, " \
f"metadata={vars(self.metadata) if self.metadata is not None else '{}'})"
[docs]
def set_annotation(self, annotation: SequenceAnnotation):
self.annotation = annotation
[docs]
def get_sequence(self, sequence_type: SequenceType = None):
"""Returns receptor_sequence (nucleotide/amino acid) that corresponds to provided sequence type or preset receptor_sequence type from
EnvironmentSettings class if no type is provided"""
sequence_type_ = EnvironmentSettings.get_sequence_type() if sequence_type is None else sequence_type
if sequence_type_ == SequenceType.AMINO_ACID:
return self.amino_acid_sequence
else:
return self.nucleotide_sequence
[docs]
def set_sequence(self, sequence: str, sequence_type: SequenceType):
if sequence_type == SequenceType.AMINO_ACID:
self.amino_acid_sequence = sequence
else:
self.nucleotide_sequence = sequence
[docs]
def get_record(self):
"""exports the sequence object as a numpy record"""
return [NumpyHelper.get_numpy_representation(getattr(self, name)) if hasattr(self, name) else getattr(ReceptorSequence, name)
for name in ReceptorSequence.FIELDS.keys()]
[docs]
def get_attribute(self, name: str):
if hasattr(self, name):
return getattr(self, name)
elif hasattr(self.metadata, name):
return getattr(self.metadata, name)
elif name in self.metadata.custom_params:
return self.metadata.custom_params[name]
elif hasattr(self.annotation, name):
return getattr(self.annotation, name)
else:
raise KeyError(f"ReceptorSequence {self.identifier} does not have attribute {name}.")