immuneML.environment package

Submodules

immuneML.environment.Constants module

class immuneML.environment.Constants.Constants[source]

Bases: object

ALLELE_DELIMITER = '*'
CACHE_PATH = 'cache_path'
CACHE_TYPE = 'cache_type'
COMMENT_SIGN = '#'
FEATURE_DELIMITER = '-'
GENE_DELIMITER = '-'
NOT_COMPUTED = 'not computed'
PLOTLY_BLACK = '#2A3F5E'
STOP_CODON = '*'
UNKNOWN = None
VERSION = '2.1.2'

immuneML.environment.EnvironmentSettings module

class immuneML.environment.EnvironmentSettings.EnvironmentSettings[source]

Bases: object

Class containing environment variables, like receptor_sequence type, root path etc.

cache_path = PosixPath('/Users/milenpa/PycharmProjects/BMIImmuneML/cache')
default_analysis_path = PosixPath('/Users/milenpa/PycharmProjects/BMIImmuneML/analysis_runs')
default_params_path = PosixPath('/Users/milenpa/PycharmProjects/BMIImmuneML/immuneML/config/default_params')
static get_cache_path(cache_type: Optional[immuneML.caching.CacheType.CacheType] = None)[source]
static get_cache_type()[source]
static get_sequence_alphabet(sequence_type: Optional[immuneML.environment.SequenceType.SequenceType] = None)[source]
Returns

alphabetically sorted receptor_sequence alphabet

static get_sequence_type() → immuneML.environment.SequenceType.SequenceType[source]
html_templates_path = PosixPath('/Users/milenpa/PycharmProjects/BMIImmuneML/immuneML/presentation/html/templates')
low_memory = True
max_sequence_length = 20
static reset_cache_path()[source]
root_path = PosixPath('/Users/milenpa/PycharmProjects/BMIImmuneML')
sequence_type = 'sequence_aas'
static set_cache_path(path: pathlib.Path)[source]
static set_sequence_type(sequence_type: immuneML.environment.SequenceType.SequenceType)[source]
source_docs_path = PosixPath('/Users/milenpa/PycharmProjects/BMIImmuneML/docs/source')
specs_docs_path = PosixPath('/Users/milenpa/PycharmProjects/BMIImmuneML/docs/specs')
tmp_cache_path = PosixPath('/Users/milenpa/PycharmProjects/BMIImmuneML/test/tmp/cache')
tmp_test_path = PosixPath('/Users/milenpa/PycharmProjects/BMIImmuneML/test/tmp')

immuneML.environment.Label module

class immuneML.environment.Label.Label(name: str, values: Optional[list] = None, auxiliary_label_names: Optional[list] = None, positive_class=None)[source]

Bases: object

immuneML.environment.LabelConfiguration module

class immuneML.environment.LabelConfiguration.LabelConfiguration(labels: Optional[list] = None)[source]

Bases: object

Class that encapsulates labels and transformers for the labels. Supports two types of labels: CLASSIFICATION and REGRESSION (as defined in LabelType class)

add_label(label_name: str, values: Optional[list] = None, auxiliary_labels: Optional[list] = None, positive_class=None)[source]
get_auxiliary_labels(label_name: str)[source]
get_label_count()[source]
get_label_object(label_name: str) → immuneML.environment.Label.Label[source]
get_label_objects() → List[immuneML.environment.Label.Label][source]
get_label_values(label_name: str)[source]
get_labels_by_name()[source]

immuneML.environment.LabelType module

class immuneML.environment.LabelType.LabelType(value)[source]

Bases: enum.Enum

An enumeration.

CLASSIFICATION = 1
REGRESSION = 2

immuneML.environment.SequenceType module

class immuneML.environment.SequenceType.SequenceType(value)[source]

Bases: enum.Enum

An enumeration.

AMINO_ACID = 'sequence_aas'
NUCLEOTIDE = 'sequences'

Module contents