immuneML.environment package

Submodules

immuneML.environment.Constants module

class immuneML.environment.Constants.Constants

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 = '2.2.6'

immuneML.environment.EnvironmentSettings module

class immuneML.environment.EnvironmentSettings.EnvironmentSettings

Bases: object

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

cache_path = PosixPath('/Users/milenpa/PycharmProjects/BMIimmuneML/cache')

compairr_paths = [PosixPath('/usr/local/bin/compairr'), PosixPath('compairr/src/compairr'), PosixPath('/Users/milenpa/PycharmProjects/BMIimmuneML/compairr/src/compairr')]

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: CacheType = None)

static get_cache_type()

static get_sequence_alphabet(sequence_type: SequenceType = None)

Returns:

alphabetically sorted receptor_sequence alphabet

static get_sequence_type() → SequenceType

html_templates_path = PosixPath('/Users/milenpa/PycharmProjects/BMIimmuneML/immuneML/presentation/html/templates')

low_memory = True

max_sequence_length = 20

static reset_cache_path()

root_path = PosixPath('/Users/milenpa/PycharmProjects/BMIimmuneML')

sequence_type = 'sequence_aas'

static set_cache_path(path: Path)

static set_sequence_type(sequence_type: SequenceType)

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: list, auxiliary_label_names: list = None, positive_class=None)

Bases: object

get_binary_negative_class()

get_desc_for_storage()

property positive_class

property values

Make sure the positive class is listed last This is needed for compatibility with ~immuneML.ml_methods.util.Util.binarize_label_classes

immuneML.environment.LabelConfiguration module

class immuneML.environment.LabelConfiguration.LabelConfiguration(labels: list = None)

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: list = None, auxiliary_labels: list = None, positive_class=None)

get_auxiliary_labels(label_name: str)

get_label_count()

get_label_object(label_name: str) → Label

get_label_objects() → List[Label]

get_label_values(label_name: str)

get_labels_by_name()

immuneML.environment.LabelType module

class immuneML.environment.LabelType.LabelType(value, names=None, *, module=None, qualname=None, type=None, start=1, boundary=None)

Bases: Enum

CLASSIFICATION = 1

REGRESSION = 2

immuneML.environment.SequenceType module

class immuneML.environment.SequenceType.SequenceType(value, names=None, *, module=None, qualname=None, type=None, start=1, boundary=None)

Bases: Enum

AMINO_ACID = 'sequence_aas'

NUCLEOTIDE = 'sequences'

Module contents