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 = '-'

GAP_LETTER = '-'

GENE_DELIMITER = '-'

NOT_COMPUTED = 'not computed'

PLOTLY_BLACK = '#2A3F5E'

SIGNAL_DELIMITER = '__'

STOP_CODON = '*'

UNKNOWN = ''

VERSION = '3.0.2'

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'), PosixPath('/Users/milenpa/PycharmProjects/BMIimmuneML/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_aa'

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()

Ensures the correct ‘negative class’ is returned when using the Label for binary classification.

get_desc_for_storage()

Method to call when storing a label to YAML format

property positive_class

Ensures the same class is always returned as the ‘positive class’, even when it was not explicitly set.

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_aa'

NUCLEOTIDE = 'sequence'

Module contents