immuneML.environment package

Submodules

immuneML.environment.Constants module

class immuneML.environment.Constants.Constants

Bases: object

ALLELE_DELIMITER = '*'

CACHE_TYPE = 'cache_type'

COMMENT_SIGN = '#'

FEATURE_DELIMITER = '///'

GENE_DELIMITER = '-'

NOT_COMPUTED = 'not computed'

PLOTLY_BLACK = '#2A3F5E'

STOP_CODON = '*'

UNKNOWN = None

VERSION = '1.2.5'

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')

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)

static get_cache_type()

static get_sequence_alphabet(sequence_type: Optional[immuneML.environment.SequenceType.SequenceType] = None)

Returns

alphabetically sorted receptor_sequence alphabet

static get_sequence_type() → immuneML.environment.SequenceType.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: pathlib.Path)

static set_sequence_type(sequence_type: immuneML.environment.SequenceType.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: Optional[list] = None, auxiliary_label_names: Optional[list] = None, positive_class=None)

Bases: object

immuneML.environment.LabelConfiguration module

class immuneML.environment.LabelConfiguration.LabelConfiguration(labels: Optional[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: str, values: Optional[list] = None, auxiliary_labels: Optional[list] = None, positive_class=None)

get_auxiliary_labels(label: str)

get_label_count()

get_label_object(label: str) → immuneML.environment.Label.Label

get_label_objects() → List[immuneML.environment.Label.Label]

get_label_values(label: str)

get_labels_by_name()

immuneML.environment.LabelType module

class immuneML.environment.LabelType.LabelType(value)

Bases: enum.Enum

An enumeration.

CLASSIFICATION = 1

REGRESSION = 2

immuneML.environment.Metric module

class immuneML.environment.Metric.Metric(value)

Bases: enum.Enum

An enumeration.

ACCURACY = 'accuracy_score'

AUC = 'roc_auc_score'

BALANCED_ACCURACY = 'balanced_accuracy_score'

CONFUSION_MATRIX = 'confusion_matrix'

F1_MACRO = 'f1_score_macro'

F1_MICRO = 'f1_score_micro'

F1_WEIGHTED = 'f1_score_weighted'

LOG_LOSS = 'log_loss'

PRECISION = 'precision_score'

RECALL = 'recall_score'

static get_probability_based_metric_types()

static get_search_criterion(metric)

immuneML.environment.SequenceType module

class immuneML.environment.SequenceType.SequenceType(value)

Bases: enum.Enum

An enumeration.

AMINO_ACID = 'sequence_aas'

NUCLEOTIDE = 'sequences'

Module contents