pypath.utils.mapping

members:

Module Attributes

UNIPROT_ID_TYPES

Classes for reading and use serving ID mapping data from custom file, function, UniProt, UniProt ID Mapping, Ensembl BioMart, PRO (Protein Ontology), miRBase or pickle file.

Functions

get_mapper(**kwargs)	The module under its mapper attribute has an instance of the Mapper object, which manages the ID translations.
guess_type(name[, entity_type])	From a string, tries to guess the ID type and optionally the entity type.
id_from_label(label[, label_id_type, ...])	For a label (e.g. Gene Symbol) returns the corresponding IDs (e.g. UniProt IDs).
id_from_label0(label[, label_id_type, ...])	For a label (e.g. Gene Symbol) returns a single ID (e.g. UniProt IDs).
id_types()	Identifier types with their labels.
init(**kwargs)	Create a new Mapper instance under the mapper attribute of this module.
label(name[, id_type, entity_type, ncbi_tax_id])	For any kind of entity, either protein, miRNA or protein complex, returns the preferred human readable label.
map_name(name, id_type, target_id_type[, ...])	Translates one instance of one ID type to a different one.
map_name0(name, id_type, target_id_type[, ...])	Translates the name and returns only one of the resulted IDs.
map_names(names[, id_type, target_id_type, ...])	Same as map_name but translates multiple IDs at once.
mapping_tables()	A list of built-in mapping tables.
translation_df(id_type, target_id_type[, ...])	Identifier translation table as a pandas.DataFrame.
translation_dict(id_type, target_id_type[, ...])	Identifier translation table as a dict of sets.

Classes

MapReader(param[, ncbi_tax_id, entity_type, ...])	Reads ID translation data and creates MappingTable instances.
Mapper([ncbi_tax_id, cleanup_period, ...])
MappingTable(data, id_type, target_id_type, ...)	This is the class directly handling ID translation data.
MappingTableKey(id_type, target_id_type, ...)