pypath.utils.go.GOCustomAnnotation

class pypath.utils.go.GOCustomAnnotation(categories, go_annot=None, ncbi_tax_id=9606)

Bases: Logger

__init__(categories, go_annot=None, ncbi_tax_id=9606)

Provides annotations by a custom set of GO terms or expressions built from multiple terms.

Parameters:

• categories (dict) – A dict with custom category labels as keys and single GO terms or names or complex expressions as values. Alternatively a set of GO terms, in this case the term names will be used as labels.

• go_annot (pypath.go.GOAnnotation) – A :class:pypath.go.GOAnnotation object.

Methods

__init__(categories[, go_annot, ncbi_tax_id])	Provides annotations by a custom set of GO terms or expressions built from multiple terms.
get_annotation(category[, uniprots])	For a category name returns a set of UniProt IDs annotated with the corresponding Gene Ontology terms or expression.
get_annotations([uniprots])	Returns a dict with set of UniProt IDs for each category.
process_categories()	Translates GO term names listed in categories to GO terms ACs.
reload()	Reloads the object from the module level.

get_annotation(category, uniprots=None)

For a category name returns a set of UniProt IDs annotated with the corresponding Gene Ontology terms or expression.

Parameters:

• category (str) – The category name, should be a key in the categories dict.

• uniprots (set) – A set or list of UniProt IDs. If None, annotations based on all UniProts in GO annotation will be returned.

get_annotations(uniprots=None)

Returns a dict with set of UniProt IDs for each category.

Parameters:

uniprots (set) – A set or list of UniProt IDs. If None, annotations based on all UniProts in GO annotation will be returned.

process_categories()

Translates GO term names listed in categories to GO terms ACs.

reload()

Reloads the object from the module level.