Annotations

class GAFAnnotation

Bases: object

Struct representing a single annotation from a GAF file.

Fields

db_object_idstr: The gene product identifier (e.g., UniProt ID).
go_termstr: The GO term ID (e.g., GO:0008150).
evidencestr: The evidence code for the annotation (e.g., IEA).

db_object_id

evidence

go_term

class TermCounter

Bases: object

Struct holding annotation counts and information content (IC) for GO terms.

Fields

countsdict: Mapping from GO term ID to annotation count.
total_by_nsdict: Mapping from namespace to total annotation count.
icdict: Mapping from GO term ID to information content (IC).

counts

ic

total_by_ns

build_term_counter(py_annotations)

Build a term counter (counts, IC) from GAF annotations.

Parameters:: py_annotations (list of GAFAnnotation) – List of GAFAnnotation Python objects.
Returns:: Struct with counts and IC values.
Return type:: TermCounter

load_gaf(path)

Load a GAF annotation file and cache the gene-to-GO mapping.

Parameters:: path (str) – Path to the GAF file.
Returns:: List of parsed GAF annotations.
Return type:: list of GAFAnnotation

Annotation Functions

import go3
go3.load_go_terms()
annots = go3.load_gaf("goa_human.gaf")
counter = go3.build_term_counter(annots)

load_gaf: Loads a GAF file and parses gene-to-GO annotations.
build_term_counter: Builds annotation counts and IC values for all terms.
GAFAnnotation: Class representing a single annotation.
TermCounter: Class holding counts and IC values.