GO

class GRATIOSA.GO.GO(filename='go-basic.obo', path2dir='/home/usr/documents/data/', obo_reload=False)

The GO (Gene Ontology) class contains the information (names, definitions) of the GO terms of the different categories (biological process, molecular function and cellular component). The associated function (GO_enrichment_test) allows the study of functional enrichment.

Parameters:

• filename (str.) – name of the Gene Ontology .obo file

• path2dir (str.) – path to the directory containing the .obo file

• obo_reload (Bool.) – if true, the Gene Ontology basic.obo file is reloaded. This file allows each GO term to be associated with a category (GOp - biological_process, GOf - molecular_function or GOc - cellular_component), a name and a description

Initializes GO object with the following attributes:

dict_GO (dict. of dict.)

dictionary containing one subdictionary per GO term. Each subdictionary contains the “Name”, the “Namespace” (biological_process, molecular_function or cellular_component) and the definition corresponding to the GO term.

dict_GOc (dict. of dict.)

dictionary containing only the GOterms from “cellular_component” namespace. This dictionary contains one subdictionary per GO term, with the following shape self.dict_GOc[“GOterm1”] = {“Name”: GO name, “Definition”: associated definition}

dict_GOf (dict. of dict.)

idem for the GOterms from “molecular_function” namespace

dict_GOp (dict. of dict.)

idem for the GOterms from “biological_process” namespace

Example

>>> from GRATIOSA import GO
>>> go = GO.GO()
>>> go.dict_GOc['GO:0000015']
{'Name': 'phosphopyruvate hydratase complex',
 'Definition': 'A multimeric enzyme complex that catalyzes the
 conversion of 2-phospho-D-glycerate to phosphoenolpyruvate and
 water. [GOC:jl, ISBN:0198506732]'}