goatools.grouper.grprdflts module

Given user GO ids and parent terms, group user GO ids under one parent term.

Given a group of GO ids with one or more higher-level grouping terms, group each user GO id under the most descriptive parent GO term.

Each GO id may have more than one parent. One of the parent(s) is chosen to best represent the user GO id’s function. The choice of parent is made by regarding how close the parent GO id is to the bottom of its hierarchy.

The estimation of how close a GO term is to “the bottom” of its GO hierarchy is estimated using the number of total Go term descendent counts below that term.

class goatools.grouper.grprdflts.GrouperDflts(gosubdag=None, goslim_filename='goslim_generic.obo', hdrgos=None)

Bases: object

Holds objects that we would like to load and initialize once.

Files used for grouping GO IDs:

http://geneontology.org/ontology/go-basic.obo http://geneontology.org/ontology/subsets/goslim_generic.obo

get_gos_d0d1()

Return GO IDs whose depth is 0 (BP, MF, CC) or depth is 1.

static get_gosubdag(gosubdag=None)

Gets a GoSubDag initialized for use by a Grouper object.