goatools.grouper.grprobj_init 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.grprobj_init.GrouperInit(goids, objpre, fnc_most_specific='dcnt')

Bases: object

Initialize Grouper object.

most_specific_fncs = {'dcnt': <function get_most_specific_dcnt>, 'tinfo': <function get_most_specific_tinfo>, 'tinfo_dcnt': <function get_most_specific_tinfo_dcnt>}

get_gos_all()

Return a flat list of all GO IDs in grouping object.

All GO IDs:

• header GO IDs that are not user GO IDs

• user GO IDs that are under header GOs

• user GO IDs that are header GOs in groups containing no other user GO IDs

class GetGoidHigh(gosubdag, gos_high, get_most_specific)

Bases: object

Given a user GO ID, return the ‘closest’ header GO.

get_goid_high(goid_main)

Return the ‘closest’ GO header to the GO ID arg.

get_go2nt(usr_go2nt)

Combine user namedtuple fields, GO object fields, and format_txt.

class NtMaker(obj)

Bases: object

Make namedtuples for GO IDs in grouper.

ntobj

alias of NtHdrIdx

get_nt(goid_user)

Get Grouper namedtuple for user GO ID.