aedera / oboder

Small library for reading OBO files.

Oboder

An extremely small python library implementing an OBO file reaDER.

Installation

pip install -U "oboder @ git+https://github.com/aedera/oboder.git"

Usage

import oboder

# read a given obo file, rels=True includes other relationships in addition to 'is_a'
go = oboder.read('data/go.obo', with_rels=True)

# get a set containing ancestors of a given GO term for all relationships
anc = go.get_ancestor_set('GO:0017011')

# or ancestors for a specific relation
anc = go.get_ancestor_set('GO:0017011', rels=['part_of'])

# get a list where elements are branches of ancestors
branches = go.get_ancestors('GO:0017011')

# loop over the terms in the obo file
for t in go.ont.keys():
  print(go.ont[t])

In addition, oboder can be used to explore an OBO file, for example, by exploring specific GO terms.

go.ont['GO:0019538']

this returns a dict with the following information of the term with id 'GO:0019538'

{
'is_a': ['GO:0043170', 'GO:0044238'],
'part_of': [],
'has_part': [],
'regulates': [],
'negatively_regulates': [],
'positively_regulates': [],
'occurs_in': [],
'ends_during': [],
'happens_during': [],
'alt_ids': {'GO:0006411'},
'is_obsolete': False,
'id': 'GO:0019538',
'name': 'protein metabolic process',
'namespace': 'biological_process',
'children': {'GO:0045558', 'GO:1901142', ..., 'GO:0072376'}
}

Note that this term has alternative ids, indicated by the key alt_ids. The reference term of an alternative id can be retrieved with this command

go.get_refterm('GO:0006411')

Alternative terms can be included when reading an obo file by using the argument include_alt_ids

go = oboder.read('data/go.obo', include_alt_ids=True)