Intro
obo2tsv
parses a gene ontology obo file to tsv. It will include for each term columns for parent terms as well as child terms.
Examples
$ obo2tsv -u http://geneontology.org/ontology/go-basic.obo \
-o go-basic.tsv -c 4 \
--organism http://geneontology.org/gene-associations/gene_association.fb.gz
Links to other --organism
can be found on http://geneontology.org/page/download-annotations.
Help
$ obo2tsv --help
usage: obo2tsv [-h] [-i INPUT] [-u URL] [-o OUTPUT] [-c CPUS]
[--organism ORGANISM]
obo to tsv parser
optional arguments:
-h, --help show this help message and exit
-i INPUT, --input INPUT
go-basic.obo file. Files can be downloaded from
http://geneontology.org/page/download-ontology.
(default: None)
-u URL, --url URL If no go-basic.obo input file is specified, a url to a
target obo file can be specified instead. (default:
http://geneontology.org/ontology/go-basic.obo)
-o OUTPUT, --output OUTPUT
Name of output tab separated file. (default: go-
basic.tsv)
-c CPUS, --cpus CPUS Number of cpus. (default: 36)
--organism ORGANISM Optional, merge GO obo.tsv with a GO annotation for an
organism: either a link to a file on geneontology.org
eg. http://geneontology.org/gene-
associations/gene_association.fb.gz or the path for
the respective downloded .gz file. (default: None)