go-show-paths-to-root.pl(1) shows all possible paths from a term to the top


go-show-paths-to-root.pl -id GO:0008021 ontology/gene_ontology.obo
go-show-paths-to-root.pl -names -id GO:0008021 ontology/gene_ontology.obo


traverses DAG showing all paths (terms and intervening relationships) to the root

This script is purely file based; it needs to parse the ontology each time

Subsequent parses can be speeded up using the use_cache option

If you wish to use the GO MySQL db, see the script go-db-show-paths-to-root.pl in the go-db-perl distribution



writes parse errors in XML - defaults to STDERR (there should be no parse errors in well formed files)


determines which parser to use; if left unspecified, will make a guess based on file suffix. See below for formats


If this switch is specified, then caching mode is turned on.

With caching mode, the first time you parse a file, then an additional file will be exported in a special format that is fast to parse. This file will have the same filename as the original file, except it will have the ``.cache'' suffix.

The next time you parse the file, this program will automatically check for the existence of the ``.cache'' file. If it exists, and is more recent than the file you specified, this is parsed instead. If it does not exist, it is rebuilt.