go-show-paths-to-root.1p

Langue: en

Autres versions - même langue

Version: 2005-03-14 (ubuntu - 24/10/10)

Section: 1 (Commandes utilisateur)

NAME

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

SYNOPSIS

   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
 
 

DESCRIPTION

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

ARGUMENTS

-e ERRFILE

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

-p FORMAT

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

-use_cache

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.

DOCUMENTATION

<http://www.godatabase.org/dev>