gmod_make_cvtermpath.pl1p

Calculates the transitive closure on the ontology terms in the cvterm table

Usage

 perl gmod_make_cvtermpath.pl -H [dbhost] -D [dbname]  [-vt] -c cvname
 perl gmod_make_cvtermpath.pl -g [GMODConf_profile] -c cvname

Parameters

`-c`	Name of ontology (cv.name) to compute the transitive closure on. (Required)
`-v`	Verbose output
`-t`	Trial mode. Do not perform any store operations at all. (Not implemented)
`-o`	outfile for writing errors and verbose messages (optional)
`-g`	GMOD database profile name (can provide host and DB name) Default: 'default'

If not using a GMOD database profile (option -g) then you must provide the following parameters

-D: Database name

-H: Hostname

-d: Database driver name (e.g. 'Pg' for postgres)

-u: [Optional- if default user is not used] Database user name

-p: [Optional- if you need a password to connect to your database] Password for your user to connect to the database

Overview

This script calculates the transitive closure on the ontology terms in the cvterm table. As this is a computationaly intensive operation, doing so on a large cv like the Gene Ontology can take several hours. For more information on what a transative closure is, please see:

  http://www.geneontology.org/GO.database.shtml#graphs

Version and date

Version 1.2, Feb. 2011.

Releases

6 releases since Debian 8 (Jessie); the text changed 3 times.