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GMOD_MAKE_CVTERMPATH(1p) User Contributed Perl Documentation GMOD_MAKE_CVTERMPATH(1p)

NAME

gmod_make_cvtermpath.pl - 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

Name of ontology (cv.name) to compute the transitive closure on. (Required)
Verbose output
Trial mode. Do not perform any store operations at all. (Not implemented)
outfile for writing errors and verbose messages (optional)
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

Database name
Hostname
Database driver name (e.g. 'Pg' for postgres)
[Optional- if default user is not used] Database user name
[Optional- if you need a password to connect to your database] Password for your user to connect to the database

DESCRIPTION

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

AUTHOR

Naama Menda <nm249@cornell.edu>

VERSION AND DATE

Version 1.2, Feb. 2011.

2019-12-05 perl v5.30.0