Provided by: chado-utils_1.31-5_all
gmod_make_cvtermpath.pl - calculates the transitive closure on the ontology terms in the cvterm table
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
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
Naama Menda <firstname.lastname@example.org>
VERSION AND DATE
Version 1.2, Feb. 2011.