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¶
- -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
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.
