perl gmod_make_cvtermpath.pl -H [dbhost] -D [dbname] [-vt] -c cvname perl gmod_make_cvtermpath.pl -g [GMODConf_profile] -c cvname
- 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
- 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
DESCRIPTIONThis 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:
AUTHORNaama Menda <[email protected]>
VERSION AND DATEVersion 1.2, Feb. 2011.