This is the command gmod_make_cvtermpath.plp that can be run in the OnWorks free hosting provider using one of our multiple free online workstations such as Ubuntu Online, Fedora Online, Windows online emulator or MAC OS online emulator
PROGRAM:
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
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