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gmod_make_cvtermpath.plp - Online in the Cloud

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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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