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.\" ========================================================================
.\"
.IX Title "GMOD_MAKE_CVTERMPATH 1p"
.TH GMOD_MAKE_CVTERMPATH 1p "2018-09-27" "perl v5.26.2" "User Contributed Perl Documentation"
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.SH "NAME"
gmod_make_cvtermpath.pl \- calculates the transitive closure on the ontology terms in the cvterm table
.SH "USAGE"
.IX Header "USAGE"
.Vb 2
\& perl gmod_make_cvtermpath.pl \-H [dbhost] \-D [dbname]  [\-vt] \-c cvname
\& perl gmod_make_cvtermpath.pl \-g [GMODConf_profile] \-c cvname
.Ve
.SS "Parameters"
.IX Subsection "Parameters"
.IP "\-c" 5
.IX Item "-c"
Name of ontology (cv.name) to compute the transitive closure on. (Required)
.IP "\-v" 5
.IX Item "-v"
Verbose output
.IP "\-t" 5
.IX Item "-t"
Trial mode. Do not perform any store operations at all. (Not implemented)
.IP "\-o" 5
.IX Item "-o"
outfile for writing errors and verbose messages (optional)
.IP "\-g" 5
.IX Item "-g"
\&\s-1GMOD\s0 database profile name (can provide host and \s-1DB\s0 name) Default: 'default'
.SS "If not using a \s-1GMOD\s0 database profile (option \-g) then you must provide the following parameters"
.IX Subsection "If not using a GMOD database profile (option -g) then you must provide the following parameters"
.IP "\-D" 5
.IX Item "-D"
Database name
.IP "\-H" 5
.IX Item "-H"
Hostname
.IP "\-d" 5
.IX Item "-d"
Database driver name (e.g. 'Pg' for postgres)
.IP "\-u" 5
.IX Item "-u"
[Optional\- if default user is not used]
Database user name
.IP "\-p" 5
.IX Item "-p"
[Optional\- if you need a password to connect to your database]
Password for your user to connect to the database
.SH "DESCRIPTION"
.IX Header "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:
.PP
.Vb 1
\&  http://www.geneontology.org/GO.database.shtml#graphs
.Ve
.SH "AUTHOR"
.IX Header "AUTHOR"
Naama Menda <nm249@cornell.edu>
.SH "VERSION AND DATE"
.IX Header "VERSION AND DATE"
Version 1.2, Feb. 2011.
