NAME

db2xml.pl: a script for export data from a Genex DB as a Gene Expression Markup Language (GeneXML) file

SYNOPSIS

  db2xml.pl --cb=outfile_name --user=name --password=passw [options]

  db2xml.pl --exp=exp_id --user=name --password=passw [options]

DESCRIPTION

db2xml.pl has two primary uses: exporting control bundles for the curation tool using the --cb option, and exporting experiment sets for download using the --exp option.

OPTIONS

Required Options

--cb=filename.xml

Specifies that the curationtool control bundle should be written to the file 'filename.xml'. The output will first be run through XMLUtils::pretty_print() to format the output to be more human-readable. This option is mutually exclusive with the --exp option. Depending on which other options are used, other supporting XML files may be written as well (array layout, user sequence feature, or canonical sequence feature).

--exp=$exp_id

Specifies that the experiment set whose primary key is $exp_id should be exported as GeneXML. The spot data for each <array> will be written to a separate external file. May be used multiple times on the command line to specify that multiple experiment sets should be exported. For example:

  db2xml.pl --exp=23 --exp=25 --user=jes --password=foo

NOTE: This option is not fully functional and should be approached with caution.

--user=$login_name

--password=$password

Retrieves the entry for $login_name from the UserSec table and matches the supplied $password against it. It will cause a not-so-graceful error if the password doesn\'t match.

Optional Options

--species=$spc_id

Used for control bundle export. Specifies that species whose primary key is $spc_id should be included in the export file. This option may be included multiple times on the command line to specify multiple species. For example:

  db2xml.pl --cb=output.xml --user=jes --password=foo --species=4 --species=8

BUGS

Please send bug reports to genex@ncgr.org

LAST UPDATED

Mon Jun 19 00:43:39 MDT 2000 by jes@ncgr.org

AUTHOR

Jason E. Stewart (jes@ncgr.org)

SEE ALSO

perl(1).