- NAME
- SYNOPSIS
- DESCRIPTION
- OPTIONS

- Required Options
- Optional Options

- BUGS
- LAST UPDATED
- AUTHOR
- SEE ALSO

# NAME

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