=head1 NAME

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

=head1 SYNOPSIS

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

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

=head1 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.

=head1 OPTIONS

=head2 Required Options

=over 4

=item --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).

=item --exp=$exp_id

Specifies that the experiment set whose primary key is $exp_id should
be exported as GEML. The spot data for each E<lt>arrayE<gt> 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

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

=item --user=$login_name

=item --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.

=back


=head2 Optional Options

=over 4

=item --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

=back


=head1 BUGS

Please send bug reports to genex@ncgr.org

=head1 LAST UPDATED

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

=head1 AUTHOR

Jason E. Stewart (jes@ncgr.org)

=head1 SEE ALSO

perl(1).

