db2xml.pl: a script for export data from a Genex DB as a Gene
Expression Markup Language (GEML) file
db2xml.pl --cb=outfile_name --user=name --password=passw [options]
db2xml.pl --exp=exp_id --user=name --password=passw [options]
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.
- --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 $password against it. It will cause a not-so-graceful
error if the password doesn\'t match.
- --species=$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
Please send bug reports to genex@ncgr.org
Mon Jun 19 00:43:39 MDT 2000 by jes@ncgr.org
Jason E. Stewart (jes@ncgr.org)
perl(1).