GenDBWiki/DeveloperDocumentation/ContributedScripts

Contributed GenDB Scripts

The following list of scripts has been contributed by various developers working with the GenDB API (only version 2.0 and higher). Since most of these scripts were implemented for some special purpose task - sometimes only for one specific GenDB project - they are not part of the GenDB distribution. Although these scripts may be useful for other projects, they are not actively maintained by the core GenDB development team.

/!\ If you intend to use one of these scripts you should carefully read (and understand!) the source code before applying it to your active project. Since you are using these scripts on your own risk we also advice you to have your backup prepared! /!\

To execute a script, just download it and copy it into the `'gendb/share/exec/'` directory of your current GenDB environment. Execute it from the `'gendb/bin/'` directory using the `'gendb_start'` wrapper script. Executing a script without any arguments should show you a detailed usage message where all available options are explained.

{i} If you have your own script and think that it could be useful for others you can send it to the GenDB mailinglist and contribute to the GenDB development. After briefly reviewing the script we will add it to the list of contributed scripts. Each script should be carefully documented, contain a short description, the authors contact address, a comprehensive usage message explaining all available options, and especially the critical parts where database content is modified should be marked and declared explicitly. You should also add a comment about the GenDB versions that you wrote and tested a script for. Notice that the option `'-d'` is reserved for activating the Perl debug mode and the option `'-p'` is usually used for specifying a GenDB project name. Use the `'GenDB_Template.pl'` script as a template for your own scripts. See section 'Writing your own GenDB Programs' for details about using the GenDB API.

* [attachment:rename_cds.pl rename_cds.pl] - rename all CDS regions in a GenDB project with a new prefix BR contributed by: Alexander Goesmann
* `getOSfromBlastHits.pl`
* `change_function_status.pl`
* `export_flanking_genes.pl`
* `export_cds_features.pl`
* `change_region_status.pl`
* `shift_orf_names_format.pl`