Bio::MAGETAB Documentation ========================== Introduction ------------ This package contains the core MAGE-TAB Utilities Perl modules. This is a beta release. All functions have now been implemented and most have test suites; the exceptions include the modules involved in export of MAGE-TAB documents, which are still a little experimental in nature. The API is mostly finalised (and fully documented), but some details may yet change where necessary to improve usability. Package Contents ---------------- This package contains the following directories: inc Modules used by the installer Makefile.PL script. lib The Bio::MAGETAB modules themselves. scripts A set of example scripts. Run without options for usage info. sql Optional SQL schema for loading data into a MySQL database. t Test suite. Dependencies ------------ Note that MAGE-TAB import, export and visualisation functions are not provided by this package, but rather by the "magetab-utils" package available from the main project SourceForge page. The Bio::MAGETAB module requires at least version 5.8.1 of perl, and depends on the following perl modules, all available from CPAN (http://www.cpan.org): Moose Moose::Policy MooseX::Types Params::Coerce URI Date::Manip DateTime DateTime::Format::DateManip Email::Valid Parse::RecDescent Text::CSV_XS The following modules are recommended, especially if you wish to use Bio::MAGETAB with the optional database integration modules or graph visualization: LWP::UserAgent Tangram DBI DBD::SQLite, DBD::mysql or similar GraphViz Scripts ------- The following example scripts are included in the package: - read_magetab.pl This is the main example script, which can read in a MAGE-TAB document (optionally loading it into a local database), and then (a) create a graph visualization diagram, and/or (b) round-trip the data back into a new set of MAGE-TAB documents. - deploy_magetab_db.pl A script which can deploy the Tangram-based schema to any Tangram-supported database engine. Note that the database schema generated by Tangram lacks indices or constraints, so performance can be poor when using databases generated using this script. For serious use with MySQL, the "tangram_with_indices.sql" script in the "sql" directory is recommended. - unload_magetab_namespace.pl A simple unloader script to remove MAGE-TAB data which has previously been loaded into a database, e.g. by read_magetab.pl - fix_ae_magetab.pl At the time of writing some of the MAGE-TAB documents made available by ArrayExpress on their FTP server do not completely conform to the MAGE-TAB specification v1.1. This script is intended to provide a quick fix for those documents and allow them to be read by Bio::MAGETAB. Contact ------- Please contact Tim Rayner (tfrayner@gmail.com) with any questions.