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.