NAME
Test::Chado::FixtureLoader::Flatfile
VERSION
version v4.1.1
SYNOPSIS
use Test::Chado::FixtureLoader::Flatfile; use Test::Chado::Factory::FixtureLoader;
my $sqlite = Test::Chado::Factory::FixtureLoader->get_instance('sqlite'); my $loader = Test::Chado::FixtureLoader::Flatfile->new(dbmanager => $sqlite); $sqlite->load_fixtures;
DESCRIPTION
This class primarilly provides a method load_fixtures to load all the default fixtures that comes bundled with distribution.
Default fixtures
Organisms entries
It's a YAML version of organism entries found in the initialize.sql file of official chado distribution.
Sequence ontology feature annotation (SOFA)
The lite version of sequence ontology.
Relation ontology
Obtained from here
NAME
Class to manage loading of test fixture from flatfile
API
Attributes
These are public attributes defined exclusively in this class. For rest of the consumed attributes look at Test::Chado::Role::Helper::WithBcs
- obo_xml
-
Name of obo xml file
- obo_xml_loader
-
Instance of <XML::Twig> with two handlers, one to load the term and other for relations
- graph
-
Instance of Graph
- traverse_graph
-
Instance of Graph::Traversal
- ontology_namespace
Methods
Other than the exclusive methods below, look at the role Test::Chado::Role::Helper::WithBcs
- load_fixtures
-
Loads all default fixtures from flatfiles.
- load_organism
-
Loads organism fixtures from organism.yaml file
=load_rel
Loads relationship ontology from relationship.obo_xml
=load_so
Loads sequence ontology(SO) from sofa.obo_xml file
AUTHOR
Siddhartha Basu <biosidd@gmail.com>
COPYRIGHT AND LICENSE
This software is copyright (c) 2011 by Siddhartha Basu.
This is free software; you can redistribute it and/or modify it under the same terms as the Perl 5 programming language system itself.