diff variant_effect_predictor/Bio/EnsEMBL/Pipeline/FASTA/FindDirs.pm @ 0:1f6dce3d34e0

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/variant_effect_predictor/Bio/EnsEMBL/Pipeline/FASTA/FindDirs.pm	Thu Apr 11 02:01:53 2013 -0400
@@ -0,0 +1,59 @@
+=pod
+
+=head1 LICENSE
+
+  Copyright (c) 1999-2012 The European Bioinformatics Institute and
+  Genome Research Limited.  All rights reserved.
+
+  This software is distributed under a modified Apache license.
+  For license details, please see
+
+    http://www.ensembl.org/info/about/code_licence.html
+
+=head1 CONTACT
+
+  Please email comments or questions to the public Ensembl
+  developers list at <[e-mail]>.
+
+  Questions may also be sent to the Ensembl help desk at
+  <[e-mail]>.
+
+=head1 NAME
+
+Bio::EnsEMBL::Pipeline::FASTA::FindDirs
+
+=head1 DESCRIPTION
+
+Finds all directories under the given species directory. This is used to
+flow any further processing only dependent on the directory and so
+inherits from JobFactory and Bio::EnsEMBL::Pipeline::FASTA::Base to bring in methods which
+know about the FTP structure.
+
+Allowed parameters are:
+
+=over 8
+
+=item species - The species to work with
+
+=back
+
+=cut
+
+package Bio::EnsEMBL::Pipeline::FASTA::FindDirs;
+
+use strict;
+use warnings;
+
+use base qw/Bio::EnsEMBL::Pipeline::FindDirs Bio::EnsEMBL::Pipeline::FASTA::Base/;
+
+use File::Spec;
+
+sub fetch_input {
+  my ($self) = @_;
+  $self->throw("No 'species' parameter specified") unless $self->param('species');
+  $self->param('path', $self->fasta_path());
+  $self->SUPER::fetch_input();
+  return;
+}
+
+1;