diff variant_effect_predictor/Bio/EnsEMBL/Variation/Pipeline/BaseVariationProcess.pm @ 0:1f6dce3d34e0

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/variant_effect_predictor/Bio/EnsEMBL/Variation/Pipeline/BaseVariationProcess.pm	Thu Apr 11 02:01:53 2013 -0400
@@ -0,0 +1,108 @@
+=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]>.
+
+=cut
+
+package Bio::EnsEMBL::Variation::Pipeline::BaseVariationProcess;
+
+use strict;
+use warnings;
+
+use Bio::EnsEMBL::Variation::Pipeline::TranscriptFileAdaptor;
+
+use Bio::EnsEMBL::Hive::AnalysisJob;
+
+use base qw(Bio::EnsEMBL::Hive::Process);
+
+sub param {
+    my $self = shift;
+    
+    unless ($self->input_job) {
+        # if we don't have an input job, add a dummy one (used when we're not 
+        # running as part of a pipeline proper)
+        $self->input_job(Bio::EnsEMBL::Hive::AnalysisJob->new);
+    }
+
+    return $self->SUPER::param(@_);
+}
+
+sub required_param {
+    my $self        = shift;
+    my $param_name  = shift;
+   
+    my $param_value = $self->param($param_name, @_);
+
+    die "$param_name is a required parameter" unless defined $param_value;
+    
+    return $param_value;
+}
+
+sub get_transcript_file_adaptor {
+    my $self = shift;
+    my $transcripts = shift;
+    
+    unless ($self->{tfa}) {
+        $self->{tfa} = Bio::EnsEMBL::Variation::Pipeline::TranscriptFileAdaptor->new(
+            fasta_file  => $self->param('fasta_file'),
+            transcripts => $transcripts,
+        );
+    }
+
+    return $self->{tfa};
+}
+
+sub get_species_adaptor {
+    my ($self, $group) = @_;
+
+    my $species = $self->required_param('species');
+    
+    return $self->get_adaptor($species, $group);
+}
+
+sub get_adaptor {
+    my ($self, $species, $group) = @_;
+   
+    my $dba;
+
+    eval {
+        $dba = Bio::EnsEMBL::Registry->get_DBAdaptor($species, $group);
+    };
+
+    unless (defined $dba) {
+        $self->_load_registry();
+        $dba = Bio::EnsEMBL::Registry->get_DBAdaptor($species, $group);
+    }
+    
+    unless (defined $dba) {
+        die "Failed to a get DBA for $species and group $group";
+    }
+    
+    return $dba;
+}
+
+sub _load_registry {
+    my ($self) = @_;
+    
+    my $reg_file = $self->required_param('ensembl_registry');
+    
+    Bio::EnsEMBL::Registry->load_all($reg_file, 0, 1);
+    
+    return;
+}
+
+1;