diff variant_effect_predictor/Bio/EnsEMBL/Funcgen/RunnableDB/Alignment.pm @ 0:1f6dce3d34e0

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/variant_effect_predictor/Bio/EnsEMBL/Funcgen/RunnableDB/Alignment.pm	Thu Apr 11 02:01:53 2013 -0400
@@ -0,0 +1,67 @@
+=pod 
+
+=head1 NAME
+
+Bio::EnsEMBL::Funcgen::RunnableDB::Alignment;
+
+=head1 DESCRIPTION
+
+'Alignment' Is a base class for other classes dealing with Alignment
+It contains virtually nothing so it may disappear and just pass to Funcgen
+
+=cut
+
+package Bio::EnsEMBL::Funcgen::RunnableDB::Alignment;
+
+use warnings;
+use strict;
+use Bio::EnsEMBL::Funcgen::Utils::Helper;
+use Bio::EnsEMBL::DBSQL::DBAdaptor;
+use Bio::EnsEMBL::Funcgen::DBSQL::DBAdaptor; 
+use Bio::EnsEMBL::Funcgen::InputSet;
+use Bio::EnsEMBL::Funcgen::DataSet;
+use Bio::EnsEMBL::Funcgen::FeatureSet;
+use Bio::EnsEMBL::Funcgen::AnnotatedFeature;
+
+use base ('Bio::EnsEMBL::Funcgen::RunnableDB::Funcgen');
+
+use Bio::EnsEMBL::Utils::Exception qw(throw warning stack_trace_dump);
+use Data::Dumper;
+
+sub fetch_input {   
+  my $self = shift @_;
+
+  $self->param("file_type","sam");
+
+  $self->SUPER::fetch_input();
+  
+  #Just override input folders... maybe consider overriding output folders too?
+  my $input_dir = $self->_work_dir()."/fastq/".$self->_species()."/".$self->_experiment_name()."/".
+    $self->_cell_type()->name."_".$self->_feature_type()->name;
+  $self->_input_dir($input_dir);
+
+  #Folder where to send the final results...
+  my $repository = $self->_work_dir()."/alignments/".$self->_species."/".$self->_assembly()."/".$self->_experiment_name();
+  $self->_repository($repository);
+  
+  return 1;
+}
+
+#Private getter / setter to the input folder
+sub _input_dir {
+  return $_[0]->_getter_setter('input_dir',$_[1]);
+}
+
+#Private getter / setter to the repository folder
+sub _repository {
+  return $_[0]->_getter_setter('repository',$_[1]);
+}
+
+#Private getter / setter to an input file
+sub _input_file {
+  return $_[0]->_getter_setter('input_file',$_[1]);
+}
+
+
+1;
+