diff variant_effect_predictor/Bio/EnsEMBL/IdMapping/InternalIdMapper/EnsemblExonGeneric.pm @ 0:1f6dce3d34e0

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/variant_effect_predictor/Bio/EnsEMBL/IdMapping/InternalIdMapper/EnsemblExonGeneric.pm	Thu Apr 11 02:01:53 2013 -0400
@@ -0,0 +1,121 @@
+=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
+
+=head1 NAME
+
+=head1 SYNOPSIS
+
+=head1 DESCRIPTION
+
+=head1 METHODS
+
+=cut
+
+package Bio::EnsEMBL::IdMapping::InternalIdMapper::EnsemblExonGeneric;
+
+use strict;
+use warnings;
+no warnings 'uninitialized';
+
+use Bio::EnsEMBL::IdMapping::InternalIdMapper::BaseMapper;
+our @ISA = qw(Bio::EnsEMBL::IdMapping::InternalIdMapper::BaseMapper);
+
+use Bio::EnsEMBL::Utils::Exception qw(throw warning);
+
+  
+#
+# basic mapping
+#
+sub init_basic {
+  my $self = shift;
+  my $num = shift;
+  my $esb = shift;
+  my $mappings = shift;
+  my $exon_scores = shift;
+
+  $self->logger->info("Basic exon mapping...\n", 0, 'stamped');
+
+  $mappings = $self->basic_mapping($exon_scores, "exon_mappings$num");
+  $num++;
+  my $new_scores = $esb->create_shrinked_matrix($exon_scores, $mappings,
+    "exon_matrix$num");
+
+  return ($new_scores, $mappings);
+}
+
+
+#
+# reduce score for mappings of exons which do not belong to mapped
+# transcripts
+#
+sub mapped_transcript {
+  my $self = shift;
+  my $num = shift;
+  my $esb = shift;
+  my $mappings = shift;
+  my $exon_scores = shift;
+
+  $self->logger->info("Exons in mapped transcript...\n", 0, 'stamped');
+
+  unless ($exon_scores->loaded) {
+    $esb->non_mapped_transcript_rescore($exon_scores, $mappings);
+    $exon_scores->write_to_file;
+  }
+
+  $mappings = $self->basic_mapping($exon_scores, "exon_mappings$num");
+  $num++;
+  my $new_scores = $esb->create_shrinked_matrix($exon_scores, $mappings,
+    "exon_matrix$num");
+
+  return ($new_scores, $mappings);
+}
+  
+
+#
+# selectively rescore by penalising scores between exons with
+# different internalIDs
+#
+sub internal_id {
+  my $self        = shift;
+  my $num         = shift;
+  my $esb         = shift;
+  my $mappings    = shift;
+  my $exon_scores = shift;
+
+  $self->logger->info( "Retry with internalID disambiguation...\n",
+                       0, 'stamped' );
+
+  if ( !$exon_scores->loaded() ) {
+    $esb->internal_id_rescore($exon_scores);
+    $exon_scores->write_to_file();
+  }
+
+  $mappings = $self->basic_mapping( $exon_scores, "exon_mappings$num" );
+  $num++;
+  my $new_scores =
+    $esb->create_shrinked_matrix( $exon_scores, $mappings,
+                                  "exon_matrix$num" );
+
+  return ( $new_scores, $mappings );
+}
+
+
+1;
+