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

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/variant_effect_predictor/Bio/EnsEMBL/IdMapping/InternalIdMapper/EnsemblGeneGeneric.pm	Thu Apr 11 02:01:53 2013 -0400
@@ -0,0 +1,188 @@
+=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
+
+Bio::EnsEMBL::IdMapping::InternalIdMapper::EnsemblGeneGeneric - default Ensembl
+InternalIdMapper implementation for genes
+
+=head1 SYNOPSIS
+
+=head1 DESCRIPTION
+
+=head1 METHODS
+
+=cut
+
+package Bio::EnsEMBL::IdMapping::InternalIdMapper::EnsemblGeneGeneric;
+
+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);
+use Bio::EnsEMBL::Utils::ScriptUtils qw(path_append);
+
+
+#
+# basic mapping
+#
+sub init_basic {
+  my $self = shift;
+  my $num = shift;
+  my $gsb = shift;
+  my $mappings = shift;
+  my $gene_scores = shift;
+
+  $self->logger->info("Basic gene mapping...\n", 0, 'stamped');
+
+  $mappings = $self->basic_mapping($gene_scores, "gene_mappings$num");
+  $num++;
+  my $new_scores = $gsb->create_shrinked_matrix($gene_scores, $mappings,
+    "gene_matrix$num");
+
+  return ($new_scores, $mappings);
+}
+
+
+#
+# build the synteny from unambiguous mappings
+#
+sub synteny {
+  my $self = shift;
+  my $num = shift;
+  my $gsb = shift;
+  my $mappings = shift;
+  my $gene_scores = shift;
+
+  unless ($gene_scores->loaded) {
+    $self->logger->info("Synteny Framework building...\n", 0, 'stamped');
+    my $dump_path = path_append($self->conf->param('basedir'), 'mapping');
+    my $sf = Bio::EnsEMBL::IdMapping::SyntenyFramework->new(
+      -DUMP_PATH    => $dump_path,
+      -CACHE_FILE   => 'synteny_framework.ser',
+      -LOGGER       => $self->logger,
+      -CONF         => $self->conf,
+      -CACHE        => $self->cache,
+    );
+    $sf->build_synteny($mappings);
+
+    # use it to rescore the genes
+    $self->logger->info("\nSynteny assisted mapping...\n", 0, 'stamped');
+    $gene_scores = $sf->rescore_gene_matrix_lsf($gene_scores);
+
+    # checkpoint
+    $gene_scores->write_to_file;
+  }
+
+  my $new_mappings = $self->basic_mapping($gene_scores, "gene_mappings$num");
+  $num++;
+  my $new_scores = $gsb->create_shrinked_matrix($gene_scores, $new_mappings,
+    "gene_matrix$num");
+
+  return ($new_scores, $new_mappings); 
+}
+
+
+#
+# rescore with simple scoring function and try again
+#
+sub best_transcript {
+  my $self = shift;
+  my $num = shift;
+  my $gsb = shift;
+  my $mappings = shift;
+  my $gene_scores = shift;
+  my $transcript_scores = shift;
+
+  $self->logger->info("Retry with simple best transcript score...\n", 0, 'stamped');
+  
+  unless ($gene_scores->loaded) {
+    $gsb->simple_gene_rescore($gene_scores, $transcript_scores);
+    $gene_scores->write_to_file;
+  }
+  
+  my $new_mappings = $self->basic_mapping($gene_scores, "gene_mappings$num");
+  $num++;
+  my $new_scores = $gsb->create_shrinked_matrix($gene_scores, $new_mappings,
+    "gene_matrix$num");
+
+  return ($new_scores, $new_mappings); 
+}
+
+
+#
+# rescore by penalising scores between genes with different biotypes  
+#
+sub biotype {
+  my $self = shift;
+  my $num = shift;
+  my $gsb = shift;
+  my $mappings = shift;
+  my $gene_scores = shift;
+
+  $self->logger->info("Retry with biotype disambiguation...\n", 0, 'stamped');
+  
+  unless ($gene_scores->loaded) {
+    $gsb->biotype_gene_rescore($gene_scores);
+    $gene_scores->write_to_file;
+  }
+
+  my $new_mappings = $self->basic_mapping($gene_scores, "gene_mappings$num");
+  $num++;
+  my $new_scores = $gsb->create_shrinked_matrix($gene_scores, $new_mappings,
+    "gene_matrix$num");
+
+  return ($new_scores, $new_mappings); 
+}
+
+
+#
+# selectively rescore by penalising scores between genes with different
+# internalIDs  
+#
+sub internal_id {
+  my $self = shift;
+  my $num = shift;
+  my $gsb = shift;
+  my $mappings = shift;
+  my $gene_scores = shift;
+
+  $self->logger->info("Retry with internalID disambiguation...\n", 0, 'stamped');
+  
+  unless ($gene_scores->loaded) {
+    $gsb->internal_id_rescore($gene_scores);
+    $gene_scores->write_to_file;
+  }
+
+  my $new_mappings = $self->basic_mapping($gene_scores, "gene_mappings$num");
+  $num++;
+  my $new_scores = $gsb->create_shrinked_matrix($gene_scores, $new_mappings,
+    "gene_matrix$num");
+
+  return ($new_scores, $new_mappings); 
+}
+
+
+1;
+