Raw content of Bio::EnsEMBL::IdMapping::InternalIdMapper::EnsemblGeneGeneric
<![CDATA[=head1 LICENSE
Copyright (c) 1999-2009 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
/info/about/code_licence.html
=head1 CONTACT
Please email comments or questions to the public Ensembl
developers list at <ensembl-dev@ebi.ac.uk>.
Questions may also be sent to the Ensembl help desk at
<helpdesk@ensembl.org>.
=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;
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