=head1 LICENSE
Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
Copyright [2016-2024] EMBL-European Bioinformatics Institute
Licensed under the Apache License, Version 2.0 (the "License");
you may not use this file except in compliance with the License.
You may obtain a copy of the License at
Unless required by applicable law or agreed to in writing, software
distributed under the License is distributed on an "AS IS" BASIS,
WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
See the License for the specific language governing permissions and
limitations under the License.
=cut
=head1 CONTACT
Please email comments or questions to the public Ensembl
Questions may also be sent to the Ensembl help desk at
=cut
=head1 NAME
Bio::EnsEMBL::IdMapping::InternalIdMapper::EnsemblGeneGeneric - default Ensembl
InternalIdMapper implementation for genes
=head1 SYNOPSIS
=head1 DESCRIPTION
=head1 METHODS
=cut
$Bio::EnsEMBL::IdMapping::InternalIdMapper::EnsemblGeneGeneric::VERSION = '112.0.0';
use strict;
no warnings 'uninitialized';
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 $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);
}
sub location {
my $self = shift;
my $num = shift;
my $gsb = shift;
my $mappings = shift;
my $gene_scores = shift;
$self->logger->info("Retry with location disambiguation...\n", 0, 'stamped');
unless ($gene_scores->loaded) {
$gsb->location_gene_rescore($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;