Mercurial > repos > mahtabm > ensembl
view variant_effect_predictor/Bio/EnsEMBL/IdMapping/InternalIdMapper/EnsemblGeneGeneric.pm @ 3:d30fa12e4cc5 default tip
Merge heads 2:a5976b2dce6f and 1:09613ce8151e which were created as a result of a recently fixed bug.
author | devteam <devteam@galaxyproject.org> |
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date | Mon, 13 Jan 2014 10:38:30 -0500 |
parents | 1f6dce3d34e0 |
children |
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=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 <dev@ensembl.org>. 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;