view variant_effect_predictor/Bio/EnsEMBL/IdMapping/InternalIdMapper/EnsemblTranscriptGeneric.pm @ 3:d30fa12e4cc5 default tip

Merge heads 2:a5976b2dce6f and 1:09613ce8151e which were created as a result of a recently fixed bug.

=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::EnsemblTranscriptGeneric;

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 $tsb = shift;
  my $mappings = shift;
  my $transcript_scores = shift;

  $self->logger->info("Basic transcript mapping...\n", 0, 'stamped');

  $mappings = $self->basic_mapping($transcript_scores,
    "transcript_mappings$num");
  $num++;
  my $new_scores = $tsb->create_shrinked_matrix($transcript_scores, $mappings,
    "transcript_matrix$num");

  return ($new_scores, $mappings);
}


#
# handle cases with exact match but different translation
#
sub non_exact_translation {
  my $self = shift;
  my $num = shift;
  my $tsb = shift;
  my $mappings = shift;
  my $transcript_scores = shift;

  $self->logger->info("Exact Transcript non-exact Translation...\n", 0, 'stamped');
  
  unless ($transcript_scores->loaded) {
    $tsb->different_translation_rescore($transcript_scores);
    $transcript_scores->write_to_file;
  }
  
  $mappings = $self->basic_mapping($transcript_scores,
    "transcript_mappings$num");
  $num++;
  my $new_scores = $tsb->create_shrinked_matrix($transcript_scores, $mappings,
    "transcript_matrix$num");

  return ($new_scores, $mappings);
}


#
# reduce score for mappings of transcripts which do not belong to mapped
# genes
#
sub mapped_gene {
  my $self = shift;
  my $num = shift;
  my $tsb = shift;
  my $mappings = shift;
  my $transcript_scores = shift;
  my $gene_mappings = shift;

  $self->logger->info("Transcripts in mapped genes...\n", 0, 'stamped');
  
  unless ($transcript_scores->loaded) {
  $tsb->non_mapped_gene_rescore($transcript_scores, $gene_mappings);
    $transcript_scores->write_to_file;
  }
  
  $mappings = $self->basic_mapping($transcript_scores,
    "transcript_mappings$num");
  $num++;
  my $new_scores = $tsb->create_shrinked_matrix($transcript_scores, $mappings,
    "transcript_matrix$num");

  return ($new_scores, $mappings);
}

#
# rescore by penalising scores between transcripts with different biotypes
#
sub biotype {
  my $self              = shift;
  my $num               = shift;
  my $tsb               = shift;
  my $mappings          = shift;
  my $transcript_scores = shift;

  $self->logger->info( "Retry with biotype disambiguation...\n",
                       0, 'stamped' );

  unless ( $transcript_scores->loaded() ) {
    $tsb->biotype_transcript_rescore($transcript_scores);
    $transcript_scores->write_to_file();
  }

  my $new_mappings = $self->basic_mapping( $transcript_scores,
                                           "transcript_mappings$num" );
  $num++;
  my $new_scores =
    $tsb->create_shrinked_matrix( $transcript_scores, $new_mappings,
                                  "transcript_matrix$num" );

  return ( $new_scores, $new_mappings );
}

#
# selectively rescore by penalising scores between transcripts with
# different internalIDs  
#
sub internal_id {
  my $self = shift;
  my $num = shift;
  my $tsb = shift;
  my $mappings = shift;
  my $transcript_scores = shift;

  $self->logger->info("Retry with internalID disambiguation...\n", 0, 'stamped');
  
  unless ($transcript_scores->loaded) {
    $tsb->internal_id_rescore($transcript_scores);
    $transcript_scores->write_to_file;
  }

  $mappings = $self->basic_mapping($transcript_scores,
    "transcript_mappings$num");
  $num++;
  my $new_scores = $tsb->create_shrinked_matrix($transcript_scores, $mappings,
    "transcript_matrix$num");

  return ($new_scores, $mappings);
}


#
# handle ambiguities between transcripts in single genes
#
sub single_gene {
  my $self = shift;
  my $num = shift;
  my $tsb = shift;
  my $mappings = shift;
  my $transcript_scores = shift;

  $self->logger->info("Transcripts in single genes...\n", 0, 'stamped');
  
  unless ($transcript_scores->loaded) {
    $transcript_scores->write_to_file;
  }
  
  $mappings = $self->same_gene_transcript_mapping($transcript_scores,
    "transcript_mappings$num");
  $num++;
  my $new_scores = $tsb->create_shrinked_matrix($transcript_scores, $mappings,
    "transcript_matrix$num");

  return ($new_scores, $mappings);
}


#
# modified basic mapper that maps transcripts that are ambiguous within one gene
#
sub same_gene_transcript_mapping {
  my $self = shift;
  my $matrix = shift;
  my $mapping_name = shift;

  # argument checks
  unless ($matrix and
          $matrix->isa('Bio::EnsEMBL::IdMapping::ScoredMappingMatrix')) {
    throw('Need a Bio::EnsEMBL::IdMapping::ScoredMappingMatrix.');
  }

  throw('Need a name for serialising the mapping.') unless ($mapping_name);

  # Create a new MappingList object. Specify AUTO_LOAD to load serialised
  # existing mappings if found
  my $dump_path = path_append($self->conf->param('basedir'), 'mapping');
  
  my $mappings = Bio::EnsEMBL::IdMapping::MappingList->new(
    -DUMP_PATH   => $dump_path,
    -CACHE_FILE  => "${mapping_name}.ser",
    -AUTO_LOAD   => 1,
  );
  
  # checkpoint test: return a previously stored MappingList
  if ($mappings->loaded) {
    $self->logger->info("Read existing mappings from ${mapping_name}.ser.\n");
    return $mappings;
  }

  my $sources_done = {};
  my $targets_done = {};

  # sort scoring matrix entries by descending score
  my @sorted_entries = sort { $b->score <=> $a->score ||
    $a->source <=> $b->source || $a->target <=> $b->target }
      @{ $matrix->get_all_Entries };

  while (my $entry = shift(@sorted_entries)) {
    
    # $self->logger->debug("\nxxx4 ".$entry->to_string." ");

    # we already found a mapping for either source or target yet
    next if ($sources_done->{$entry->source} or
             $targets_done->{$entry->target});

    #$self->logger->debug('d');

    my $other_sources = [];
    my $other_targets = [];
    my %source_genes = ();
    my %target_genes = ();

    if ($self->ambiguous_mapping($entry, $matrix, $other_sources, $other_targets)) {
      #$self->logger->debug('a');

      $other_sources = $self->filter_sources($other_sources, $sources_done);
      $other_targets = $self->filter_targets($other_targets, $targets_done);

      $source_genes{$self->cache->get_by_key('genes_by_transcript_id',
        'source', $entry->source)} = 1;
      $target_genes{$self->cache->get_by_key('genes_by_transcript_id',
        'target', $entry->target)} = 1;

      foreach my $other_source (@{ $other_sources }) {
        $source_genes{$self->cache->get_by_key('genes_by_transcript_id',
          'source', $other_source)} = 1;
      }
        
      foreach my $other_target (@{ $other_targets }) {
        $target_genes{$self->cache->get_by_key('genes_by_transcript_id',
          'target', $other_target)} = 1;
      }
      
      # only add mapping if only one source and target gene involved
      if (scalar(keys %source_genes) == 1 and scalar(keys %target_genes) == 1) {
        #$self->logger->debug('O');
        $mappings->add_Entry($entry);
      }

    } else {
      #$self->logger->debug('A');

      # this is the best mapping, add it
      $mappings->add_Entry($entry);
    }

    $sources_done->{$entry->source} = 1;
    $targets_done->{$entry->target} = 1;
  }

  # create checkpoint
  $mappings->write_to_file;

  return $mappings;
}


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