Inheritance diagram for Bio::EnsEMBL::IdMapping::TranscriptScoreBuilder:

Public Member Functions
public	score_transcripts ()

public	scores_from_exon_scores ()

public	build_scores ()

public	flag_matrix_from_exon_scores ()

public	score_matrix_from_flag_matrix ()

public	biotype_transcript_rescore ()

public	different_translation_rescore ()

public	non_mapped_gene_rescore ()

public	get_biotype_group ()

Public Member Functions inherited from Bio::EnsEMBL::IdMapping::ScoreBuilder
public Bio::EnsEMBL::IdMapping::ScoredMappingMatrix	create_shrinked_matrix ()

public void	internal_id_rescore ()

public void	log_matrix_stats ()

Public Member Functions inherited from Bio::EnsEMBL::IdMapping::BaseObject
public $this	new ()

public Filehandle	get_filehandle ()

public Boolean	file_exists ()

public SQLStatement	fetch_value_from_db ()

public Int	dump_table_to_file ()

public Int	upload_file_into_table ()

public Bio::EnsEMBL::Utils::Logger	logger ()

public Bio::EnsEMBL::Utils::ConfParser	conf ()

public Bio::EnsEMBL::IdMapping::Cache	cache ()

Detailed Description

Synopsis

Description

Combines ExonScoreBuilder, ExonDirectMapper and ExonerateRunner from
Java application.

Definition at line 19 of file TranscriptScoreBuilder.pm.

Member Function Documentation

◆ biotype_transcript_rescore()

public Bio::EnsEMBL::IdMapping::TranscriptScoreBuilder::biotype_transcript_rescore ( )

Undocumented method

Code:

click to view

◆ build_scores()

public Bio::EnsEMBL::IdMapping::TranscriptScoreBuilder::build_scores ( )

Undocumented method

Code:

click to view

◆ different_translation_rescore()

public Bio::EnsEMBL::IdMapping::TranscriptScoreBuilder::different_translation_rescore ( )

Undocumented method

Code:

click to view

◆ flag_matrix_from_exon_scores()

public Bio::EnsEMBL::IdMapping::TranscriptScoreBuilder::flag_matrix_from_exon_scores ( )

Undocumented method

Code:

click to view

◆ get_biotype_group()

public Bio::EnsEMBL::IdMapping::TranscriptScoreBuilder::get_biotype_group ( )

Undocumented method

Code:

click to view

◆ non_mapped_gene_rescore()

public Bio::EnsEMBL::IdMapping::TranscriptScoreBuilder::non_mapped_gene_rescore ( )

Undocumented method

Code:

click to view

◆ score_matrix_from_flag_matrix()

public Bio::EnsEMBL::IdMapping::TranscriptScoreBuilder::score_matrix_from_flag_matrix ( )

Undocumented method

Code:

click to view

sub score_matrix_from_flag_matrix {
  my $self = shift;
  my $flag_matrix = shift;
  my $exon_matrix = shift;
 
  unless ($flag_matrix and
          $flag_matrix->isa('Bio::EnsEMBL::IdMapping::ScoredMappingMatrix')) {
    throw('Need a transcript Bio::EnsEMBL::IdMapping::ScoredMappingMatrix.');
  }
  
  unless ($exon_matrix and
          $exon_matrix->isa('Bio::EnsEMBL::IdMapping::ScoredMappingMatrix')) {
    throw('Need an exon Bio::EnsEMBL::IdMapping::ScoredMappingMatrix.');
  }
 
  my $transcript_score_threshold =
    $self->conf->param('transcript_score_threshold') || 0;
 
  # create a new scoring matrix which will replace the flag matrix
  my $matrix = Bio::EnsEMBL::IdMapping::ScoredMappingMatrix->new(
    -DUMP_PATH   => $flag_matrix->dump_path,
    -CACHE_FILE  => $flag_matrix->cache_file_name,
  );
 
  # initialise progress logger
  my $i;
  my $num_transcripts =
    scalar(keys %{ $self->cache->get_by_name('transcripts_by_id', 'source') });
  my $progress_id = $self->logger->init_progress($num_transcripts, 100);
 
  $self->logger->info("Creating score matrix from flag matrix...\n", 1);
 
  # debug
  my $fmt_d1 = "%-14s%-15s%-14s%-14s%-14s\n";
  my $fmt_d2 = "%.6f";
  
  # loop over source transcripts
  foreach my $source_transcript (values %{ $self->cache->get_by_name('transcripts_by_id', 'source') }) {
    
    # log progress
    $self->logger->log_progress($progress_id, ++$i, 1);
 
    # We are only interested in scoring with exons that are in the target
    # transcript. The ScoredMappingMatrix may contain scores for exons that
    # aren't in this transcript so create a hash of the target transcript's
    # exons
    my %source_exons = map { $_->id => 1 }
      @{ $source_transcript->get_all_Exons };
 
    my $source_transcript_length = $source_transcript->length;
 
    # get all corresponding target transcripts from the flag matrix
    foreach my $target_transcript_id (@{ $flag_matrix->get_targets_for_source($source_transcript->id) }) {
      
      my $target_transcript = $self->cache->get_by_key('transcripts_by_id', 'target', $target_transcript_id);
 
      my $source_transcript_score = 0;
      my $target_transcript_score = 0;
      my $target_transcript_length = $target_transcript->length;
 
      my %target_exons = map { $_->id => 1 }
        @{ $target_transcript->get_all_Exons };
 
      # now loop over source exons and find the highest scoring target exon
      # belonging to the target transcript
      
      foreach my $source_exon (@{ $source_transcript->get_all_Exons }) {
 
        my $max_source_score = -1;
        
        foreach my $target_exon_id (@{ $exon_matrix->get_targets_for_source($source_exon->id) }) {
 
          next unless ($target_exons{$target_exon_id});
 
          my $score = $exon_matrix->get_score($source_exon->id,
            $target_exon_id);
          $max_source_score = $score if ($score > $max_source_score);
        }
 
        if ($max_source_score > 0) {
          $source_transcript_score += ($max_source_score * $source_exon->length);
 
        }
      }
 
      # now do the same for target exons
      
      foreach my $target_exon (@{ $target_transcript->get_all_Exons }) {
 
        my $max_target_score = -1;
        
        foreach my $source_exon_id (@{ $exon_matrix->get_sources_for_target($target_exon->id) }) {
 
          next unless ($source_exons{$source_exon_id});
 
          my $score = $exon_matrix->get_score(
            $source_exon_id, $target_exon->id);
          $max_target_score = $score if ($score > $max_target_score);
        }
 
        if ($max_target_score > 0) {
          $target_transcript_score += ($max_target_score * $target_exon->length);
 
        }
      }
 
      #
      # calculate transcript score and add to scoring matrix
      #
      if (($source_transcript_length + $target_transcript_length) > 0) {
 
        # sanity check
        if (($source_transcript_score > $source_transcript_length) or
            ($target_transcript_score > $target_transcript_length)) {
 
          $self->logger->warning("Score > length for source ($source_transcript_score <> $source_transcript_length) or target ($target_transcript_score <> $target_transcript_length).\n", 1);
 
        } else {
 
          my $source_transcript_biotype_group = $self->get_biotype_group($source_transcript->biotype());
          my $target_transcript_biotype_group = $self->get_biotype_group($target_transcript->biotype());
 
          # debug
          $self->logger->info($source_transcript->id.":".$target_transcript->id.
            " source score: $source_transcript_score".
            " source length: $source_transcript_length".
            " source biotype:" . $source_transcript->biotype() .
            " source group: $source_transcript_biotype_group".
            " target score: $target_transcript_score".
            " target biotype:" . $target_transcript->biotype() .
            " target group: $target_transcript_biotype_group".
            " target length: $target_transcript_length\n");
 
          my $transcript_score =
            ($source_transcript_score + $target_transcript_score) /
            ($source_transcript_length + $target_transcript_length);
 
## Add penalty if biotypes are different
          if ($source_transcript->biotype() ne $target_transcript->biotype()) {
            $transcript_score = $transcript_score * 0.9;
          }
 
## Add penalty if biotype groups are different
          if ($source_transcript_biotype_group ne $target_transcript_biotype_group) {
            $transcript_score = $transcript_score * 0.8;
          }
 
          # everything is fine, add score to matrix
          if ($transcript_score > $transcript_score_threshold) {
            $matrix->add_score($source_transcript->id, $target_transcript->id,
              $transcript_score);
          }
          
        }
      
      } else {
      
        $self->logger->warning("Combined length of source (".$source_transcript->id.") and target (".$target_transcript->id.") transcript is zero!\n", 1);
      
      }
 
    }
  }
 
  $self->logger->info("\n");
 
  return $matrix;
    
}

◆ score_transcripts()

public Bio::EnsEMBL::IdMapping::TranscriptScoreBuilder::score_transcripts ( )

Undocumented method

Code:

click to view

◆ scores_from_exon_scores()

public Bio::EnsEMBL::IdMapping::TranscriptScoreBuilder::scores_from_exon_scores ( )

Undocumented method

Code:

click to view

The documentation for this class was generated from the following file:

ensembl/modules/Bio/EnsEMBL/IdMapping/TranscriptScoreBuilder.pm

Public Member Functions

Detailed Description

Synopsis

Description

Member Function Documentation

◆ biotype_transcript_rescore()

◆ build_scores()

◆ different_translation_rescore()

◆ flag_matrix_from_exon_scores()

◆ get_biotype_group()

◆ non_mapped_gene_rescore()

◆ score_matrix_from_flag_matrix()

◆ score_transcripts()

◆ scores_from_exon_scores()