Bio::EnsEMBL::IdMapping GeneScoreBuilder
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Summary
Package variables
No package variables defined.
Included modules
Bio::EnsEMBL::IdMapping::ScoreBuilder
Bio::EnsEMBL::IdMapping::ScoredMappingMatrix
Bio::EnsEMBL::Utils::Exception qw ( throw warning )
Bio::EnsEMBL::Utils::ScriptUtils qw ( path_append )
Inherit
Bio::EnsEMBL::IdMapping::ScoreBuilder
Synopsis
Description
Combines ExonScoreBuilder, ExonDirectMapper and ExonerateRunner from
Java application.
Methods
biotype_gene_rescore
No description
Code
build_scores
No description
Code
complex_gene_gene_score
No description
Code
flag_matrix_from_transcript_scores
No description
Code
score_genes
No description
Code
score_matrix_from_flag_matrix
No description
Code
scores_from_transcript_scores
No description
Code
simple_gene_gene_score
No description
Code
simple_gene_rescore
No description
Code
Methods description
None available.
Methods code
biotype_gene_rescoredescriptionprevnextTop
sub biotype_gene_rescore {
  my $self = shift;
  my $matrix = shift;

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

  my $i = 0;

  foreach my $entry (@{ $matrix->get_all_Entries }) {

    my $source_gene = $self->cache->get_by_key('genes_by_id', 'source',
      $entry->source);

    my $target_gene = $self->cache->get_by_key('genes_by_id', 'target',
      $entry->target);

    if ($source_gene->biotype ne $target_gene->biotype) {
      #$self->logger->debug("biotype ".$entry->to_string."\n");
$matrix->set_score($entry->source, $entry->target, ($entry->score * 0.8)); $i++; } } $self->logger->debug("Scored genes with biotype mismatch: $i\n", 1); } 1;
}
build_scoresdescriptionprevnextTop
sub build_scores {
  my $self = shift;
  my $matrix = shift;
  my $transcript_matrix = shift;

  unless ($matrix and
          $matrix->isa('Bio::EnsEMBL::IdMapping::ScoredMappingMatrix')) {
    throw('Need a gene Bio::EnsEMBL::IdMapping::ScoredMappingMatrix.');
  }
  
  unless ($transcript_matrix and
          $transcript_matrix->isa('Bio::EnsEMBL::IdMapping::ScoredMappingMatrix')) {
    throw('Need a transcript Bio::EnsEMBL::IdMapping::ScoredMappingMatrix.');
  }

  # first find out which source and target genes have scoring transcripts and
# build a "flag" matrix for these genes (all scores are 1)
$self->flag_matrix_from_transcript_scores($matrix, $transcript_matrix); # now calculate the actual scores for the genes in the flag matrix
my $final_matrix = $self->score_matrix_from_flag_matrix($matrix, $transcript_matrix); return $final_matrix;
}
complex_gene_gene_scoredescriptionprevnextTop
sub complex_gene_gene_score {
  my $self = shift;
  my $source_gene = shift;
  my $target_gene = shift;
  my $transcript_matrix = shift;

  my $source_gene_score = 0;
  my $target_gene_score = 0;
  my $source_gene_accum_length = 0; # sum of all transcript lengths
my $target_gene_accum_length = 0; # sum of all transcript lengths
# We are only interested in scoring with transcripts that are in the target
# gene. The scored mapping matrix may contain scores for transcripts that
# aren't in this gene so create a hash of the target genes's transcripts
my %target_transcripts = map { $_->id => 1 } @{ $target_gene->get_all_Transcripts }; # loop over source transcripts
foreach my $source_transcript (@{ $source_gene->get_all_Transcripts }) { # now loop over target transcripts and find the highest scoring target
# transcript belonging to the target gene
my $max_source_score = -1; foreach my $target_transcript_id (@{ $transcript_matrix->get_targets_for_source($source_transcript->id) }) { next unless ($target_transcripts{$target_transcript_id}); my $score = $transcript_matrix->get_score( $source_transcript->id, $target_transcript_id); $max_source_score = $score if ($score > $max_source_score); } if ($max_source_score > 0) { $source_gene_score += ($max_source_score * $source_transcript->length); } $source_gene_accum_length += $source_transcript->length; } # now do the same for target genes
my %source_transcripts = map { $_->id => 1 } @{ $source_gene->get_all_Transcripts }; # loop over target transcripts
foreach my $target_transcript (@{ $target_gene->get_all_Transcripts }) { # now loop over source transcripts and find the highest scoring source
# transcript belonging to the source gene
my $max_target_score = -1; foreach my $source_transcript_id (@{ $transcript_matrix->get_sources_for_target($target_transcript->id) }) { next unless ($source_transcripts{$source_transcript_id}); my $score = $transcript_matrix->get_score( $source_transcript_id, $target_transcript->id); $max_target_score = $score if ($score > $max_target_score); } if ($max_target_score > 0) { $target_gene_score += ($max_target_score * $target_transcript->length); } $target_gene_accum_length += $target_transcript->length; } # calculate overall score for this gene
my $gene_score = 0; if (($source_gene_accum_length + $target_gene_accum_length) > 0) { $gene_score = ($source_gene_score + $target_gene_score) /
(
$source_gene_accum_length + $target_gene_accum_length);
} else { $self->logger->warning("Combined transcript length of source (".$source_gene->id.") and target (".$target_gene->id.") gene is zero!\n", 1); } if ($gene_score > 1) { $self->logger->warning("Illegal gene score: $gene_score (". join("|", $source_gene_score, $target_gene_score, $source_gene_accum_length, $target_gene_accum_length).")\n", 1); } return $gene_score; } #
# Simplified scoring for genes. Score is best scoring transcript pair.
# This is used when the more elaborate gene representing score does not
# distinguish very well.
#
}
flag_matrix_from_transcript_scoresdescriptionprevnextTop
sub flag_matrix_from_transcript_scores {
  my $self = shift;
  my $matrix = shift;
  my $transcript_matrix = shift;

  unless ($matrix and
          $matrix->isa('Bio::EnsEMBL::IdMapping::ScoredMappingMatrix')) {
    throw('Need a gene Bio::EnsEMBL::IdMapping::ScoredMappingMatrix.');
  }
  
  unless ($transcript_matrix and
          $transcript_matrix->isa('Bio::EnsEMBL::IdMapping::ScoredMappingMatrix')) {
    throw('Need a transcript Bio::EnsEMBL::IdMapping::ScoredMappingMatrix.');
  }

  # initialise progress logger
my $i; my $num_entries = $transcript_matrix->get_entry_count; my $progress_id = $self->logger->init_progress($num_entries, 100); $self->logger->info("Creating flag matrix...\n", 1); # for every transcript scoring matrix entry, make an entry in the gene flag
# matrix.
foreach my $entry (@{ $transcript_matrix->get_all_Entries }) { $self->logger->log_progress($progress_id, ++$i, 1); my $source_gene = $self->cache->get_by_key('genes_by_transcript_id', 'source', $entry->source); my $target_gene = $self->cache->get_by_key('genes_by_transcript_id', 'target', $entry->target); $matrix->add_score($source_gene->id, $target_gene->id, 1); } $self->logger->info("\n"); return $matrix;
}
score_genesdescriptionprevnextTop
sub score_genes {
  my $self = shift;
  my $transcript_matrix = shift;

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

  $self->logger->info("-- Scoring genes...\n\n", 0, 'stamped');

  # build scores based on transcript scores
my $matrix = $self->scores_from_transcript_scores($transcript_matrix); # debug logging
if ($self->logger->loglevel eq 'debug') { $matrix->log('gene', $self->conf->param('basedir')); } # log stats of combined matrix
my $fmt = "%-40s%10.0f\n"; $self->logger->info("Scoring matrix:\n"); $self->logger->info(sprintf($fmt, "Total source genes:", $self->cache->get_count_by_name('genes_by_id', 'source')), 1); $self->logger->info(sprintf($fmt, "Total target genes:", $self->cache->get_count_by_name('genes_by_id', 'target')), 1); $self->log_matrix_stats($matrix); $self->logger->info("\nDone with gene scoring.\n\n"); return $matrix;
}
score_matrix_from_flag_matrixdescriptionprevnextTop
sub score_matrix_from_flag_matrix {
  my $self = shift;
  my $flag_matrix = shift;
  my $transcript_matrix = shift;
  my $simple_scoring = shift;

  unless ($flag_matrix and
          $flag_matrix->isa('Bio::EnsEMBL::IdMapping::ScoredMappingMatrix')) {
    throw('Need a gene Bio::EnsEMBL::IdMapping::ScoredMappingMatrix.');
  }
  
  unless ($transcript_matrix and
          $transcript_matrix->isa('Bio::EnsEMBL::IdMapping::ScoredMappingMatrix')) {
    throw('Need a transcript Bio::EnsEMBL::IdMapping::ScoredMappingMatrix.');
  }

  # 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_entries = $flag_matrix->get_entry_count; my $progress_id = $self->logger->init_progress($num_entries, 100); $self->logger->info("Creating score matrix from flag matrix...\n", 1); # loop over flag matrix and do proper scoring for each entry
foreach my $entry (@{ $flag_matrix->get_all_Entries }) { $self->logger->log_progress($progress_id, ++$i, 1); my $score = 0; my $source_gene = $self->cache->get_by_key('genes_by_id', 'source', $entry->source); my $target_gene = $self->cache->get_by_key('genes_by_id', 'target', $entry->target); if ($simple_scoring) { # simple scoring (used for rescoring purposes)
$score = $self->simple_gene_gene_score($source_gene, $target_gene, $transcript_matrix); } else { # full scoring
$score = $self->complex_gene_gene_score($source_gene, $target_gene, $transcript_matrix); } $matrix->add_score($entry->source, $entry->target, $score); } $self->logger->info("\n"); return $matrix;
}
scores_from_transcript_scoresdescriptionprevnextTop
sub scores_from_transcript_scores {
  my $self = shift;
  my $transcript_matrix = shift;

  unless ($transcript_matrix and
          $transcript_matrix->isa('Bio::EnsEMBL::IdMapping::ScoredMappingMatrix')) {
    throw('Need a Bio::EnsEMBL::IdMapping::ScoredMappingMatrix.');
  }
  
  my $dump_path = path_append($self->conf->param('basedir'), 'matrix');
  
  my $matrix = Bio::EnsEMBL::IdMapping::ScoredMappingMatrix->new(
    -DUMP_PATH   => $dump_path,
    -CACHE_FILE  => 'gene_matrix.ser',
  );

  my $gene_cache = $matrix->cache_file;

  if (-s $gene_cache) {
    
    # read from file
$self->logger->info("Reading gene scoring matrix from file...\n", 0, 'stamped'); $self->logger->debug("Cache file $gene_cache.\n", 1); $matrix->read_from_file; $self->logger->info("Done.\n\n", 0, 'stamped'); } else { # build scoring matrix
$self->logger->info("No gene scoring matrix found. Will build new one.\n"); $self->logger->info("Gene scoring...\n", 0, 'stamped'); $matrix = $self->build_scores($matrix, $transcript_matrix); $self->logger->info("Done.\n\n", 0, 'stamped'); # write scoring matrix to file
$matrix->write_to_file; } return $matrix;
}
simple_gene_gene_scoredescriptionprevnextTop
sub simple_gene_gene_score {
  my $self = shift;
  my $source_gene = shift;
  my $target_gene = shift;
  my $transcript_matrix = shift;

  my $gene_score = 0;

  foreach my $source_transcript (@{ $source_gene->get_all_Transcripts }) {
    foreach my $target_transcript (@{ $target_gene->get_all_Transcripts }) {
      
      my $score = $transcript_matrix->get_score($source_transcript->id,
        $target_transcript->id);

      $gene_score = $score if ($score > $gene_score);
    }
  }

  return $gene_score;
}
simple_gene_rescoredescriptionprevnextTop
sub simple_gene_rescore {
  my $self = shift;
  my $gene_matrix = shift;
  my $transcript_matrix = shift;

  $gene_matrix = $self->score_matrix_from_flag_matrix($gene_matrix,
    $transcript_matrix, 1);
}

#
# penalise scores between genes with different biotypes.
# entries are modified in place
#
}
General documentation
LICENSETop
  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
CONTACTTop
  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>.