Inheritance diagram for Bio::EnsEMBL::IdMapping::ScoreBuilder:

Public Member Functions
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

This class is not instantiated. Please see subclasses for usage examples

(e.g. GeneScoreBuilder).

Description

This is the base class for the score builders used in the stable Id
mapping application. It contains methods which are used by more than one
ScoreBuilder.

Definition at line 22 of file ScoreBuilder.pm.

Member Function Documentation

◆ create_shrinked_matrix()

public Bio::EnsEMBL::IdMapping::ScoredMappingMatrix Bio::EnsEMBL::IdMapping::ScoreBuilder::create_shrinked_matrix ( )

  Arg[1]      : Bio::EnsEMBL::Idmapping::ScoredMappingMatrix $matrix - a scoring
                matrix
  Arg[2]      : Bio::EnsEMBL::Idmapping::MappingList $mappings - mappings
  Arg[3]      : String $cache_file - base name of a cache file (extension '.ser'
                will be added automatically) for the returned matrix
  Example     :

my $new_scores = $score_builder->create_shrinked_matrix(

$gene_scores, $mappings, "gene_matrix1");

  Description : Create a shrinked scoring matrix which doesn't contain entries
                which were already mapped. It also logs how many new mappings
                were added in this process.
  Return type : Bio::EnsEMBL::IdMapping::ScoredMappingMatrix
  Exceptions  : thrown on wrong or missing arguments
  Caller      : InternalIdMapper plugin
  Status      : At Risk
              : under development

Code:

click to view

sub create_shrinked_matrix {
  my $self = shift;
  my $matrix = shift;
  my $mappings = shift;
  my $cache_file = shift; # base name, extension '.ser' will be added
 
  # argument checks
  unless ($matrix and
          $matrix->isa('Bio::EnsEMBL::IdMapping::ScoredMappingMatrix')) {
    throw('Need a Bio::EnsEMBL::IdMapping::ScoredMappingMatrix.');
  }
  
  unless ($mappings and
          $mappings->isa('Bio::EnsEMBL::IdMapping::MappingList')) {
    throw('Need a gene Bio::EnsEMBL::IdMapping::MappingList.');
  }
 
  throw('Need a cache file name.') unless ($cache_file);
 
  my $dump_path = path_append($self->conf->param('basedir'), 'matrix');
  $cache_file .= '.ser';
 
  my $shrinked_matrix = Bio::EnsEMBL::IdMapping::ScoredMappingMatrix->new(
    -DUMP_PATH   => $dump_path,
    -CACHE_FILE  => $cache_file,
    -AUTO_LOAD   => 1,
  );
 
  # if we already found a saved matrix, just return it
  if ($shrinked_matrix->loaded) {
  
    $self->logger->info("Read existing scoring matrix from $cache_file.\n");
  
  } else {
    
    # create lookup hashes for sources and targets in the MappingList
    my %sources = ();
    my %targets = ();
 
    foreach my $entry (@{ $mappings->get_all_Entries }) {
      $sources{$entry->source} = 1;
      $targets{$entry->target} = 1;
    }
 
    # add all entries to shrinked matrix which are not in the MappingList
    foreach my $entry (@{ $matrix->get_all_Entries }) {
      unless ($sources{$entry->source} or $targets{$entry->target}) {
        $shrinked_matrix->add_Entry($entry);
      }
    }
 
  }
 
  # log shrinking stats
  $self->logger->info('Sources '.$matrix->get_source_count.' --> '.
    $shrinked_matrix->get_source_count."\n");
  $self->logger->info('Targets '.$matrix->get_target_count.' --> '.
    $shrinked_matrix->get_target_count."\n");
  $self->logger->info('Entries '.$matrix->get_entry_count.' --> '.
    $shrinked_matrix->get_entry_count."\n");
  $self->logger->info('New mappings: '.$mappings->get_entry_count."\n\n");
 
  return $shrinked_matrix;
}

◆ internal_id_rescore()

public void Bio::EnsEMBL::IdMapping::ScoreBuilder::internal_id_rescore ( )

  Arg[1]      : Bio::EnsEMBL::Idmapping::ScoredMappingMatrix $matrix - a scoring
                matrix
  Example     :

$score_builder->internal_id_rescore($gene_scores);

  Description : Rescore ambiguous mappings based on internal Ids. This is the
                last disambiguation step and is only useful if objects with the
                same internal Id were used in source and target dbs (e.g. in
                patch builds or if objects were copied from source to target).

                If a source and target gene have the same internal Id and there
                are mappings to other target genes then these *other* mappings
                are penalised.
  Return type : none
  Exceptions  : thrown on wrong or missing argument
  Caller      : InternalIdMapper plugins
  Status      : At Risk
              : under development

Code:

click to view

◆ log_matrix_stats()

public void Bio::EnsEMBL::IdMapping::ScoreBuilder::log_matrix_stats ( )

  Arg[1]      : Bio::EnsEMBL::Idmapping::ScoredMappingMatrix $matrix - a scoring
                matrix
  Example     :

$score_builder->log_matrix_stats;

  Description : Logs scoring matrix statistics (number of entries, min/max/avg
                scores).
  Return type : none
  Exceptions  : thrown on wrong or missing argument
  Caller      : general
  Status      : At Risk
              : under development

Code:

click to view

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

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

Public Member Functions

Detailed Description

Synopsis

Description

Member Function Documentation

◆ create_shrinked_matrix()

◆ internal_id_rescore()

◆ log_matrix_stats()