Inheritance diagram for Bio::EnsEMBL::IdMapping::InternalIdMapper::EnsemblTranscriptGeneric:

Public Member Functions
public	init_basic ()

public	non_exact_translation ()

public	mapped_gene ()

public	biotype ()

public	internal_id ()

public	single_gene ()

public	same_gene_transcript_mapping ()

Public Member Functions inherited from Bio::EnsEMBL::IdMapping::InternalIdMapper::BaseMapper
public	basic_mapping ()

public	higher_score_exists ()

public	ambiguous_mapping ()

public	scores_similar ()

public	filter_sources ()

public	filter_targets ()

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

Definition at line 15 of file EnsemblTranscriptGeneric.pm.

Member Function Documentation

◆ biotype()

public Bio::EnsEMBL::IdMapping::InternalIdMapper::EnsemblTranscriptGeneric::biotype ( )

Undocumented method

Code:

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◆ init_basic()

public Bio::EnsEMBL::IdMapping::InternalIdMapper::EnsemblTranscriptGeneric::init_basic ( )

Undocumented method

Code:

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◆ internal_id()

public Bio::EnsEMBL::IdMapping::InternalIdMapper::EnsemblTranscriptGeneric::internal_id ( )

Undocumented method

Code:

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◆ mapped_gene()

public Bio::EnsEMBL::IdMapping::InternalIdMapper::EnsemblTranscriptGeneric::mapped_gene ( )

Undocumented method

Code:

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◆ non_exact_translation()

public Bio::EnsEMBL::IdMapping::InternalIdMapper::EnsemblTranscriptGeneric::non_exact_translation ( )

Undocumented method

Code:

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◆ same_gene_transcript_mapping()

public Bio::EnsEMBL::IdMapping::InternalIdMapper::EnsemblTranscriptGeneric::same_gene_transcript_mapping ( )

Undocumented method

Code:

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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;
}

◆ single_gene()

public Bio::EnsEMBL::IdMapping::InternalIdMapper::EnsemblTranscriptGeneric::single_gene ( )

Undocumented method

Code:

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

ensembl/modules/Bio/EnsEMBL/IdMapping/InternalIdMapper/EnsemblTranscriptGeneric.pm

Public Member Functions

Detailed Description

Synopsis

Description

Member Function Documentation

◆ biotype()

◆ init_basic()

◆ internal_id()

◆ mapped_gene()

◆ non_exact_translation()

◆ same_gene_transcript_mapping()

◆ single_gene()