Public Member Functions
public	gene_description_sources ()

public	gene_description_filter_regexps ()

public	transcript_display_xref_sources ()

public	gene_display_xref_sources ()

public	remove_source_priorities ()

public	new ()

public	mapper ()

public	genes_and_transcripts_attributes_set ()

public	set_gene_descriptions_from_display_xref ()

public	set_display_xrefs_from_stable_table ()

public	load_translation_to_transcript ()

public	build_genes_to_transcripts ()

public	build_meta_timestamp ()

public	set_display_xrefs ()

protected	_apply_ignore ()

public	transcript_names_from_gene ()

public	check_label ()

public	set_source_id_to_external_name ()

public	set_gene_descriptions ()

public	filter_by_regexp ()

public	check_desc ()

Detailed Description

Definition at line 7 of file DisplayXrefs.pm.

Member Function Documentation

◆ _apply_ignore()

protected XrefMapper::DisplayXrefs::_apply_ignore ( )

Undocumented method

Code:

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◆ build_genes_to_transcripts()

public XrefMapper::DisplayXrefs::build_genes_to_transcripts ( )

Undocumented method

Code:

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◆ build_meta_timestamp()

public XrefMapper::DisplayXrefs::build_meta_timestamp ( )

Undocumented method

Code:

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◆ check_desc()

public XrefMapper::DisplayXrefs::check_desc ( )

Undocumented method

Code:

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◆ check_label()

public XrefMapper::DisplayXrefs::check_label ( )

Undocumented method

Code:

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◆ filter_by_regexp()

public XrefMapper::DisplayXrefs::filter_by_regexp ( )

Undocumented method

Code:

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◆ gene_description_filter_regexps()

public XrefMapper::DisplayXrefs::gene_description_filter_regexps ( )

Undocumented method

Code:

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sub gene_description_filter_regexps {
 
  return ('[0-9A-Z]{10}RIK PROTEIN[ \.]',
          '\(?[0-9A-Z]{10}RIK PROTEIN\)?[ \.]',
          '^BA\S+\s+\(NOVEL PROTEIN\)\.?',
          '^BC\d+\_\d+\.?',
          'CDNA SEQUENCE\s?,? [A-Z]+\d+[ \.;]',
          '^CGI\-\d+ PROTEIN\.?\;?',
          '^CHROMOSOME\s+\d+\s+OPEN\s+READING\s+FRAME\s+\d+\.?.*',
          'CLONE MGC:\d+[ \.;]',
          '^\(CLONE REM\d+\) ORF \(FRAGMENT\)\.*',
          '\(CLONE \S+\)\s+',
          '^DJ\S+\s+\(NOVEL PROTEIN\)\.?',
          '^DKFZP[A-Z0-9]+\s+PROTEIN[\.;]?.*',
          'DNA SEGMENT, CHR.*',
          'EST [A-Z]+\d+[ \.;]',
          'EXPRESSED SEQUENCE [A-Z]+\d+[ \.;]',
          '^FKSG\d+\.?.*',
          '^FLJ\d+\s+PROTEIN.*',
          '^HSPC\d+.*',
          '^HSPC\d+\s+PROTEIN\.?.*',
          'HYPOTHETICAL PROTEIN,',
          'HYPOTHETICAL PROTEIN \S+[\.;]',
          '^\(*HYPOTHETICAL\s+.*',
          '\(*HYPOTHETICAL\s+.*',
          '^KIAA\d+\s+GENE\s+PRODUCT\.?.*',
          '^KIAA\d+\s+PROTEIN\.?.*',
          '^LOC\d+\s*(PROTEIN)?\.?',
          ' MGC:\s*\d+[ \.;]',
          'MGC:\s*\d+[ \.;]',
          '^ORF.*',
          '^ORF\s*\d+\s+PROTEIN\.*',
          '^PRED\d+\s+PROTEIN.*',
          '^PRO\d+\.?.*',
          '^PRO\d+\s+PROTEIN\.?.*',
          '^PROTEIN C\d+ORF\d+\.*',
          'PROTEIN KIAA\d+[ \.].*',
          'PROTEIN \S+ HOMOLOG\.?',
          '^Putative uncharacterized protein.*',
          'R\d{5}_\d[ \.,].*',
          'RIKEN CDNA [0-9A-Z]{10}[ \.;]',
          'RIKEN CDNA [0-9A-Z]{10}[ \.]',
          '.*RIKEN FULL-LENGTH ENRICHED LIBRARY.*',
          '.*RIKEN FULL-LENGTH ENRICHED LIBRARY.*PRODUCT:',
          '^\s*\(\d*\)\s*[ \.]$',
          '^\s*\(\d*\)\s*[ \.]$',
          '^\s*\(?FRAGMENT\)?\.?\s*$',
          '^\s*\(FRAGMENT\)\.?\s*$',
          '\s*\(?GENE\)?\.?;?',
          '^\s*\(?GENE\)?\.?;?\s*$',
          '^\s*\(?GENE\)?\.?\s*$',
          'SIMILAR TO GENBANK ACCESSION NUMBER\s+\S+',
          '^SIMILAR TO GENE.*',
          '^SIMILAR TO HYPOTHETICAL.*',
          '^SIMILAR TO (KIAA|LOC).*',
          'SIMILAR TO (KIAA|LOC|RIKEN).*',
          '^SIMILAR TO PUTATIVE[ \.]',
          'SIMILAR TO PUTATIVE[ \.]',
          '^SIMILAR TO\s+$',
          'SIMILAR TO\s+$',
          '\s*\(?PRECURSOR\)?\.?;?',
          '^\s*\(?PROTEIN\)?\.?\s*$',
          '^\s+\(?\s*$',
          '^\s*\(\s*\)\s*$',
          '^UNKNOWN\s+.*',
          '^WUGSC:H_.*',
          '^WUGSC:.*\s+PROTEIN\.?.*');
 
}

◆ gene_description_sources()

public XrefMapper::DisplayXrefs::gene_description_sources ( )

Undocumented method

Code:

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◆ gene_display_xref_sources()

public XrefMapper::DisplayXrefs::gene_display_xref_sources ( )

Undocumented method

Code:

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◆ genes_and_transcripts_attributes_set()

public XrefMapper::DisplayXrefs::genes_and_transcripts_attributes_set ( )

Undocumented method

Code:

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◆ load_translation_to_transcript()

public XrefMapper::DisplayXrefs::load_translation_to_transcript ( )

Undocumented method

Code:

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◆ mapper()

public XrefMapper::DisplayXrefs::mapper ( )

Undocumented method

Code:

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◆ new()

public XrefMapper::DisplayXrefs::new ( )

Undocumented method

Code:

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◆ remove_source_priorities()

public XrefMapper::DisplayXrefs::remove_source_priorities ( )

Undocumented method

Code:

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◆ set_display_xrefs()

public XrefMapper::DisplayXrefs::set_display_xrefs ( )

Undocumented method

Code:

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sub set_display_xrefs{
  my $self = shift;
 
 
  print "Building Transcript and Gene display_xrefs\n" if ($self->verbose);
 
  my $xref_offset = $self->get_meta_value("xref_offset");
  my $core_dbi = $self->core->dbc();
  my $xref_dbi = $self->xref->dbc();
 
  print "Using xref_off set of $xref_offset\n" if($self->verbose);
 
  my $reset_sth = $core_dbi->prepare("UPDATE transcript SET display_xref_id = null WHERE biotype NOT IN ('LRG_gene')");
  $reset_sth->execute();
  $reset_sth->finish;
 
  my $update_gene_sth = $core_dbi->prepare("UPDATE gene g SET g.display_xref_id= ? WHERE g.gene_id=? and g.display_xref_id IS NULL");
  my $update_tran_sth = $core_dbi->prepare("UPDATE transcript t SET t.display_xref_id= ? WHERE t.transcript_id=?");
 
 
 
  my $ins_p_sth = $xref_dbi->prepare("INSERT ignore into display_xref_priority (ensembl_object_type,source_id, priority) values(?, ?, ?)");
  my $get_source_id_sth = $xref_dbi->prepare("select source_id from source where name like ? order by priority");
  my $list_sources_sth = $xref_dbi->prepare("select distinct name from display_xref_priority d join source using(source_id) where ensembl_object_type = ? order by d.priority");
 
 
  my %object_types = ('gene' => 'Gene', 'transcript' => 'Transcript'); 
  
  foreach my $object_type (keys %object_types) {
 
      my $precedence;
      my $ignore; 
      my $method = $object_type . '_display_xref_sources';
      if( $self->mapper->can($method) ){
      ($precedence, $ignore) = @{$self->mapper->$method()};
      }
      else{
      ($precedence, $ignore) = @{$self->$method()};
      }
 
      # The lower the priority number the better then 
      my $i=0;
      foreach my $name (@$precedence){
      $i++;
      $get_source_id_sth->execute($name);
      my $source_id;
      $get_source_id_sth->bind_columns(\$source_id);
      while($get_source_id_sth->fetch){
          $ins_p_sth->execute($object_types{$object_type},$source_id, $i);
      }
      }
      $ins_p_sth->finish;
      $get_source_id_sth->finish;
 
      $i = 0;
      if ($self->verbose) {
      print "Precedence for $object_type display xrefs (1- best name)\n";
      $list_sources_sth->execute($object_types{$object_type});
      my $source_name;
      $list_sources_sth->bind_columns(\$source_name);
      while ($list_sources_sth->fetch() ) {
          $i++;
          print "\t$i\t$source_name\n";
      }
 
      }
 
      $self->_apply_ignore($ignore, $xref_dbi);
 
 
#look at sources of display xrefs which are relevant for this object type
#(listed in gene_display_xref_sources() or transcript_display_xref_sources() )
#but get xrefs for all levels Gene, its Transcripts and Translations 
#######################################################################
my $display_xref_sql =(<<DXS);
select  CASE ox.ensembl_object_type
           WHEN 'Gene' THEN gtt_gene.gene_id
       WHEN 'Transcript' THEN gtt_transcript.gene_id
       WHEN 'Translation' THEN gtt_translation.gene_id
    END AS d_gene_id,
        CASE ox.ensembl_object_type
           WHEN 'Gene' THEN gtt_gene.transcript_id
       WHEN 'Transcript' THEN gtt_transcript.transcript_id
       WHEN 'Translation' THEN gtt_translation.transcript_id
        END AS d_transcript_id,
        p.priority as priority,
        x.xref_id
from    (   display_xref_priority p
    join  (   source s
      join    (   xref x
        join      (   object_xref ox
          join        (   identity_xref ix
                      ) using (object_xref_id)
                  ) using (xref_id)
              ) using (source_id)
          ) using (source_id)
        )
  left join gene_transcript_translation gtt_gene
    on (gtt_gene.gene_id = ox.ensembl_id)
  left join gene_transcript_translation gtt_transcript
    on (gtt_transcript.transcript_id = ox.ensembl_id)
  left join gene_transcript_translation gtt_translation
    on (gtt_translation.translation_id = ox.ensembl_id)
where   ox.ox_status = 'DUMP_OUT'
        and p.ensembl_object_type = ?
order by d_gene_id, ox.ensembl_object_type, 
    p.priority, (ix.target_identity + ix.query_identity) DESC, unused_priority DESC, x.accession;
 
DXS
 
 
########################################################################
 
      my %object_seen;
 
      my $display_xref_sth = $xref_dbi->prepare($display_xref_sql);
 
      my $display_xref_count = 0;
      $display_xref_sth->execute($object_type);
      my ($gene_id, $transcript_id, $priority, $xref_id);  
      $display_xref_sth->bind_columns(\$gene_id, \$transcript_id, \$priority, \$xref_id);
      while($display_xref_sth->fetch()){
      my $object_id;
      if ($object_type eq 'gene') {
          $object_id = $gene_id;
      } elsif ($object_type eq 'transcript') {
          $object_id = $transcript_id;
      }
 
      if (!exists($object_seen{$object_id}) ) {
          if ($object_type eq 'gene') {
          $update_gene_sth->execute($xref_id+$xref_offset, $object_id);
          } elsif ($object_type eq 'transcript') {
          $update_tran_sth->execute($xref_id+$xref_offset, $object_id);
          }    
          $display_xref_count++;
          $object_seen{$object_id} = 1;
      }
      } 
  
      $display_xref_sth->finish;
      $update_gene_sth->finish;
      $update_tran_sth->finish;
 
      print "Updated $display_xref_count $object_type display_xrefs\n" if($self->verbose);
 
  }
 
  #
  # reset the status to DUMP_OUT fro object_xrefs that where ignored for the display_xref;
  #
 
  my $reset_status_sth = $xref_dbi->prepare('UPDATE object_xref SET ox_status = "DUMP_OUT" where ox_status = "NO_DISPLAY"');
  $reset_status_sth->execute();
  $reset_status_sth->finish;
 
  #
  # Clean up synonyms linked to xrefs which are not the display xref
  # Synonyms are only used as alternative gene names, so should be synonyms of the gene symbol chosen
  #
 
  my $syn_clean_sth = $core_dbi->prepare("DELETE es FROM external_synonym es, xref x LEFT JOIN gene g ON g.display_xref_id = x.xref_id WHERE es.xref_id = x.xref_id AND isnull(g.display_xref_id)");
  $syn_clean_sth->execute();
  $syn_clean_sth->finish();
 
 
}

◆ set_display_xrefs_from_stable_table()

public XrefMapper::DisplayXrefs::set_display_xrefs_from_stable_table ( )

Undocumented method

Code:

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sub set_display_xrefs_from_stable_table{
  my $self = shift;
  print "Setting Transcript and Gene display_xrefs from xref database into core and setting the desc\n" if ($self->verbose);
 
  my $xref_offset = $self->get_meta_value("xref_offset");
  my $core_dbi = $self->core->dbc;
  my $xref_dbi = $self->xref->dbc;
 
  print "Using xref_off set of $xref_offset\n" if($self->verbose);
 
  my $reset_sth = $core_dbi->prepare("UPDATE gene SET display_xref_id = null");
  $reset_sth->execute();
  $reset_sth->finish;
 
  # Remove any leftover transcript description, as it is not used anywhere
  $reset_sth = $core_dbi->prepare("UPDATE transcript SET display_xref_id = null");
  $reset_sth->execute();
  $reset_sth->finish;
 
  # Remove descriptions assigned through the xref pipeline, recognisable by the 'Source' field
  # This will maintain any manually added descriptions
  $reset_sth = $core_dbi->prepare("UPDATE gene SET description = null WHERE description like '%[Source:%]%'");
  $reset_sth->execute();
  $reset_sth->finish;
 
  my %name_to_external_name;
  my $sql = "select external_db_id, db_name, db_display_name from external_db";
  my $sth = $core_dbi->prepare($sql);
  $sth->execute();
  my ($id, $name, $display_name);
  $sth->bind_columns(\$id, \$name, \$display_name);
  while($sth->fetch()){
    $name_to_external_name{$name} = $display_name;
   }
  $sth->finish;
 
  my %source_id_to_external_name;
 
  $sql = 'select s.source_id, s.name from source s, xref x where x.source_id = s.source_id group by s.source_id'; # only get those of interest
  $sth = $xref_dbi->prepare($sql);
  $sth->execute();
  $sth->bind_columns(\$id, \$name);
 
  while($sth->fetch()){
     if(defined($name_to_external_name{$name})){
      $source_id_to_external_name{$id} = $name_to_external_name{$name};
    }
  }
  $sth->finish;
 
 
  my $update_gene_sth = $core_dbi->prepare("UPDATE gene g SET g.display_xref_id= ? WHERE g.gene_id=?");
  my $update_gene_desc_sth = $core_dbi->prepare("UPDATE gene g SET g.description= ? WHERE g.gene_id=?");
 
  my $update_tran_sth = $core_dbi->prepare("UPDATE transcript t SET t.display_xref_id= ? WHERE t.transcript_id=?");
 
  my $get_gene_display_xref = $xref_dbi->prepare("SELECT gsi.internal_id, gsi.display_xref_id, x.description ,x.source_id, x.accession
                                                              FROM gene_stable_id gsi, xref x 
                                                                 WHERE gsi.display_xref_id = x.xref_id");
 
  my $get_tran_display_xref = $xref_dbi->prepare("SELECT gsi.internal_id, gsi.display_xref_id from transcript_stable_id gsi");
 
  $reset_sth = $xref_dbi->prepare("UPDATE gene_stable_id gsi SET gsi.desc_set=0");
  $reset_sth->execute();
 
  my $set_desc_done_sth = $xref_dbi->prepare("UPDATE gene_stable_id gsi SET gsi.desc_set=1 WHERE gsi.internal_id=?");
 
  $get_gene_display_xref->execute();
  my $xref_id;
  my $desc;
  my $gene_id;
  my $source_id;
  my $label;
  $get_gene_display_xref->bind_columns(\$gene_id, \$xref_id, \$desc, \$source_id, \$label);
  my $gene_count =0;
  while($get_gene_display_xref->fetch()){
 
    $update_gene_sth->execute($xref_id+$xref_offset, $gene_id);
 
    if (defined($desc) and $desc ne "") {
      $desc .= " [Source:".$source_id_to_external_name{$source_id}.";Acc:".$label."]";
      $update_gene_desc_sth->execute($desc,$gene_id);
      $set_desc_done_sth->execute($gene_id);
      $gene_count++;
    }
 
  }
 
  $update_gene_desc_sth->finish;
  $update_gene_sth->finish;
 
  print "$gene_count gene descriptions added\n" if($self->verbose);
 
  $get_tran_display_xref->execute();
  my $tran_id;
  $get_tran_display_xref->bind_columns(\$tran_id, \$xref_id);
 
  while($get_tran_display_xref->fetch()){
    if(defined($xref_id)){
      $update_tran_sth->execute($xref_id+$xref_offset, $tran_id);
      if(!defined($tran_id) || !defined($xref_id) || !defined($xref_offset)){
    print "PROB: tran_id = $tran_id\nxref_id = $xref_id\n$xref_offset = $xref_offset\n";
      }
    }
  } 
 
  #
  # Clean up synonyms linked to xrefs which are not the display xref
  # Synonyms are only used as alternative gene names, so should be synonyms of the gene symbol chosen
  #
 
  my $syn_clean_sth = $core_dbi->prepare("DELETE es FROM external_synonym es, xref x LEFT JOIN gene g ON g.display_xref_id = x.xref_id WHERE es.xref_id = x.xref_id AND isnull(g.display_xref_id)");
  $syn_clean_sth->execute();
  $syn_clean_sth->finish();
 
}

◆ set_gene_descriptions()

public XrefMapper::DisplayXrefs::set_gene_descriptions ( )

Undocumented method

Code:

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sub set_gene_descriptions{
  my $self = shift;
  my $only_those_not_set = shift || 0;
  my $sql;
  my $core_dbi = $self->core->dbc;
  my $xref_dbi = $self->xref->dbc;
 
  my $update_gene_desc_sth =  $core_dbi->prepare("UPDATE gene SET description = ? where gene_id = ? and description IS NULL");
 
  if(!$only_those_not_set){
    my $reset_sth = $core_dbi->prepare("UPDATE gene SET description = null");
    $reset_sth->execute();
    $reset_sth->finish;
  }
 
  my %ignore;
  if($only_those_not_set){
    print "Only setting those not already set\n";
    $sql = "select internal_id from gene_stable_id where desc_set = 1";
    my $sql_sth = $xref_dbi->prepare($sql);
    $sql_sth->execute;
    my $id;
    $sql_sth->bind_columns(\$id);
    while($sql_sth->fetch){
      $ignore{$id} = 1;
    }
    $sql_sth->finish;
  } 
 
  ##########################################
  # Get source_id to external_disaply_name #
  ##########################################
 
  my %name_to_external_name;
  $sql = "select external_db_id, db_name, db_display_name from external_db";
  my $sth = $core_dbi->prepare($sql);
  $sth->execute();
  my ($id, $name, $display_name);
  $sth->bind_columns(\$id, \$name, \$display_name);
  while($sth->fetch()){
    $name_to_external_name{$name} = $display_name;
   }
  $sth->finish;
  
  my ($source_id_to_external_name_href, $name_to_source_id_href);
  if( $self->mapper->can("set_source_id_to_external_name") ){
      ($source_id_to_external_name_href, $name_to_source_id_href) = $self->mapper->set_source_id_to_external_name (\%name_to_external_name);
  }
  else{
      ($source_id_to_external_name_href, $name_to_source_id_href) = $self->set_source_id_to_external_name (\%name_to_external_name);
  }
 
  my %source_id_to_external_name = %$source_id_to_external_name_href;
  my %name_to_source_id = %$name_to_source_id_href;
  
 
  my @precedence;
  my @regexps;
  my ($ignore, $precedence);
  if( $self->mapper->can("gene_description_sources") ){
    @precedence = $self->mapper->gene_description_sources();
  }
  else{
    ($precedence, $ignore) = @{$self->gene_description_sources()};
    @precedence = @$precedence;
  }
 
  if( $self->mapper->can("gene_description_filter_regexps") ){
    @regexps = $self->mapper->gene_description_filter_regexps();
  }
  else{
    @regexps = $self->gene_description_filter_regexps();
  }
  
  my $ins_p_sth = $xref_dbi->prepare("INSERT ignore into gene_desc_priority (source_id, priority) values(?, ?)");
  my $get_source_id_sth = $xref_dbi->prepare("select source_id from source where name like ?");
  my $list_sources_sth = $xref_dbi->prepare("select distinct name from gene_desc_priority d join source using(source_id) order by d.priority");
 
  # The lower the priority number the better then 
  my $i=0;
  foreach my $name (@precedence){
     $i++;
     $get_source_id_sth->execute($name);
     my $source_id;
     $get_source_id_sth->bind_columns(\$source_id);
     while($get_source_id_sth->fetch){
      $ins_p_sth->execute($source_id, $i);
     }
  }
  $ins_p_sth->finish;
  $get_source_id_sth->finish;
 
 
  $i = 0;
  if ($self->verbose) {
      print "Precedence for gene descriptions (1- best description)\n";
      $list_sources_sth->execute();
      my $source_name;
      $list_sources_sth->bind_columns(\$source_name);
      while ($list_sources_sth->fetch() ) {
      $i++;
      print "\t$i\t$source_name\n";
      }
 
  }
 
  $self->_apply_ignore($ignore, $xref_dbi);
 
 
 
#######################################################################
my $gene_desc_sql =(<<DXS);
select  CASE ox.ensembl_object_type
           WHEN 'Gene' THEN gtt_gene.gene_id
       WHEN 'Transcript' THEN gtt_transcript.gene_id
       WHEN 'Translation' THEN gtt_translation.gene_id
    END AS d_gene_id,
        x.description AS description,
        s.source_id AS source_id,
        x.accession AS accession
from    (   gene_desc_priority p
    join  (   source s
      join    (   xref x
        join      (   object_xref ox
          join        (   identity_xref ix
                      ) using (object_xref_id)
                  ) using (xref_id)
              ) using (source_id)
          ) using (source_id)
        )
  left join gene_transcript_translation gtt_gene
    on (gtt_gene.gene_id = ox.ensembl_id)
  left join gene_transcript_translation gtt_transcript
    on (gtt_transcript.transcript_id = ox.ensembl_id)
  left join gene_transcript_translation gtt_translation
    on (gtt_translation.translation_id = ox.ensembl_id)
where   ox.ox_status = 'DUMP_OUT'
order by    d_gene_id,
            ox.ensembl_object_type,
            p.priority,
            (ix.target_identity+ix.query_identity) desc
 
DXS
 
######################################################################## 
  
  my $gene_sth = $core_dbi->prepare("select g.description from gene g where g.gene_id = ?"); 
 
  my %no_source_name_in_desc;
  if( $self->mapper->can("no_source_label_list") ){
    foreach my $name (@{$self->mapper->no_source_label_list()}){
      my $id = $name_to_source_id{$name};
      print "$name will not have [Source:...] info in desc\n";
      $no_source_name_in_desc{$id} = 1;
    }
  }
 
  my $gene_desc_sth = $xref_dbi->prepare($gene_desc_sql);
 
  $gene_desc_sth->execute();
  my ($gene_id, $desc,$source_id,$label);  
  $gene_desc_sth->bind_columns(\$gene_id, \$desc, \$source_id,\$label);
  
  my %gene_desc_updated;
 
  while($gene_desc_sth->fetch()){
     
    next if(exists($ignore{$gene_id}) || exists($gene_desc_updated{$gene_id}));
    
    if(defined($desc) ){
      my $filtered_desc = $self->filter_by_regexp($desc, \@regexps);
      if ($filtered_desc ne "") {
    if(!defined($no_source_name_in_desc{$source_id})){
      $filtered_desc .= " [Source:".$source_id_to_external_name{$source_id}.";Acc:".$label."]";
    }
    $update_gene_desc_sth->execute($filtered_desc,$gene_id);
    $gene_desc_updated{$gene_id} = 1;
      }
    }
  }
  $update_gene_desc_sth->finish;
  $gene_desc_sth->finish;
  print scalar(keys %gene_desc_updated) ." gene descriptions added\n";
 
  # reset the status to DUMP_OUT fro object_xrefs that where ignored for the display_xref;
 
  my $reset_status_sth = $xref_dbi->prepare('UPDATE object_xref SET ox_status = "DUMP_OUT" where ox_status = "NO_DISPLAY"');
  $reset_status_sth->execute();
  $reset_status_sth->finish;
  
 
}

◆ set_gene_descriptions_from_display_xref()

public XrefMapper::DisplayXrefs::set_gene_descriptions_from_display_xref ( )

Undocumented method

Code:

click to view

◆ set_source_id_to_external_name()

public XrefMapper::DisplayXrefs::set_source_id_to_external_name ( )

Undocumented method

Code:

click to view

◆ transcript_display_xref_sources()

public XrefMapper::DisplayXrefs::transcript_display_xref_sources ( )

Undocumented method

Code:

click to view

◆ transcript_names_from_gene()

public XrefMapper::DisplayXrefs::transcript_names_from_gene ( )

Undocumented method

Code:

click to view

sub transcript_names_from_gene {
  my $self = shift;
  my $core_dbi = $self->core->dbc;
  my $xref_dbi = $self->xref->dbc;
 
  print "Assigning transcript names from gene names\n" if ($self->verbose);
 
  my $reset_sth = $core_dbi->prepare("UPDATE transcript SET display_xref_id = null WHERE biotype NOT IN ('LRG_gene')");
  $reset_sth->execute();
  $reset_sth->finish;
 
  my $xref_id_sth = $core_dbi->prepare("SELECT max(xref_id) FROM xref");
  my $ox_id_sth = $core_dbi->prepare("SELECT max(object_xref_id) FROM object_xref");
  my $del_xref_sth = $core_dbi->prepare("DELETE x FROM xref x, object_xref ox WHERE x.xref_id = ox.xref_id AND ensembl_object_type = 'Transcript' AND display_label REGEXP '-2[0-9]{2}\$'");
  my $reuse_xref_sth = $core_dbi->prepare("SELECT xref_id FROM xref x WHERE external_db_id = ? AND display_label = ? AND info_type = 'MISC'");
  my $del_ox_sth = $core_dbi->prepare("DELETE ox FROM object_xref ox LEFT JOIN xref x ON x.xref_id = ox.xref_id WHERE isnull(x.xref_id)");
  my $ins_xref_sth = $core_dbi->prepare("INSERT IGNORE into xref (xref_id, external_db_id, dbprimary_acc, display_label, version, description, info_type, info_text) values(?, ?, ?, ?, 0, ?, 'MISC', ?)");
  my $ins_ox_sth = $core_dbi->prepare("INSERT into object_xref (object_xref_id, ensembl_id, ensembl_object_type, xref_id) values(?, ?, 'Transcript', ?)");
  my $update_tran_sth = $core_dbi->prepare("UPDATE transcript t SET t.display_xref_id= ? WHERE t.transcript_id=?");
 
  my $get_genes = $core_dbi->prepare("SELECT g.gene_id, e.db_name, x.dbprimary_acc, x.display_label, x.description FROM gene g, xref x, external_db e where g.display_xref_id = x.xref_id and e.external_db_id = x.external_db_id");
  my $get_transcripts = $core_dbi->prepare("SELECT transcript_id FROM transcript WHERE gene_id = ? ORDER BY seq_region_start, seq_region_end");
  my $get_source_id = $core_dbi->prepare("SELECT external_db_id FROM external_db WHERE db_name like ?");
 
  $get_genes->execute();
  my ($gene_id, $external_db, $external_db_id, $acc, $label, $description, $transcript_id, $xref_id, $ox_id, $ext, $reuse_xref_id, $info_text);
  $get_genes->bind_columns(\$gene_id, \$external_db, \$acc, \$label, \$description);
  $xref_id_sth->execute();
  $xref_id_sth->bind_columns(\$xref_id);
  $xref_id_sth->fetch();
  $ox_id_sth->execute();
  $ox_id_sth->bind_columns(\$ox_id);
  $ox_id_sth->fetch();
  $del_xref_sth->execute();
  while ($get_genes->fetch()) {
    $ext = '201';
    $get_source_id->execute($external_db . "_trans_name");
    $get_source_id->bind_columns(\$external_db_id);
    $get_source_id->fetch();
    $get_transcripts->execute($gene_id);
    $get_transcripts->bind_columns(\$transcript_id);
    while ($get_transcripts->fetch) {
      $xref_id++;
      $ox_id++;
      $reuse_xref_sth->execute($external_db_id, $label . '-' . $ext);
      $reuse_xref_sth->bind_columns(\$reuse_xref_id);
      if ($reuse_xref_sth->fetch()) {
        $ins_ox_sth->execute($ox_id, $transcript_id, $reuse_xref_id);
        $update_tran_sth->execute($reuse_xref_id, $transcript_id);
      } else {
        $info_text = 'via gene ' . $acc;
        $ins_xref_sth->execute($xref_id, $external_db_id, $label. "-" . $ext, $label . "-" . $ext, $description, $info_text);
        $ins_ox_sth->execute($ox_id, $transcript_id, $xref_id); 
        $update_tran_sth->execute($xref_id, $transcript_id);
      }
      $ext++;
    }
  }
 
  $del_xref_sth->finish();
  $del_ox_sth->execute();
  $del_ox_sth->finish();
  $reuse_xref_sth->finish();
  $xref_id_sth->finish();
  $ox_id_sth->finish();
  $get_genes->finish();
  $get_source_id->finish();
  $get_transcripts->finish();
  $ins_xref_sth->finish();
  $ins_ox_sth->finish();
  $update_tran_sth->finish();
}

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

ensembl/misc-scripts/xref_mapping/XrefMapper/DisplayXrefs.pm

Public Member Functions

Detailed Description

Member Function Documentation

◆ _apply_ignore()

◆ build_genes_to_transcripts()

◆ build_meta_timestamp()

◆ check_desc()

◆ check_label()

◆ filter_by_regexp()

◆ gene_description_filter_regexps()

◆ gene_description_sources()

◆ gene_display_xref_sources()

◆ genes_and_transcripts_attributes_set()

◆ load_translation_to_transcript()

◆ mapper()

◆ new()

◆ remove_source_priorities()

◆ set_display_xrefs()

◆ set_display_xrefs_from_stable_table()

◆ set_gene_descriptions()

◆ set_gene_descriptions_from_display_xref()

◆ set_source_id_to_external_name()

◆ transcript_display_xref_sources()

◆ transcript_names_from_gene()