Public Member Functions
public	run ()
Detailed Description

Definition at line 4 of file RefSeqDatabaseParser.pm.
Member Function Documentation

◆ run()

public XrefParser::RefSeqDatabaseParser::run ( )
Undocumented method
Code:
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sub run {
 
  my ($self, $ref_arg) = @_;
  my $source_id    = $ref_arg->{source_id};
  my $species_id   = $ref_arg->{species_id};
  my $dbi          = $ref_arg->{dbi};
  my $xref_source  = $ref_arg->{xref_source};
 
  if((!defined $source_id) or (!defined $species_id) or (!defined $xref_source)){
    croak "Need to pass source_id, species_id and xref_source";
  }
 
  my $source_name = $self->get_source_name_for_source_id($source_id, $dbi);
  my @source_ids;
 
  if ($source_name =~ /RefSeq_dna/) {
    my $mrna_source_id = $self->get_source_id_for_source_name('RefSeq_mRNA','refseq', $dbi);
    push @source_ids, $mrna_source_id;
    my $pred_mrna_source_id = $self->get_source_id_for_source_name('RefSeq_mRNA_predicted','refseq', $dbi);
    push @source_ids, $pred_mrna_source_id;
    my $ncrna_source_id = $self->get_source_id_for_source_name('RefSeq_ncRNA', undef, $dbi);
    push @source_ids, $ncrna_source_id;
    my $pred_ncrna_source_id = $self->get_source_id_for_source_name('RefSeq_ncRNA_predicted', undef, $dbi);
    push @source_ids, $pred_ncrna_source_id;
  } elsif ($source_name =~ /RefSeq_peptide/) {
    my $peptide_source_id = $self->get_source_id_for_source_name('RefSeq_peptide', undef, $dbi);
    push @source_ids, $peptide_source_id;
    my $pred_peptide_source_id = $self->get_source_id_for_source_name('RefSeq_peptide_predicted', undef, $dbi);
    push @source_ids, $pred_peptide_source_id;
  }
 
  my $entrez_source_id = $self->get_source_id_for_source_name('EntrezGene', undef, $dbi);
  my $wiki_source_id = $self->get_source_id_for_source_name('WikiGene', undef, $dbi);
 
  # Retrieve existing NCBIGene xrefs
  my (%entrez)     = %{$self->get_acc_to_label("EntrezGene",$species_id, undef, $dbi)};
 
  # Get existing mrna, entrezgene and wikigene accession => xref_id
  my (%refseq_ids, %entrez_ids, %wiki_ids, $add_dependent_xref_sth);
  if ($source_name =~ /RefSeq_peptide/) {
    (%refseq_ids) = %{ $self->get_valid_codes("RefSeq_mRNA", $species_id, $dbi) };
    (%entrez_ids) = %{ $self->get_valid_codes("EntrezGene", $species_id, $dbi) };
    (%wiki_ids) = %{ $self->get_valid_codes("WikiGene", $species_id, $dbi) };
    $add_dependent_xref_sth = $dbi->prepare("INSERT INTO dependent_xref  (master_xref_id, dependent_xref_id, linkage_source_id) VALUES (?,?, $entrez_source_id)");
  }
 
  my $get_xref_sql = "SELECT xref_id, accession, version, label, description, info_type ".
  "FROM xref WHERE species_id = ? AND source_id = ?";
  my $get_xref_sth = $xref_source->prepare($get_xref_sql);
  my $get_dependent_sql = "SELECT x.xref_id, x.accession, x.version, x.label, x.description, x.source_id, x.species_id, dx.linkage_source_id FROM xref x, dependent_xref dx ".
  "WHERE dx.dependent_xref_id = x.xref_id and dx.master_xref_id = ?";
  my $get_dependent_sth = $xref_source->prepare($get_dependent_sql);
  my $get_sequence_sql = "SELECT sequence, sequence_type, status FROM primary_xref WHERE xref_id = ?";
  my $get_sequence_sth = $xref_source->prepare($get_sequence_sql);
  my $get_synonym_sql = "SELECT synonym FROM synonym WHERE xref_id = ?";
  my $get_synonym_sth = $xref_source->prepare($get_synonym_sql);
  my $get_pair_sql = "SELECT accession2 FROM pairs where accession1 = ?";
  my $get_pair_sth = $xref_source->prepare($get_pair_sql);
  my ($xref_id, $accession, $version, $label, $description, $info_type, $parsed_seq, $type, $status, $dep_xref_id, $dep_accession, $dep_version, $dep_label, $dep_description, $dep_source_id, $dep_species_id, $linkage_source_id, $synonym, $refseq_pair);
 
  my @xrefs;
  my @dep_refseq_ids;
  my @dep_entrez_ids;
  my $count = 0;
  foreach my $xref_source_id (@source_ids) {
    $get_xref_sth->execute($species_id, $xref_source_id);
    $get_xref_sth->bind_columns(\$xref_id, \$accession, \$version, \$label, \$description, \$info_type);
    while ($get_xref_sth->fetch()) {
      my $xref = {};
      $count++;
 
      $xref->{ACCESSION} = $accession;
      $xref->{LABEL} = $label;
      $xref->{VERSION} = $version;
      $xref->{SPECIES_ID} = $species_id;
      $xref->{INFO_TYPE} = $info_type;
      $xref->{SOURCE_ID} = $xref_source_id;
      $xref->{DESCRIPTION} = $description;
 
      # Add sequence if there is some
      $get_sequence_sth->execute($xref_id);
      $get_sequence_sth->bind_columns(\$parsed_seq, \$type, \$status);
      while ($get_sequence_sth->fetch) {
        $xref->{SEQUENCE_TYPE} = $type;
        $xref->{STATUS} = $status;
        $xref->{SEQUENCE} = $parsed_seq;
      }
 
      # Add pair information if there is some
      $get_pair_sth->execute($accession);
      $get_pair_sth->bind_columns(\$refseq_pair);
      while ($get_pair_sth->fetch) {
        $xref->{PAIR} = $refseq_pair;
      }
 
      # Look for synonyms
      $get_synonym_sth->execute($xref_id);
      $get_synonym_sth->bind_columns(\$synonym);
      while ($get_synonym_sth->fetch) {
        push (@{$xref->{SYNONYMS} }, $synonym);
      }
 
      # Add any dependent xrefs
      $get_dependent_sth->execute($xref_id);
      $get_dependent_sth->bind_columns(\$dep_xref_id, \$dep_accession, \$dep_version, \$dep_label, \$dep_description, \$dep_source_id, \$dep_species_id, \$linkage_source_id);
      while ($get_dependent_sth->fetch) {
        if ($dep_species_id != $species_id) { next; }
        if (defined $entrez{$dep_accession}) {
      push(@{$xref->{DEPENDENT_XREFS}}, {
            ACCESSION => $dep_accession,
            LABEL => $entrez{$dep_accession},
            VERSION => $dep_version,
            DESCRIPTION => $dep_description,
            SOURCE_ID => $entrez_source_id,
            LINKAGE_SOURCE_ID => $linkage_source_id
          });
 
          push(@{$xref->{DEPENDENT_XREFS}}, {
            ACCESSION => $dep_accession,
            LABEL => $entrez{$dep_accession},
            VERSION => $dep_version,
            DESCRIPTION => $dep_description,
            SOURCE_ID => $wiki_source_id,
            LINKAGE_SOURCE_ID => $linkage_source_id
          });
 
          # Add dependent xrefs for RefSeq mRNA as well where available
          # only after they are added in priority 1
          $refseq_pair =~ s/\.[0-9]*// if $refseq_pair;
          if (defined $refseq_pair) {
            if ($refseq_ids{$refseq_pair}) {
              foreach my $refseq_id (@{ $refseq_ids{$refseq_pair} }) {
                foreach my $entrez_id (@{ $entrez_ids{$dep_accession} }) {
                  push(@dep_refseq_ids, $refseq_id);
                  push(@dep_entrez_ids, $entrez_id);
                }
                foreach my $wiki_id (@{ $wiki_ids{$dep_accession} }) {
                  push(@dep_refseq_ids, $refseq_id);
                  push(@dep_entrez_ids, $wiki_id);
                }
              }
            }
          }
        }
      }
 
      push @xrefs, $xref;
 
      if (scalar(@dep_refseq_ids) > 0) {
        my @tuple_status;
        my $tuples = $add_dependent_xref_sth->execute_array(
          { ArrayTupleStatus => \@tuple_status },
          \@dep_refseq_ids,
          \@dep_entrez_ids,
        );
        $dbi->commit;
        undef @dep_refseq_ids;
        undef @dep_entrez_ids;
      }
 
      if ($count > 1000) {
        $self->upload_xref_object_graphs( \@xrefs, $dbi );
        $count = 0;
        undef @xrefs;
      }
    }
  }
  $get_xref_sth->finish();
 
  $self->upload_xref_object_graphs(\@xrefs, $dbi) if scalar(@xrefs) > 0;
 
  return 0; # successful
 
}
The documentation for this class was generated from the following file:
ensembl/misc-scripts/xref_mapping/XrefParser/RefSeqDatabaseParser.pm
Public Member Functions

Detailed Description

Member Function Documentation

◆ run()
