Public Member Functions
public	run ()
Detailed Description

Definition at line 6 of file PHIbaseParser.pm.
Member Function Documentation

◆ run()

public XrefParser::PHIbaseParser::run ( )
Undocumented method
Code:
click to view
sub run {
 
 
  my ($self, $ref_arg) = @_;
  my $source_id    = $ref_arg->{source_id};
  my $species_id   = $ref_arg->{species_id};
  my $files        = $ref_arg->{files};
  my $verbose      = $ref_arg->{verbose};
 
  if((!defined $source_id) or (!defined $species_id) or (!defined $files) ){
    croak "Need to pass source_id, species_id and file as pairs";
  }
  $verbose |=0;
 
  my $phi_xml_file = @{$files}[0];
  
  print STDERR "PhiBase file to parse, $phi_xml_file\n" if($verbose);
 
  my %phi_mapping;
  my %taxIds;
 
  my $term = undef;
  my $desc = undef;
  
  my $phi_parser = XML::LibXML->new();
  my $phi_doc    = $phi_parser->parse_file($phi_xml_file);
 
  my $concepts_count = 0;
  
  foreach my $concept ($phi_doc->findnodes('ondex:ondexdata/ondexdataseq/concepts/concept')) {
    my ($pid_node) = $concept->findnodes('./pid');
    my $pid = $pid_node->to_literal;
    my $concept_accessions_aref = $concept->findnodes('./coaccessions/concept_accession');
    my $uniprot_acc = undef;
 
    foreach my $concept_accession (@$concept_accessions_aref) {
    
    # get the one associated with UniProt
    my ($elementOf) = $concept_accession->findnodes('./elementOf');
 
    if ($elementOf->to_literal =~ /UPROT/) {
        my ($accession) = $concept_accession->findnodes('./accession');
        $uniprot_acc = $accession->to_literal;
    }
    }
 
    if (!defined $uniprot_acc) {
    # print STDERR "phi id, $pid, no uniprot mapping found in xml file!\n";
    }
    else {
      if (!defined $phi_mapping{$uniprot_acc}) {
    $phi_mapping{$uniprot_acc} = 
      {
       -phi_ids => [$pid],
       -tax_id  => undef,
      };
      }
      else {
    my $phi_href = $phi_mapping{$uniprot_acc};
    my $aref = $phi_href->{-phi_ids};
    push (@$aref, $pid);
      }
    }
 
      # Get the TaxId
 
    my $concept_gds_aref = $concept->findnodes('./cogds/concept_gds');
    my $taxId = undef;
 
    foreach my $concept_gds (@$concept_gds_aref) {
 
      # get the one associated with Taxid
      my ($attrname) = $concept_gds->findnodes('./attrname');
      if ($attrname->to_literal =~ /TAXID/) {
    my ($value) = $concept_gds->findnodes('./value');
    $taxId = $value->to_literal;
    $taxId =~ s/\D//g;
    
    if (! defined $taxIds{$taxId}) {
      $taxIds{$taxId} = 1;
    }
    
    if (defined $uniprot_acc) {
      my $phi_href = $phi_mapping{$uniprot_acc};
      $phi_href->{-tax_id} = $taxId;
    }
      }
    }
    $concepts_count++;
  }
 
  my @phis = keys (%phi_mapping);
 
  print  "Parsed $concepts_count concepts\n";
  print  "Found " . @phis . " with UniProt mapping!\n";
 
  print  "Found " . keys (%taxIds) . " different taxIds\n";
 
  #get the "main" PHIbase source id.
  $source_id = $self->get_source_id_for_source_name("PHIbase");
 
 
  #get the mapping that are already there so that we don't get lots of duplicates.
  # stored in the global hash xref_dependent_mapped.
  $self->get_dependent_mappings($source_id);
 
  #if(!defined($species_id)){
  #  $species_id = $self->get_species_id_for_filename($phi_xml_file);
  #}
 
  my $swiss_miss=0;
  my (%swiss) = %{$self->get_valid_codes("uniprot/", $species_id)};
 
  print "got " . keys (%swiss) . " Uniprot entries\n";
   
  print "species_id, source_id: $species_id, $source_id\n";
 
  # Don't check only the species_id, but all taxIds specified in xref_config.ini
 
  my %species2tax = $self->species_id2taxonomy();
  my @tax_ids = @{$species2tax{$species_id}};
 
  print "tax_ids from xref_config.ini file: " . join (', ', @tax_ids) . "\n";
 
  my $added = 0;
 
  foreach my $uniprot_acc (keys (%phi_mapping)) {
    my $phis_href = $phi_mapping{$uniprot_acc};
    my $taxId = $phis_href->{-tax_id};
    if (grep {$_ eq $taxId} @tax_ids) {
      # Get the master_xref_id
      # and the linkage
 
      if(!defined($swiss{$uniprot_acc})){
    print STDERR "failed to get the master_xref_if for UniProt, $uniprot_acc!\n";
    # one reason it happens is that the UniProt identifier is attached to a different tax node in Phibase that it is in UniProt
      }
      else{
    foreach my $master_xref_id (@{$swiss{$uniprot_acc}}){
      #       print STDERR "master_xref_id, $master_xref_id\n";
      my $linkage = undef;
      my $phis_aref = $phis_href->{-phi_ids};
      foreach my $phibase_id (@$phis_aref) {
        #         print STDERR "Adding xrefs for phibase id, $phibase_id\n";
        $self->add_dependent_xref({ master_xref_id => $master_xref_id,
                    acc            => $phibase_id,
                    label          => $phibase_id,
                    source_id      => $source_id,
                    species_id     => $species_id });
        $added++;
      }
    }
      }
    }
  }
 
  print "Added $added PHIbase xrefs\n";
 
  return 0;
 
}
The documentation for this class was generated from the following file:
ensembl/misc-scripts/xref_mapping/XrefParser/PHIbaseParser.pm
Public Member Functions

Detailed Description

Member Function Documentation

◆ run()
