CoreXrefParser.pm

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=head1 LICENSE
 
See the NOTICE file distributed with this work for additional information
regarding copyright ownership.
 
Licensed under the Apache License, Version 2.0 (the "License");
you may not use this file except in compliance with the License.
You may obtain a copy of the License at
 
     http://www.apache.org/licenses/LICENSE-2.0
 
Unless required by applicable law or agreed to in writing, software
distributed under the License is distributed on an "AS IS" BASIS,
WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
See the License for the specific language governing permissions and
limitations under the License.
 
=cut
 
package XrefParser::CoreXrefParser;
 
use strict;
use warnings;
use Carp;
use DBI;
 
use base qw( XrefParser::BaseParser );
use Bio::EnsEMBL::Registry;
 
sub run_script {
 
  my ($self, $ref_arg) = @_;
  my $source_id    = $ref_arg->{source_id};
  my $species_id   = $ref_arg->{species_id};
  my $file         = $ref_arg->{file};
  my $verbose      = $ref_arg->{verbose};
  my $dbi          = $ref_arg->{dbi};
  $dbi = $self->dbi unless defined $dbi;
 
  if((!defined $source_id) or (!defined $species_id) or (!defined $file) ){
    croak "Need to pass source_id, species_id and file as pairs";
  }
  $verbose |=0;
 
  my $logic_name;
  my $biotype;
  my $object_type;
  my $project;
  my $copy_description_from_object;
 
  if($file =~ /logic_name[=][>](\S+?)[,]/){
    $logic_name = $1;
  }
  if($file =~ /biotype[=][>](\S+?)[,]/){
    $biotype = $1;
  }
  if($file =~ /object_type[=][>](\S+?)[,]/){
    $object_type = $1;
  }
  if($file =~ /project[=][>](\S+?)[,]/){
    $project = $1;
  }
  if($file =~ /copy_description_from_object[=][>](\S+?)[,]/){
    $copy_description_from_object = $1;
  }
 
  my $external_db_name = $self->get_source_name_for_source_id($source_id, $dbi);
 
  #copy object xrefs from core
 
  my $registry = "Bio::EnsEMBL::Registry";
 
  if ($project eq 'ensembl') {
      $registry->load_registry_from_multiple_dbs( 
      {
          '-host'    => 'mysql-ensembl-mirror.ebi.ac.uk',
          '-port'    => 4240,
          '-user'    => 'ensro',
      },
       );
  } elsif ($project eq 'ensemblgenomes') {
 
      $registry->load_registry_from_multiple_dbs( 
      {
          '-host'     => 'mysql-eg-staging-1.ebi.ac.uk',
          '-port'     => 4160,
          '-user'     => 'ensro',
      },
      {
          '-host'     => 'mysql-eg-staging-2.ebi.ac.uk',
          '-port'     => 4275,
          '-user'     => 'ensro',
      },
      );
 
  } else {
      die("Missing or unsupported project value. Supported values: ensembl, ensemblgenomes");
  }
 
  #get the species name
  my %id2name = $self->species_id2name($dbi);
  my $species_name = $id2name{$species_id}[0];
 
  if (!$object_type) {
      $object_type = 'gene';
  }
 
  my %valid_object_types = (
 
      gene => 'Gene',
      transcript => 'Transcript',
      translation => 'Translation',
      Gene => 'Gene',
      Transcript => 'Transcript',
      Translation => 'Translation',
  );
 
  if (!exists($valid_object_types{$object_type}) ) {
 
      die("Unsupported object type value. Supported values: ", join(',', keys %valid_object_types) );
  }
 
  if ($biotype &&  $object_type ne 'gene' && $object_type ne 'transcript') {
      die("Incorrect parser argument values: expecting gene or transcript object type when biotype provided.\n");
  }
 
  my $object_adaptor = $registry->get_adaptor($species_name, 'core', $object_type);
 
  my @genes;
 
  if ($verbose) {
      print STDERR "fetching genes...\n";
  }
  
  if ($biotype) {
      @genes = @{$object_adaptor->fetch_all_by_biotype($biotype)};
      if ($biotype eq "tRNA") {
      # Fetch also all tRNA_pseudogene genes
      push (@genes, @{$object_adaptor->fetch_all_by_biotype('tRNA_pseudogene')});
      }
  } elsif ($logic_name) {
 
      if ($verbose) {
      print STDERR "Fetching by logic_name, $logic_name\n";
      }
 
      # This way we get all ncRNA genes (rRNAs, tRNAs, and all ncRNAs which can be under multiple biotypes)
 
      @genes = @{$object_adaptor->fetch_all_by_logic_name($logic_name)};
  }
  
  my %added_xref;
  my $direct_count = 0;
 
  print STDERR "Fetched " . @genes . " genes\n";
 
  foreach my $object (@genes) {
 
      #my @xrefs = @{$object->get_all_DBEntries($external_db_name)};
      # as we use a generic ncRNA source, which maps to multiple external_db_id
      my @xrefs = @{$object->get_all_DBEntries()};
 
      # print STDERR "processing " . @xrefs . " xrefs\n";
 
      if (@xrefs == 0) {
      print STDERR "No xrefs for gene, " . $object->stable_id() . "!\n";
      }
 
      foreach my $xref (@xrefs) {
 
      my $xref_id;
      my $db_name = $xref->dbname();
 
      # $source_id maps to nCRNA_EG
      # but we need to attach them specifcally
      # to RNAmmer, tRNAScan or RFAM
      # so get the source based on the db_name from the core db
      my $external_source_id = $self->get_source_id_for_source_name($db_name, undef, $dbi);
      
      if (! defined $external_source_id) {
          warn ("can't get a source_id for external_db, $db_name!\n");
          return 1;
      }
      
      if (!exists($added_xref{$xref->primary_id()})) {
          
          my $description = $xref->description();
 
          if ($copy_description_from_object && !$description) {
 
          if ($object->description()) {
                      #populate xref description with object description stripping the [Source: .. part
              ($description) = $object->description() =~ /([^\[]+)/;
              #trim trailing spaces
              $description =~ s/\s+$//;
          }
          }
          
          $xref_id = $self->add_xref({ acc        => $xref->primary_id(),
                      version    => $xref->version(),
                      label      => $xref->display_id(),
                      desc       => $description,
                      source_id  => $external_source_id,
                      species_id => $species_id,
                                      dbi        => $dbi,
                      info_type  => "DIRECT"} );
 
 
          $added_xref{$xref->primary_id()} = $xref_id;
      } 
 
      if (!$xref_id) {
          $xref_id = $added_xref{$xref->primary_id()};
      }
      
      $self->add_direct_xref($xref_id, $object->stable_id(), $valid_object_types{$object_type}, "", $dbi);
      $direct_count++;
      }
  }
 
  my $xref_count = scalar(keys %added_xref);
 
  print "Added $xref_count $external_db_name xrefs and $direct_count $object_type direct xrefs\n" if($verbose);
  if ( !$xref_count ) {
      return 1;    # 1 error
  }
 
  return 0; # successfull
 
 
}
 
1;