CreateHomology_dNdSJobs documentation.

Bio::EnsEMBL::Compara::RunnableDB::CreateHomology_dNdSJobs

No package variables defined.

my $aa = $sdba->get_AnalysisAdaptor;
my $analysis = $aa->fetch_by_logic_name('CreateHomology_dNdSJobs');
my $rdb = new Bio::EnsEMBL::Compara::RunnableDB::CreateHomology_dNdSJobs(
-input_id => [[1,2,3,14],[4,13],[11,16]]
-analysis => $analysis);
$rdb->fetch_input
$rdb->run;

This is a homology compara specific runnableDB, that based on an input
of arrayrefs of genome_db_ids, creates Homology_dNdS jobs in the hive
analysis_job table.

sub create_analysis_jobs {

  my $self = shift;
  my $species_sets_aref = shift;

  my $aa = $self->db->get_AnalysisAdaptor;
  my $Homology_dNdS_analysis = $aa->fetch_by_logic_name('Homology_dNdS');

#   my $sql = "insert ignore into analysis_job (analysis_id,input_id,status) select " .
#     $Homology_dNdS_analysis->dbID .
#       ",homology_id,'READY' from homology where method_link_species_set_id = ?";

  my $sql = "select homology_id from homology where method_link_species_set_id = ?";
  my $sth = $self->db->dbc->prepare($sql);

  my $mlssa = $self->{'comparaDBA'}->get_MethodLinkSpeciesSetAdaptor;
  my @homologies;
  foreach my $species_set (@{$species_sets_aref}) {
    while (my $genome_db_id1 = shift @{$species_set}) {
      foreach my $genome_db_id2 (@{$species_set}) {

        foreach my $mlt(@{$self->{'method_link_types'}||[]}){
          my $mlss = $mlssa->fetch_by_method_link_type_genome_db_ids
              ($mlt,[$genome_db_id1,$genome_db_id2]);
	  next unless($mlss);
          $sth->execute($mlss->dbID);
          while( my $ref  = $sth->fetchrow_arrayref() ) {
            my ($homology_id) = @$ref;
            push @homologies, $homology_id;
          }
        }
      }
    }
  }

  my $job_size = int(((scalar @homologies)/25000));
  $job_size = 1 if ($job_size < 1);
  $job_size = 25 if ($job_size > 20); # limit of 255 chars in input_id

  my $analysis_id = $Homology_dNdS_analysis->dbID;
  while (@homologies) {
    my @job_array = splice(@homologies,0,$job_size);
    my $input_id = "[" . join(',',@job_array) . "]";
    my $input_string = "{'ids'=>" . $input_id . "}";
    my $sql = "insert ignore into analysis_job (analysis_id,input_id,status) VALUES ($analysis_id,\"$input_string\",'READY')";
    my $sth2 = $self->db->dbc->prepare($sql);
    $sth2->execute;
  }

  $sth->finish;
}

1;

}

sub fetch_input {

  my( $self) = @_;

  $self->{'species_sets_aref'} = undef;
  $self->throw("No input_id") unless defined($self->input_id);

  #create a Compara::DBAdaptor which shares the same DBI handle
  #with the pipeline DBAdaptor that is based into this runnable
  $self->{'comparaDBA'} = Bio::EnsEMBL::Compara::DBSQL::DBAdaptor->new(-DBCONN=>$self->db->dbc);

  $self->get_params($self->input_id);
  return 1;

}

sub get_params {

  my $self         = shift;
  my $param_string = shift;

  return unless($param_string);
  print("parsing parameter string : ",$param_string,"\n");
  
  my $params = eval($param_string);

  return unless($params);
  if (!defined($params->{method_link_types})) {
    # Default will be orthologues
    $params->{method_link_types} = ['ENSEMBL_ORTHOLOGUES'];
  }

  foreach my $key (keys %$params) {
    print("  $key : ", $params->{$key}, "\n");
  }

  if (defined $params->{'species_sets'}) {
    $self->{'species_sets_aref'} = [@{$params->{'species_sets'}}];
  }
  if (defined $params->{'method_link_types'}){
    $self->{'method_link_types'} = [@{$params->{'method_link_types'}}];
  }
  elsif (defined $params->{'method_link_type'}) {
    warn( 'The method_link_type paramerter is deprecated. '.
          'Please use method_link_types with an arrayref value instead' );
    $self->{'method_link_types'} = [$params->{'method_link_type'}];
  }
  
  return;

}

sub run {

  my $self = shift;
  return 1 unless($self->{'species_sets_aref'});

  $self->create_analysis_jobs($self->{'species_sets_aref'});
  
  return 1;

}

sub write_output {

  my $self = shift;
  return 1;
}

##########################################
#
# internal methods
#
##########################################

}

General documentation

The rest of the documentation details each of the object methods.
Internal methods are usually preceded with a _

create_analysis_jobs	No description	Code
fetch_input	No description	Code
get_params	No description	Code
run	No description	Code
write_output	No description	Code