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Summary

Bio::EnsEMBL::Compara::RunnableDB::CreateHclusterPrepareJobs

Package variables

Included modules

Inherit

Bio::EnsEMBL::Hive::Process

Synopsis

my $aa = $sdba->get_AnalysisAdaptor;
my $analysis = $aa->fetch_by_logic_name('CreateHclusterPrepareJobs');
my $rdb = new Bio::EnsEMBL::Compara::RunnableDB::CreateHclusterPrepareJobs();
$rdb->fetch_input;
$rdb->run;

Description

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.

Methods

Methods description

None available.

Methods code

sub create_analysis_jobs {

  my $self = shift;

  my $aa = $self->db->get_AnalysisAdaptor;
  my $hclusterprepare_analysis = $aa->fetch_by_logic_name('HclusterPrepare');

  foreach my $species (@{$self->{species_set}}) {
    my $analysis_id = $hclusterprepare_analysis->dbID;
    my $sql = "insert ignore into analysis_job (analysis_id,input_id,status) VALUES ($analysis_id,$species,'READY')";
    my $sth = $self->dbc->prepare($sql);
    $sth->execute;
    $sth->finish;
  }
}

1;

}

sub fetch_input {

  my( $self) = @_;

  $self->{'species_set'} = 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->parameters);
  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);

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

  if (defined $params->{'species_set'}) {
    $self->{'species_set'} = $params->{'species_set'};
  }

  print("parameters...\n");
  printf("  species_set    : (%s)\n", join(',', @{$self->{'species_set'}}));

  return;

}

sub run {

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

  $self->create_analysis_jobs($self->{'species_set'});

  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 _