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Summary

Bio::EnsEMBL::Compara::RunnableDB::CreateRules

Package variables

Included modules

Inherit

Bio::EnsEMBL::Pipeline::RunnableDB

Synopsis

my $db = Bio::EnsEMBL::Compara::DBAdaptor->new($locator);
my $repmask = Bio::EnsEMBL::Pipeline::RunnableDB::CreateRules->new (
-db => $db,
-input_id => $input_id
-analysis => $analysis );
$repmask->fetch_input(); #reads from DB
$repmask->run();
$repmask->output();
$repmask->write_output(); #writes to DB

Description

Methods

Methods description

None available.

Methods code

sub createBlastRules {

  my $self = shift;

  my $dataflowRuleDBA = $self->db->get_DataflowRuleAdaptor;
  my $analysisList = $self->db->get_AnalysisAdaptor->fetch_all();

  my @fromList = ();

  foreach my $analysis (@{$analysisList}) {
    next unless($analysis->logic_name =~ /^$self->{'from_prefix'}/);
    push @fromList, $analysis;
    print("FROM: ", $analysis->logic_name,"\n");
  }

  foreach my $to_analysis (@{$analysisList}) {
    next unless($to_analysis->logic_name =~ /^$self->{'to_prefix'}/);
    next if($to_analysis->logic_name eq $self->{'to_prefix'});
    foreach my $from_analysis (@fromList) {
      print("  ",$from_analysis->logic_name," -> ", $to_analysis->logic_name, "\n");
      $dataflowRuleDBA->create_rule($from_analysis, $to_analysis);
    }
  }

  foreach my $from_analysis (@fromList) {
    my $stats = $from_analysis->stats;
    $stats->status('LOADING');
    $stats->update;
  }
}


1;

}

sub fetch_input {

  my $self = shift;

  $self->throw("No input_id") unless defined($self->input_id);
  $self->throw("Improper formated input_id") unless ($self->input_id =~ /{/);

  return 1;

}

sub run {

  return 1;

}

sub write_output {

  my $self = shift;

  my $input_hash = eval($self->input_id);
  $self->{'from_prefix'} = $input_hash->{'from'};
  $self->{'to_prefix'} = $input_hash->{'to'};

  $self->createBlastRules();
  return 1;
}




##################################
#
# subroutines
#
##################################

}

General documentation

Describe contact details here

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