Raw content of Bio::EnsEMBL::Compara::Production::GenomicAlignBlock::CreateRules
<![CDATA[#
# You may distribute this module under the same terms as perl itself
#
# POD documentation - main docs before the code
=pod
=head1 NAME
Bio::EnsEMBL::Compara::RunnableDB::CreateRules
=cut
=head1 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
=cut
=head1 DESCRIPTION
=cut
=head1 CONTACT
Describe contact details here
=cut
=head1 APPENDIX
The rest of the documentation details each of the object methods.
Internal methods are usually preceded with a _
=cut
package Bio::EnsEMBL::Compara::Production::GenomicAlignBlock::CreateRules;
use strict;
use Bio::EnsEMBL::DBSQL::DBAdaptor;
use Bio::EnsEMBL::Pipeline::RunnableDB;
use Bio::EnsEMBL::Compara::DBSQL::DBAdaptor;
use Bio::EnsEMBL::Hive;
use vars qw(@ISA);
@ISA = qw(Bio::EnsEMBL::Pipeline::RunnableDB);
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
#
##################################
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;
]]>