Raw content of Bio::EnsEMBL::Compara::RunnableDB::CreateHclusterPrepareJobs
<![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::CreateHclusterPrepareJobs
=cut
=head1 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;
=cut
=head1 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.
=cut
=head1 CONTACT
avilella@ebi.ac.uk
=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::RunnableDB::CreateHclusterPrepareJobs;
use strict;
use Bio::EnsEMBL::Compara::DBSQL::DBAdaptor;
use Bio::EnsEMBL::Hive;
use Bio::EnsEMBL::Hive::Process;
our @ISA = qw(Bio::EnsEMBL::Hive::Process);
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
#
##########################################
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;
]]>