Raw content of Bio::EnsEMBL::Compara::RunnableDB::CreateHomology_dNdSJobs
<![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::CreateHomology_dNdSJobs
=cut
=head1 SYNOPSIS
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;
=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
abel@ebi.ac.uk, jessica@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::CreateHomology_dNdSJobs;
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_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
#
##########################################
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;
]]>