Raw content of Bio::EnsEMBL::Compara::RunnableDB::CreateBuildHomologyJobs
<![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::CreateBuildHomologyJobs
=cut
=head1 SYNOPSIS
my $aa = $sdba->get_AnalysisAdaptor;
my $analysis = $aa->fetch_by_logic_name('CreateBuildHomologyJobs');
my $rdb = new Bio::EnsEMBL::Compara::RunnableDB::CreateBuildHomologyJobs(
-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
Contact Jessica Severin on module implemetation/design detail: jessica@ebi.ac.uk
Contact Abel Ureta-Vidal on EnsEMBL/Compara: abel@ebi.ac.uk
Contact Ewan Birney on EnsEMBL in general: birney@sanger.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::CreateBuildHomologyJobs;
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);
foreach my $key (keys %$params) {
print(" $key : ", $params->{$key}, "\n");
}
if (defined $params->{'species_sets'}) {
$self->{'species_sets_aref'} = $params->{'species_sets'};
}
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;
foreach my $species_set (@{$species_sets_aref}) {
while (my $gdb1 = shift @{$species_set}) {
my $genome_db1 = $self->{'comparaDBA'}->get_GenomeDBAdaptor->fetch_by_dbID($gdb1);
next unless($genome_db1);
foreach my $gdb2 (@{$species_set}) {
my $genome_db2 = $self->{'comparaDBA'}->get_GenomeDBAdaptor->fetch_by_dbID($gdb2);
next unless($genome_db2);
$self->createBuildHomologyJob($genome_db1, $genome_db2);
}
}
}
}
sub createBuildHomologyJob
{
my $self = shift;
my $genome_db1 = shift;
my $genome_db2 = shift;
my $noRHS = shift;
my $logic_name1 = 'blast_' .$genome_db1->dbID."_".$genome_db1->assembly;
my $logic_name2 = 'blast_' .$genome_db2->dbID."_".$genome_db2->assembly;
my $phylum1 = $self->phylumForGenomeDBID($genome_db1->dbID);
my $phylum2 = $self->phylumForGenomeDBID($genome_db2->dbID);
$noRHS='noRHS' if(!defined($noRHS) and $phylum1 ne $phylum2);
my $output_id;
if($genome_db1->dbID < $genome_db2->dbID) {
$output_id = "{blasts=>['".$logic_name1 . "','". $logic_name2 . "']";
} else {
$output_id = "{blasts=>['".$logic_name2 . "','". $logic_name1 . "']";
}
if($noRHS and ($noRHS eq 'noRHS')) { $output_id .= ",noRHS=>1"; }
$output_id .= "}";
print("HOMOLOGY '$output_id'\n");
# dataflow the output_id on branch_code 2, which will be configured in the graph
# to flow into BuildHomology
$self->dataflow_output_id($output_id, 2);
}
sub phylumForGenomeDBID
{
my $self = shift;
my $genome_db_id = shift;
my $phylum;
unless($genome_db_id) { return undef; }
my $sql = "SELECT phylum FROM genome_db_extn " .
"WHERE genome_db_id=$genome_db_id;";
my $sth = $self->db->dbc->prepare( $sql );
$sth->execute();
$sth->bind_columns( undef, \$phylum );
$sth->fetch();
$sth->finish();
return $phylum;
}
1;
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