Raw content of Bio::EnsEMBL::Compara::Production::GenomicAlignBlock::CreatePairAlignerJobs
<![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::CreatePairAlignerJobs
=cut
=head1 SYNOPSIS
my $db = Bio::EnsEMBL::Compara::DBAdaptor->new($locator);
my $repmask = Bio::EnsEMBL::Pipeline::RunnableDB::CreatePairAlignerJobs->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::CreatePairAlignerJobs;
use strict;
use Bio::EnsEMBL::Hive;
use Bio::EnsEMBL::Compara::Production::DBSQL::DBAdaptor;
use Bio::EnsEMBL::Compara::Production::DnaFragChunk;
use Bio::EnsEMBL::Compara::Production::DnaFragChunkSet;
use Bio::EnsEMBL::Compara::Production::DnaCollection;
use Bio::EnsEMBL::Analysis::RunnableDB;
use Bio::EnsEMBL::Hive::Process
our @ISA = qw(Bio::EnsEMBL::Hive::Process);
sub fetch_input {
my $self = shift;
#
# parameters which can be set either via
# $self->parameters OR
# $self->input_id
#
$self->{'pair_aligner_logic_name'} = undef;
$self->{'query_dna'} = undef;
$self->{'target_dna'} = undef;
$self->{'method_link_species_set_id'} = undef;
$self->get_params($self->parameters);
$self->get_params($self->input_id);
# create a Compara::DBAdaptor which shares my DBConnection
$self->{'comparaDBA'} = Bio::EnsEMBL::Compara::Production::DBSQL::DBAdaptor->new(-DBCONN => $self->db->dbc);
# get the PairAligner analysis
throw("must specify pair_aligner to identify logic_name of PairAligner analysis")
unless(defined($self->{'pair_aligner_logic_name'}));
$self->{'pair_aligner'} = $self->db->get_AnalysisAdaptor->fetch_by_logic_name($self->{'pair_aligner_logic_name'});
throw("unable to find analysis with logic_name ". $self->{'pair_aligner_logic_name'})
unless(defined($self->{'pair_aligner'}));
# get DnaCollection of query
throw("must specify 'query_collection_name' to identify DnaCollection of query")
unless(defined($self->{'query_collection_name'}));
$self->{'query_collection'} = $self->{'comparaDBA'}->get_DnaCollectionAdaptor->
fetch_by_set_description($self->{'query_collection_name'});
throw("unable to find DnaCollection with name : ". $self->{'query_collection_name'})
unless(defined($self->{'query_collection'}));
# get DnaCollection of target
throw("must specify 'target_collection_name' to identify DnaCollection of query")
unless(defined($self->{'target_collection_name'}));
$self->{'target_collection'} = $self->{'comparaDBA'}->get_DnaCollectionAdaptor->
fetch_by_set_description($self->{'target_collection_name'});
throw("unable to find DnaCollection with name : ". $self->{'target_collection_name'})
unless(defined($self->{'target_collection'}));
$self->print_params;
return 1;
}
sub run
{
my $self = shift;
$self->createPairAlignerJobs();
return 1;
}
sub write_output
{
my $self = shift;
return 1;
}
##################################
#
# subroutines
#
##################################
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");
}
$self->{'pair_aligner_logic_name'} = $params->{'pair_aligner'} if(defined($params->{'pair_aligner'}));
$self->{'query_collection_name'} = $params->{'query_collection_name'} if(defined($params->{'query_collection_name'}));
$self->{'target_collection_name'} = $params->{'target_collection_name'} if(defined($params->{'target_collection_name'}));
$self->{'method_link_species_set_id'} = $params->{'method_link_species_set_id'}
if(defined($params->{'method_link_species_set_id'}));
return;
}
sub print_params {
my $self = shift;
printf(" params:\n");
printf(" method_link_species_set_id : %d\n", $self->{'method_link_species_set_id'});
printf(" pair_aligner : (%d) %s\n",
$self->{'pair_aligner'}->dbID, $self->{'pair_aligner'}->logic_name);
printf(" query_collection : (%d) %s\n",
$self->{'query_collection'}->dbID, $self->{'query_collection'}->description);
printf(" target_collection : (%d) %s\n",
$self->{'target_collection'}->dbID, $self->{'target_collection'}->description);
}
sub createPairAlignerJobs
{
my $self = shift;
my $query_dna_list = $self->{'query_collection'}->get_all_dna_objects;
my $target_dna_list = $self->{'target_collection'}->get_all_dna_objects;
my $count=0;
foreach my $target_dna (@{$target_dna_list}) {
my $input_hash = {};
$input_hash->{'dbChunk'} = undef;
$input_hash->{'dbChunkSetID'} = undef;
if($target_dna->isa('Bio::EnsEMBL::Compara::Production::DnaFragChunk')) {
$input_hash->{'dbChunk'} = $target_dna->dbID;
}
if($target_dna->isa('Bio::EnsEMBL::Compara::Production::DnaFragChunkSet')) {
$input_hash->{'dbChunkSetID'} = $target_dna->dbID;
}
foreach my $query_dna (@{$query_dna_list}) {
$input_hash->{'qyChunk'} = undef
$input_hash->{'qyChunkSetID'} = undef;
if($query_dna->isa('Bio::EnsEMBL::Compara::Production::DnaFragChunk')) {
$input_hash->{'qyChunk'} = $query_dna->dbID;
}
if($query_dna->isa('Bio::EnsEMBL::Compara::Production::DnaFragChunkSet')) {
$input_hash->{'qyChunkSetID'} = $query_dna->dbID;
}
my $input_id = main::encode_hash($input_hash);
#printf("create_job : %s : %s\n", $self->{'pair_aligner'}->logic_name, $input_id);
Bio::EnsEMBL::Hive::DBSQL::AnalysisJobAdaptor->CreateNewJob (
-input_id => $input_id,
-analysis => $self->{'pair_aligner'},
-input_job_id => 0,
);
$count++;
}
}
printf("created %d jobs for pair aligner\n", $count);
}
1;
]]>