Raw content of Bio::EnsEMBL::Compara::RunnableDB::CreateBlastRules
<![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::CreateBlastRules
=cut
=head1 SYNOPSIS
my $db = Bio::EnsEMBL::Compara::DBAdaptor->new($locator);
my $repmask = Bio::EnsEMBL::Compara::RunnableDB::CreateBlastRules->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
This object wraps Bio::EnsEMBL::Analysis::Runnable::Blast to add
functionality to read and write to databases.
The appropriate Bio::EnsEMBL::Analysis object must be passed for
extraction of appropriate parameters.
=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::RunnableDB::CreateBlastRules;
use strict;
use Bio::EnsEMBL::DBSQL::DBAdaptor;
use Bio::EnsEMBL::Compara::DBSQL::DBAdaptor;
use Bio::EnsEMBL::Hive::DBSQL::DataflowRuleAdaptor;
use Bio::EnsEMBL::Utils::Exception;
use Bio::EnsEMBL::Hive::Process;
our @ISA = qw(Bio::EnsEMBL::Hive::Process);
sub fetch_input {
my $self = shift;
throw("No input_id") unless defined($self->input_id);
print("input_id = ".$self->input_id."\n");
throw("Improper formated input_id") unless ($self->input_id =~ /\s*\{/);
$self->{'selfBlast'} = 1;
$self->{'phylumBlast'} = 0;
if($self->analysis->parameters =~ /\s*\{/) {
my $paramHash = eval($self->analysis->parameters);
if($paramHash) {
$self->{'phylumBlast'}=1 if($paramHash->{'phylumBlast'}==1);
$self->{'selfBlast'}=0 if($paramHash->{'selfBlast'}==0);
$self->{'cr_analysis_logic_name'} = $paramHash->{'cr_analysis_logic_name'} if(defined $paramHash->{'cr_analysis_logic_name'});
}
}
#create a new Compara::DBAdaptor which points to the same database
#as the pipeline DBAdaptor passed in ($self->db)
#the -DBCONN options uses the dbname,user,pass,port,host,driver from the
#variable DBConnection to create the new connection (in essence a copy)
$self->{'comparaDBA'} = Bio::EnsEMBL::Compara::DBSQL::DBAdaptor->new(-DBCONN => $self->db->dbc);
if (defined $self->{'cr_analysis_logic_name'}) {
$self->{'cr_analysis'} = $self->db->get_AnalysisAdaptor->fetch_by_logic_name($self->{'cr_analysis_logic_name'});
throw($self->{'cr_analysis_logic_name'} . " analysis is missing, can't proceed\n")
unless(defined($self->{'cr_analysis'}));
}
return 1;
}
sub run
{
#need to subclass otherwise it defaults to a version that fails
#just return 1 so success
return 1;
}
sub write_output
{
my $self = shift;
my $input_hash = eval($self->input_id);
if($input_hash and $input_hash->{'peps'} and $input_hash->{'blast'}) {
my $conditionLogicName = $input_hash->{'peps'};
my $goalLogicName = $input_hash->{'blast'};
print("create rule $conditionLogicName => $goalLogicName\n");
my $conditionAnalysis = $self->db->get_AnalysisAdaptor->fetch_by_logic_name($conditionLogicName);
my $goalAnalysis = $self->db->get_AnalysisAdaptor->fetch_by_logic_name($goalLogicName);
$self->linkSubmitBlastPair($conditionAnalysis, $goalAnalysis);
}
else {
$self->createAllBlastRules();
}
return 1;
}
##################################
#
# subroutines
#
##################################
sub createAllBlastRules
{
my $self = shift;
my $analysisList = $self->db->get_AnalysisAdaptor->fetch_all();
my @submitList;
my @blastList;
foreach my $submitAnalysis (@{$analysisList}) {
next unless($submitAnalysis->logic_name =~ /SubmitPep_(.*)/);
my $blast_name = "blast_".$1;
printf("found submit %s\n", $submitAnalysis->logic_name);
push @submitList, $submitAnalysis;
$self->db->get_AnalysisCtrlRuleAdaptor->create_rule($submitAnalysis, $self->{'cr_analysis'});
my $blastAnalysis = $self->db->get_AnalysisAdaptor->fetch_by_logic_name($blast_name);
if($blastAnalysis) {
push @blastList, $blastAnalysis;
$self->db->get_AnalysisCtrlRuleAdaptor->create_rule($blastAnalysis, $self->{'cr_analysis'});
}
}
foreach my $submitAnalysis (@submitList) {
foreach my $blastAnalysis (@blastList) {
if (!$self->{'selfBlast'}) {
my ($submit_id) = $submitAnalysis->logic_name =~ /SubmitPep_(.*)/;
my ($blast_id) = $blastAnalysis->logic_name =~ /blast_(.*)/;
next if ($submit_id eq $blast_id);
}
# If it uses BlastcomparaPepAcross, we only create one Blast job 1
# job only across all the sps in 'species_set' in PAFCluster
# instead of a job per sp. This is to avoid creating an
# exponentially large ((n*n-1)/2) number of jobs that collapses
# the analysis_job table.
if ($blastAnalysis->module eq 'Bio::EnsEMBL::Compara::RunnableDB::BlastComparaPepAcross') {
my ($submit_id) = $submitAnalysis->logic_name =~ /SubmitPep_(.*)/;
my ($blast_id) = $blastAnalysis->logic_name =~ /blast_(.*)/;
next unless ($submit_id eq $blast_id);
}
$self->linkSubmitBlastPair($submitAnalysis, $blastAnalysis);
}
}
}
sub linkSubmitBlastPair
{
my $self = shift;
my $conditionAnalysis = shift;
my $goalAnalysis = shift;
printf("link %s => %s\n", $conditionAnalysis->logic_name, $goalAnalysis->logic_name);
if($self->db->get_DataflowRuleAdaptor->create_rule($conditionAnalysis, $goalAnalysis)) {
printf("reset_all_jobs_for_analysis %s\n", $conditionAnalysis->logic_name);
$self->db->get_AnalysisJobAdaptor->reset_all_jobs_for_analysis_id($conditionAnalysis->dbID);
}
}
1;
]]>