Raw content of Bio::EnsEMBL::Analysis::RunnableDB::Finished::Augustus
<![CDATA[# Ensembl module for Bio::EnsEMBL::Analysis::RunnableDB::Finished::Augustus
#
# Copyright (c) 2004 Ensembl
#
=head1 NAME
=head1 SYNOPSIS
my $runnabledb = Bio::EnsEMBL::Analysis::RunnableDB::Finished::Augustus->
new(
-input_id => 'contig::AL805961.22.1.166258:1:166258:1',
-db => $db,
-analysis => $analysis,
);
$runnabledb->fetch_input;
$runnabledb->run;
$runnabledb->write_output;
=head1 DESCRIPTION
fetches sequence data from database an instantiates and runs the
augustus runnable, this inherits from the Genscan runnableDB an as such doesnt
implement much itself
=head1 CONTACT
Post questions to : anacode-people@sanger.ac.uk
=cut
package Bio::EnsEMBL::Analysis::RunnableDB::Finished::Augustus;
use strict;
use warnings;
use Bio::EnsEMBL::Analysis::RunnableDB::Genscan;
use Bio::EnsEMBL::Analysis::Runnable::Finished::Augustus;
use Bio::EnsEMBL::Analysis::Config::General;
use Bio::EnsEMBL::Utils::Exception qw(throw warning);
use vars qw(@ISA);
@ISA = qw(Bio::EnsEMBL::Analysis::RunnableDB::Genscan);
=head2 runnable_path
Arg [1] : Bio::EnsEMBL::Analysis::RunnableDB::Finished::Augustus
Function : return the runnable path
Returntype: string
Exceptions:
Example : my $runnable = $self->runnable_path->new
(
-query => $self->query,
-program => $self->analysis->program_file,
-analysis => $self->analysis,
%parameters,
);
=cut
sub runnable_path{
my ($self);
return "Bio::EnsEMBL::Analysis::Runnable::Finished::Augustus";
}
sub write_output{
my ($self) = @_;
my $adaptor = $self->db->get_PredictionTranscriptAdaptor;
my $dbh = $self->db->dbc->db_handle;
my @output = @{$self->output};
my $ff = $self->feature_factory;
$dbh->begin_work;
eval {
foreach my $pt(@output){
$pt->analysis($self->analysis);
$pt->slice($self->query) if(!$pt->slice);
print STDERR "Validate transcript ".$pt->seqname."\n";
# dismiss transcript with invalid translation
eval {
$ff->validate_prediction_transcript($pt, 1);
};
if($@){ warning($@); next; }
$adaptor->store($pt);
}
$dbh->commit;
};
if ($@) {
$dbh->rollback;
throw("UNABLE TO WRITE PREDICTION TRANSCRIPTS IN DATABASE\n[$@]\n");
}
}
1;
]]>