Raw content of Bio::EnsEMBL::Analysis::RunnableDB::tRNAscan_SE
<![CDATA[# Ensembl module for Bio::EnsEMBL::Analysis::RunnableDB::tRNAscan_SE
#
# Copyright (c) 2004 Ensembl
#
=head1 NAME
Bio::EnsEMBL::Analysis::RunnableDB::tRNAscan_SE
=head1 SYNOPSIS
my $runnable = Bio::EnsEMBL::Analysis::RunnableDB::tRNAscan_SE->
new(
-input_id => 'contig::AL805961.22.1.166258:1:166258:1',
-db => $db,
-analysis => $analysis,
);
$runnable->fetch_input;
$runnable->run;
$runnable->write_output;
=head1 DESCRIPTION
This module provides an interface between the ensembl database and
the Runnable tRNAscan_SE which wraps the program tRNAscan_SE
This module can fetch appropriate input from the database
pass it to the runnable then write the results back to the database
in the simple_feature table
=head1 CONTACT
Post questions to the Ensembl development list: ensembl-dev@ebi.ac.uk
=cut
package Bio::EnsEMBL::Analysis::RunnableDB::tRNAscan_SE;
use strict;
use warnings;
use Bio::EnsEMBL::Analysis::RunnableDB;
use Bio::EnsEMBL::Analysis::Runnable::tRNAscan_SE;
use vars qw(@ISA);
@ISA = qw(Bio::EnsEMBL::Analysis::RunnableDB);
=head2 fetch_input
Arg [1] : Bio::EnsEMBL::Analysis::RunnableDB::tRNAscan_SE
Function : fetch data out of database and create runnable
Returntype: 1
Exceptions: none
Example :
=cut
sub fetch_input{
my ($self) = @_;
my $slice = $self->fetch_sequence;
$self->query($slice);
my %parameters;
if($self->parameters_hash){
%parameters = %{$self->parameters_hash};
}
my $runnable = Bio::EnsEMBL::Analysis::Runnable::tRNAscan_SE->new
(
-query => $self->query,
-program => $self->analysis->program_file,
-analysis => $self->analysis,
%parameters,
);
$self->runnable($runnable);
return 1;
}
=head2 get_adaptor
Arg [1] : Bio::EnsEMBL::Analysis::RunnableDB::tRNAscan_SE
Function : get simple_feature adaptor
Returntype: Bio::EnsEMBL::DBSQL::SimpleFeatureAdaptor
Exceptions: none
Example :
=cut
sub get_adaptor{
my ($self) = @_;
return $self->db->get_SimpleFeatureAdaptor;
}
1;
]]>