Raw content of Bio::EnsEMBL::Analysis::RunnableDB::Genefinder
<![CDATA[# Ensembl module for Bio::EnsEMBL::Analysis::RunnableDB::Genefinder
#
# Copyright (c) 2005 Ensembl
#
=head1 NAME
=head1 SYNOPSIS
my $runnabledb = Bio::EnsEMBL::Analysis::RunnableDB::Genefinder->
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
genefinder runnable
=head1 CONTACT
Post questions to the Ensembl development list: ensembl-dev@ebi.ac.uk
=cut
package Bio::EnsEMBL::Analysis::RunnableDB::Genefinder;
use strict;
use warnings;
use Bio::EnsEMBL::Analysis::RunnableDB::Genscan;
use Bio::EnsEMBL::Analysis::Runnable::Genefinder;
use Bio::EnsEMBL::Analysis::Config::General;
use vars qw(@ISA);
@ISA = qw(Bio::EnsEMBL::Analysis::RunnableDB::Genscan);
=head2 runnable_path
Arg [1] : Bio::EnsEMBL::Analysis::RunnableDB::Genefinder
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::Genefinder";
}
=head2 standard_args
Arg [1] : Bio::EnsEMBL::Analysis::RunnableDB::Genefinder
Function : to return a hash which contains the
standard constructor args for the genscan runnable
Returntype: hashref
Exceptions: none
Example :
=cut
sub standard_args{
my ($self) = @_;
my %parameters;
if($self->parameters_hash){
%parameters = %{$self->parameters_hash};
}
return {
-query => $self->query,
-program => $self->analysis->program_file,
-analysis => $self->analysis,
%parameters,
};
}
1;
]]>