Raw content of Bio::EnsEMBL::Analysis::RunnableDB::FirstEF
<![CDATA[# Ensembl module for Bio::EnsEMBL::Analysis::RunnableDB::FirstEF
#
# Copyright (c) 2004 Ensembl
#
=head1 NAME
Bio::EnsEMBL::Analysis::RunnableDB::FirstEF
=head1 SYNOPSIS
my $runnabledb = Bio::EnsEMBL::Analysis::RunnableDB::FirstEF->
new(
-input_id => 'contig::AL805961.22.1.166258:1:166258:1',
-db => $db,
-analysis => $analysis,
);
$runnabledb->fetch_input;
$runnabledb->run;
$runnabledb->write_output;
=head1 DESCRIPTION
This module provides an interface between the ensembl database and
the Runnable FirstEF which wraps the program FirstEF
This module can fetch appropriate input from the database
pass it to the runnable then write the results back to the database
in the simple_feature table
=head1 CONTACT
Post questions to the Ensembl development list: ensembl-dev@ebi.ac.uk
=cut
package Bio::EnsEMBL::Analysis::RunnableDB::FirstEF;
use strict;
use warnings;
use Bio::EnsEMBL::Analysis::RunnableDB;
use Bio::EnsEMBL::Analysis::Runnable::FirstEF;
use Bio::EnsEMBL::Analysis::Config::General qw(PARAMETERS_DIR PARSE_SCRIPT) ;
use vars qw(@ISA);
@ISA = qw(Bio::EnsEMBL::Analysis::RunnableDB);
=head2 fetch_input
Arg [1] : Bio::EnsEMBL::Analysis::RunnableDB::FirstEF
Function : fetch data out of database and create runnable
Returntype: 1
Exceptions: none
Example :
=cut
sub fetch_input{
my ($self) = @_;
my $slice = $self->fetch_sequence($self->input_id, $self->db, ['']);
#hard coded array is used here as it always wants all repeats in
#the table masked at somepoint the general variables will be replaced by
#analysis specific variables and this will move back into confi
$self->query($slice);
if(!$self->analysis->program_file){
$self->analysis->program_file('firstef');
}
my %parameters;
if($self->parameters_hash){
%parameters = %{$self->parameters_hash};
}
my $runnable = Bio::EnsEMBL::Analysis::Runnable::FirstEF->new
(
-query => $self->query,
-program => $self->analysis->program_file,
-analysis => $self->analysis,
-param_dir => $PARAMETERS_DIR,
-parse_script => $PARSE_SCRIPT,
%parameters,
);
$self->runnable($runnable);
return 1;
}
=head2 get_adaptor
Arg [1] : Bio::EnsEMBL::Analysis::RunnableDB::FirstEF
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;
]]>