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