Raw content of Bio::EnsEMBL::Analysis::RunnableDB::EPCR
<![CDATA[# Ensembl module for Bio::EnsEMBL::Analysis::RunnableDB::EPCR
#
# Copyright (c) 2004 Ensembl
#
=head1 NAME
=head1 SYNOPSIS
my $runnabledb = Bio::EnsEMBL::Analysis::RunnableDB::EPCR->
new(
-input_id => 'contig::AL805961.22.1.166258:1:166258:1',
-db => $db,
-analysis => $analysis,
);
$runnabledb->fetch_input;
$runnabledb->run;
$runnabledb->write_output;
=head1 DESCRIPTION
=head1 CONTACT
Post questions to the Ensembl development list: ensembl-dev@ebi.ac.uk
=cut
package Bio::EnsEMBL::Analysis::RunnableDB::EPCR;
use strict;
use warnings;
use Bio::EnsEMBL::Analysis::RunnableDB;
use Bio::EnsEMBL::Analysis::Runnable::EPCR;
use vars qw(@ISA);
@ISA = qw(Bio::EnsEMBL::Analysis::RunnableDB);
=head2 fetch_input
Arg [1] : Bio::EnsEMBL::Analysis::RunnableDB::EPCR
Function : fetch data out of database and create runnable
Returntype: none
Exceptions: throws if no markers in the database when no -STS_FILE
is defined
Example :
=cut
sub fetch_input{
my ($self) = @_;
my %parameters = %{$self->parameters_hash};
if($self->analysis->db_file){
$parameters{'-STS_FILE'} = $self->analysis->db_file
unless($parameters{'-STS_FILE'});
}
if(!$parameters{'-STS_FILE'}){
my $sts = $self->db->get_MarkerAdaptor->fetch_all;
throw("No markers in ".$self->db->dbname) unless(@$sts);
$parameters{'-STS_FEATURES'} = $sts;
}
my $slice = $self->fetch_sequence;
$self->query($slice);
my $runnable = Bio::EnsEMBL::Analysis::Runnable::EPCR->new
(
-query => $slice,
-program => $self->analysis->program_file,
-analysis => $self->analysis,
%parameters
);
$self->runnable($runnable);
}
=head2 get_adaptor
Arg [1] : Bio::EnsEMBL::Analysis::RunnableDB::EPCR
Function : get marker feature adaptor
Returntype: Bio::EnsEMBL::Map::DBSQL::MarkerFeatureAdaptor
Exceptions: none
Example :
=cut
sub get_adaptor{
my ($self) = @_;
return $self->db->get_MarkerFeatureAdaptor;
}
]]>