Raw content of Bio::EnsEMBL::Analysis::RunnableDB::Finished::EPCR
<![CDATA[=head1 NAME
EPCR.pm
=head1 SYNOPSIS
my $runnabledb = Bio::EnsEMBL::Analysis::RunnableDB::Finished::EPCR->
new(
-input_id => 'contig::AL805961.22.1.166258:1:166258:1',
-db => $db,
-analysis => $analysis,
);
$runnabledb->fetch_input;
$runnabledb->run;
$runnabledb->write_output;
=head1 DESCRIPTION
The Finished version of EPCR.
=head1 CONTACT
anacode@sanger.ac.uk
=cut
package Bio::EnsEMBL::Analysis::RunnableDB::Finished::EPCR;
use strict;
use warnings;
use Bio::EnsEMBL::Analysis::RunnableDB::EPCR;
use Bio::EnsEMBL::Analysis::Runnable::Finished::EPCR;
use vars qw(@ISA);
@ISA = qw(Bio::EnsEMBL::Analysis::RunnableDB::EPCR);
sub fetch_input{
my ($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::Finished::EPCR->new
(
-query => $slice,
-program => $self->analysis->program_file,
-analysis => $self->analysis,
%parameters
);
$self->runnable($runnable);
}
1;]]>