Raw content of Bio::EnsEMBL::Analysis::RunnableDB::ProteinAnnotation::Pfam
<![CDATA[#
#
#
=pod
=head1 NAME
Bio::EnsEMBL::Pipeline::RunnableDB::ProteinAnnotation::Pfam
=head1 SYNOPSIS
my $seg = Bio::EnsEMBL::Pipeline::RunnableDB::ProteinAnnotation::Pfam->
new ( -db => $db,
-input_id => $input_id,
-analysis => $analysis,
);
$seg->fetch_input; # gets sequence from DB
$seg->run;
$seg->write_output; # writes features to to DB
=head1 DESCRIPTION
This object wraps Bio::EnsEMBL::Pipeline::Runnable::Hmmpfam
to add functionality to read and write to databases in
a Pfam-specific way.
=head1 CONTACT
=cut
package Bio::EnsEMBL::Analysis::RunnableDB::ProteinAnnotation::Pfam;
use strict;
use vars qw(@ISA);
use Bio::EnsEMBL::Analysis::RunnableDB::ProteinAnnotation;
use Bio::EnsEMBL::Analysis::Runnable::ProteinAnnotation::Pfam;
@ISA = qw(Bio::EnsEMBL::Analysis::RunnableDB::ProteinAnnotation);
sub fetch_input {
my ($self) = @_;
$self->SUPER::fetch_input;
my $run = Bio::EnsEMBL::Analysis::Runnable::ProteinAnnotation::Pfam->
new(-query => $self->query,
-analysis => $self->analysis,
-database => $self->analysis->db_file,
%{$self->parameters_hash}
);
$self->runnable($run);
}
]]>