Raw content of Bio::EnsEMBL::Analysis::RunnableDB::ProteinAnnotation::Seg
<![CDATA[
=pod
=head1 NAME
Bio::EnsEMBL::Analysis::RunnableDB::ProteinAnnotation::Seg
=head1 SYNOPSIS
my $seg = Bio::EnsEMBL::Analysis::RunnableDB::ProteinAnnotation::Seg->new ( -db => $db,
-input_id => $input_id,
-analysis => $analysis,
);
$seg->fetch_input; # gets sequence from DB
$seg->run;
$seg->output;
$seg->write_output; # writes features to to DB
NB: The input_id can either be a peptide id or the location for a protein file.
=head1 DESCRIPTION
This object wraps Bio::EnsEMBL::Analysis::Runnable::ProteinAnnotation::Seg
to add functionality to read and write to databases.
The query sequence is provided through the input_id.
The appropriate Bio::EnsEMBL::Analysis object
must be passed for extraction of parameters.
=head1 CONTACT
Marc Sohrmann: ms2@sanger.ac.uk
=head1 APPENDIX
The rest of the documentation details each of the object methods.
Internal methods are usually preceded with a _.
=cut
package Bio::EnsEMBL::Analysis::RunnableDB::ProteinAnnotation::Seg;
use strict;
use vars qw(@ISA);
use Bio::EnsEMBL::Analysis::RunnableDB::ProteinAnnotation;
use Bio::EnsEMBL::Analysis::Runnable::ProteinAnnotation::Seg;
@ISA = qw(Bio::EnsEMBL::Analysis::RunnableDB::ProteinAnnotation);
sub fetch_input {
my ($self, @args) = @_;
$self->SUPER::fetch_input(@args);
my $run = Bio::EnsEMBL::Analysis::Runnable::ProteinAnnotation::Seg->new(-query => $self->query,
-analysis => $self->analysis);
$self->runnable($run);
}
1;
]]>