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