Raw content of Bio::EnsEMBL::Analysis::RunnableDB::EPCR # 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; }