Raw content of Bio::EnsEMBL::Analysis::RunnableDB::HavanaAdder
<![CDATA[#
# Cared for by EnsEMBL <ensembl-dev@ebi.ac.uk>
#
# written by Michele Clamp
#
# You may distribute this module under the same terms as perl itself
#
# POD documentation - main docs before the code
=pod
=head1 NAME
Bio::EnsEMBL::Analysis::RunnableDB::HavanaAdder
=head1 SYNOPSIS
my $obj = Bio::EnsEMBL::Analysis::RunnableDB::HavanaAdder->new(
-db => $db,
-input_id => $id,
);
$obj->fetch_input
$obj->run
my @newfeatures = $obj->output;
=head1 DESCRIPTION
=head1 CONTACT
Describe contact details here
=head1 APPENDIX
The rest of the documentation details each of the object methods.
Internal methods are usually preceded with a _
=cut
# Let the code begin...
package Bio::EnsEMBL::Analysis::RunnableDB::HavanaAdder;
use vars qw(@ISA);
use strict;
# Object preamble
use Bio::EnsEMBL::Analysis::RunnableDB;
use Bio::EnsEMBL::Analysis::Runnable::HavanaAdder;
use Bio::EnsEMBL::Analysis::RunnableDB::BaseGeneBuild;
use Bio::EnsEMBL::Utils::Exception qw(throw warning);
use Bio::EnsEMBL::Analysis::Config::GeneBuild::General qw (
GB_INPUTID_REGEX
);
use Bio::EnsEMBL::Analysis::Config::HavanaAdder qw (
GB_ENSEMBL_INPUT_GENETYPE
HAVANA_GENE_OUTPUT_BIOTYPE
MERGED_GENE_OUTPUT_BIOTYPE
ENSEMBL_GENE_OUTPUT_BIOTYPE
MERGED_TRANSCRIPT_OUTPUT_TYPE
);
@ISA = qw(Bio::EnsEMBL::Analysis::RunnableDB::BaseGeneBuild);
############################################################
=head2 new
Usage : $self->new(-DBOBJ => $db,
-INPUT_ID => $id,
-SEQFETCHER => $sf,
-ANALYSIS => $analysis,
);
Function: creates a Bio::EnsEMBL::Analysis::RunnableDB::HavanaAdder object
Returns : A Bio::EnsEMBL::Analysis::RunnableDB::HavanaAdder object
Args : -dbobj: A Bio::EnsEMBL::DBSQL::DBAdaptor (required),
-input_id: Contig input id (required),
-seqfetcher: A Sequence Fetcher Object,
-analysis: A Bio::EnsEMBL::Analysis (optional)
-extend: determines the extension of the virtual contig
note: not implemented yet!
-golden_path: determines the name of the golden path to use
=cut
sub new {
my ($class,@args) = @_;
my $self = $class->SUPER::new(@args);
return $self;
}
############################################################
sub input_id {
my ($self,$arg) = @_;
if (defined($arg)) {
$self->{_input_id} = $arg;
}
return $self->{_input_id};
}
############################################################
=head2 write_output
Title : write_output
Usage : $self->write_output
Function: Writes output data to db
Returns : array of exons (with start and end)
Args : none
=cut
sub write_output {
my($self,@genes) = @_;
# write genes out to a different database from the one we read genewise genes from.
my $db = $self->get_dbadaptor("GENEBUILD_DB") ;
# sort out analysis
my $analysis = $self->analysis;
unless ($analysis){
$self->throw("an analysis logic name must be defined in the command line");
}
my %contighash;
my $gene_adaptor = $db->get_GeneAdaptor;
# this now assummes that we are building on a single VC.
my $genebuilders = $self->get_genebuilders;
foreach my $contig ( keys %$genebuilders ){
my $vc = $genebuilders->{$contig}->query;
@genes = $genebuilders->{$contig}->final_genes;
return unless ($#genes >= 0);
my @newgenes;
foreach my $gene (@genes) {
my %trans_types;
$gene->analysis($analysis);
#$gene->type($GB_GENE_OUTPUT_BIOTYPE);
# poke the caches
my %s_pfhash;
foreach my $tran (@{$gene->get_all_Transcripts}) {
$trans_types{$tran->biotype} = 1;
#$tran->stable_id(undef);
my @tsf = @{$tran->get_all_supporting_features};
my @exons= @{$tran->get_all_Exons};
my $tln = $tran->translation;
$tln->{'stable_id'} = undef;
foreach my $exon (@exons) {
my @esf = @{$exon->get_all_supporting_features};
#$exon->{'stable_id'} = undef;
}
}
my @total_biotypes;
foreach my $t_biotype (keys %trans_types){
push (@total_biotypes, $t_biotype);
}
if (scalar(@total_biotypes)>1 || (scalar(@total_biotypes) == 1 &&
$total_biotypes[0] eq $MERGED_TRANSCRIPT_OUTPUT_TYPE)){
$gene->biotype($MERGED_GENE_OUTPUT_BIOTYPE);
}elsif(scalar(@total_biotypes) == 1 &&
$total_biotypes[0] eq $GB_ENSEMBL_INPUT_GENETYPE){
$gene->biotype($ENSEMBL_GENE_OUTPUT_BIOTYPE);
}else{
$gene->biotype($HAVANA_GENE_OUTPUT_BIOTYPE);
}
# store
eval {
$gene_adaptor->store($gene);
#print STDERR "wrote gene " . $gene->dbID . " to database ".
# $gene->adaptor->db->dbname."\n";
};
if( $@ ) {
warning("UNABLE TO WRITE GENE:\n$@");
}
}
}
return 1;
}
############################################################
=head2 fetch_input
Function: It fetches the slice or contig according to the input_id,
and it defines the database where the
previous annotations are stored and create a Bio::EnsEMBL::Pipeline::GeneBuilder
object for that genomic, input_id and db
Returns : nothing
Args : none
=cut
sub fetch_input {
my( $self) = @_;
$self->throw("No input id") unless defined($self->input_id);
$self->fetch_sequence();
my $discarded_db = $self->get_dbadaptor("DISCARDED_DB");
print "DISCARDED GENE DB: ", $discarded_db->dbname,"\n";
# database where the genebuild produced genes are
my $ensembl_db = $self->get_dbadaptor("PSEUDO_DB") ;
print "ENSEMBL DB : ", $ensembl_db->dbname,"\n";
my $havana_db = $self->get_dbadaptor("HAVANA_DB") ;
print "HAVANA DB : ", $havana_db->dbname,"\n";
my $ref_db = $self->get_dbadaptor("REFERENCE_DB");
print $self->input_id,"\n";
my $slice = $ref_db->get_SliceAdaptor->fetch_by_name($self->input_id);
print $slice,"\n";
$self->query($slice);
print "QUERY: ",$self->query->seq_region_name,"\n";
my $genebuilder = new Bio::EnsEMBL::Analysis::Runnable::HavanaAdder
(
'-slice' => $self->query,
'-input_id' => $self->input_id,
);
$genebuilder->discarded_db($discarded_db);
$genebuilder->ensembl_db($ensembl_db);
$genebuilder->havana_db($havana_db);
# store the object and the piece of genomic where it will run
$self->addgenebuilder($genebuilder,$self->query);
}
############################################################
sub addgenebuilder {
my ($self,$arg,$contig) = @_;
if (defined($arg) && defined($contig)) {
$self->{_genebuilder}{$contig->id} = $arg;
}
else {
$self->throw("Wrong number of inputs [$arg,$contig]\n");
}
}
############################################################
sub get_genebuilders {
my ($self) = @_;
return $self->{_genebuilder};
}
############################################################
sub run {
my ($self) = @_;
# get a hash, with keys = contig/slice and value = genebuilder object
my $genebuilders = $self->get_genebuilders;
my @genes;
foreach my $contig (keys %{ $genebuilders } ) {
my $query = $genebuilders->{$contig}->query;
#print(STDERR "GeneBuilding for $contig\n");
$genebuilders->{$contig}->build_Genes;
@genes = $genebuilders->{$contig}->final_genes;
}
$self->output( @genes );
}
############################################################
# override the evil RunnableDB output method:
sub output{
my ($self, @genes ) = @_;
unless ( $self->{_output} ){
$self->{_output} = [];
}
if (@genes){
push( @{$self->{_output}}, @genes );
}
return @{$self->{_output}};
}
############################################################
1;
]]>