Raw content of Bio::EnsEMBL::Analysis::RunnableDB::HaplotypeProjection
<![CDATA[#
# Cared for by EnsEMBL <ensembl-dev@ebi.ac.uk>
#
=pod
=head1 NAME
Bio::EnsEMBL::Analysis::RunnableDB::HaplotypeProjection
=head1 SYNOPSIS
my $obj = Bio::EnsEMBL::Analysis::RunnableDB::HaplotypeProjection->new(
-db => $db,
-input_id => $id,
);
$obj->fetch_input
$obj->run
my @newfeatures = $obj->output;
=head1 DESCRIPTION
This method is used to get project the genes annotated in the reference chromosome into the Haplotype regions.
=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::HaplotypeProjection;
use vars qw(@ISA);
use strict;
# Object preamble
use Bio::EnsEMBL::Analysis::RunnableDB;
use Bio::EnsEMBL::Analysis::Runnable::HaplotypeProjection;
use Bio::EnsEMBL::Analysis::RunnableDB::BaseGeneBuild;
use Bio::EnsEMBL::Utils::Exception qw(throw warning);
#use Bio::EnsEMBL::Analysis::Config::HaplotypeProjection qw (
# );
@ISA = qw(Bio::EnsEMBL::Analysis::RunnableDB::BaseGeneBuild);
############################################################
=head2 new
Usage : $self->new(-DBOBJ => $db,
-INPUT_ID => $id,
-SEQFETCHER => $sf,
-ANALYSIS => $analysis,
);
Function: creates a Bio::EnsEMBL::Analysis::RunnableDB::HaplotypeProjection object
Returns : A Bio::EnsEMBL::Analysis::RunnableDB::HaplotypeProjection object
Args : -dbobj: A Bio::EnsEMBL::DBSQL::DBAdaptor (required),
-input_id: Hap_pair input id (required),
-seqfetcher: A Sequence Fetcher Object,
-analysis: A Bio::EnsEMBL::Analysis (optional)
-extend: determines the extension of the virtual contig
note: not implemented yet!
-golden_path: determines the name of the golden path to use
=cut
sub new {
my ($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) = @_;
my $db = $self->get_dbadaptor("REFERENCE_DB") ;
# sort out analysis
my $analysis = $self->analysis;
unless ($analysis){
$self->throw("an analysis logic name must be defined in the command line");
}
my $gene_adaptor = $db->get_GeneAdaptor;
@genes = $self->output;
foreach my $gene (@genes) {
my $before = scalar(@{$gene->get_all_Transcripts});
unless (scalar(@{$gene->get_all_Transcripts})){
warning("GENE DOES NOT HAVE TRANSCRIPTS:\n");
next;
}
my %trans_types;
$gene->analysis($analysis);
$gene->{'stable_id'} = '';
# poke the caches
my %s_pfhash;
foreach my $tran (@{$gene->get_all_Transcripts}) {
$tran->{'stable_id'} = '';
my @tsf = @{$tran->get_all_supporting_features};
my @exons= @{$tran->get_all_Exons};
my $tln = $tran->translation;
if ($tln){
$tln->{'stable_id'} = '';
}
foreach my $exon (@exons) {
if ($tran->seq_region_name != $exon->seq_region_name){
print "NO EXON WAS NOT TRANSFORMED BEFORE STORAGE\n";
}else{
print "TRANSFORMED transcript: ",$tran->seq_region_name , " exon: ", $exon->seq_region_name,"\n";
}
$exon->{'stable_id'} = '';
my @esf = @{$exon->get_all_supporting_features};
}
}
# store
# eval {
if ($before > scalar(@{$gene->get_all_Transcripts})){
print "MISSING TRANSCRIPTS IN WRITTING\n";
}
$gene_adaptor->store($gene);
#print STDERR "wrote gene " . $gene->dbID . " to database ".$gene->adaptor->db->dbname."\n";
# };
# if( $@ ) {
# warning("UNABLE TO WRITE GENE:\n$@");
# }
}
my $genebuilders = $self->get_genebuilders;
foreach my $target (keys %{ $genebuilders } ) {
foreach my $query (keys %{$genebuilders->{$target}}){
$genebuilders->{$target}->{$query}->clean_tables;
}
}
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);
my $discarded_db = $self->get_dbadaptor("DISCARDED_DB");
print "DISCARDED GENE DB: ", $discarded_db->dbname,"\n";
# database where the genebuild produced genes are
my $ref_db = $self->get_dbadaptor("REFERENCE_DB");
print "ENSEMBL DB : ", $ref_db->dbname,"\n";
print $self->input_id,"\n";
my @input_id = split(/:/,$self->input_id);
my $hap_slice = $ref_db->get_SliceAdaptor->fetch_by_region($input_id[0],$input_id[2],$input_id[3],$input_id[4],1,$input_id[2]);
my $slice = $ref_db->get_SliceAdaptor->fetch_by_region($input_id[5],$input_id[7],$input_id[8],$input_id[9],1,$input_id[6]);
#$self->fetch_sequence();
print "HAP_slice: ",$hap_slice,"\n";
print "REF_slice: ",$slice,"\n";
$self->query($hap_slice);
$self->target($slice);
print "QUERY: ",$self->query->seq_region_name,"\n";
print "TARGET: ",$self->target->seq_region_name,"\n";
my $genebuilder = new Bio::EnsEMBL::Analysis::Runnable::HaplotypeProjection
(
'-hap_slice' => $self->query,
'-slice' => $self->target,
'-input_id' => $self->input_id,
);
$genebuilder->discarded_db($discarded_db);
$genebuilder->ensembl_db($ref_db);
# store the object and the piece of genomic where it will run
$self->addgenebuilder($genebuilder,$self->target,$self->query);
}
############################################################
sub addgenebuilder {
my ($self,$arg,$target,$query) = @_;
if (defined($arg) && defined($target) && defined($query)) {
$self->{_genebuilder}{$target->id}{$query->id} = $arg;
}
else {
$self->throw("Wrong number of inputs [$arg,$target,$query]\n");
}
}
############################################################
sub get_genebuilders {
my ($self) = @_;
return $self->{_genebuilder};
}
############################################################
sub run {
my ($self) = @_;
my @genes;
# get a hash, with keys = contig/slice and value = genebuilder object
my $genebuilders = $self->get_genebuilders;
foreach my $target (keys %{ $genebuilders } ) {
foreach my $query (keys %{$genebuilders->{$target}}){
@genes = $genebuilders->{$target}->{$query}->project_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 @{$self->{_output}};
}
############################################################
sub target {
my ($self,$slice) = @_;
if (defined($slice)) {
$self->{_target} = $slice;
}
return $self->{_target};
}
1;
]]>