Raw content of Bio::EnsEMBL::Analysis::RunnableDB::HaplotypeMapper
<![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::HaplotypeMapper;
use vars qw(@ISA);
use strict;
# Object preamble
use Bio::EnsEMBL::Analysis::RunnableDB;
use Bio::EnsEMBL::Analysis::Runnable::HaplotypeMapper;
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,@mappings) = @_;
#my $db = $self->get_dbadaptor("REFERENCE_DB") ;
@mappings = $self->output;
print "REACH TEST 2 position\n";
print "now I have mappings: ",@mappings,"\n";
my $genebuilders = $self->get_genebuilders;
foreach my $target (keys %{ $genebuilders } ) {
foreach my $query (keys %{$genebuilders->{$target}}){
$genebuilders->{$target}->{$query}->load_tables(@mappings);
}
}
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[1]);
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::HaplotypeMapper
(
'-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 @mapping;
# get a hash, with keys = contig/slice and value = genebuilder object
my $genebuilders = $self->get_genebuilders;
#my @genes;
foreach my $target (keys %{ $genebuilders } ) {
foreach my $query (keys %{$genebuilders->{$target}}){
$genebuilders->{$target}->{$query}->create_alignment;
$genebuilders->{$target}->{$query}->filter_alignment;
@mapping = $genebuilders->{$target}->{$query}->make_map_regions;
print "I got mappings: ",@mapping,"\n";
}
}
$self->output( @mapping );
}
############################################################
# override the evil RunnableDB output method:
sub output{
my ($self, @output ) = @_;
unless ( $self->{_output} ){
$self->{_output} = [];
}
if (@output){
push( @{$self->{_output}}, @output );
}
return @{$self->{_output}};
}
############################################################
sub target {
my ($self,$slice) = @_;
if (defined($slice)) {
$self->{_target} = $slice;
}
return $self->{_target};
}
1;
]]>