Enscoresw 1481

Created by: premanand17

lib/EnsEMBL/REST/Controller/Map.pm

@@ -44,10 +44,15 @@ sub cdna_GET {  }
 sub cdna: Chained('/') Args(2) PathPart('map/cdna') ActionClass('REST') {
   my ($self, $c, $id, $region) = @_;
   $c->stash()->{id} = $id;
+  
   my $transcript = $c->model('Lookup')->find_object_by_stable_id($id);
   my $ref = ref($transcript);
   $c->go('ReturnError', 'custom', ["Expected a Bio::EnsEMBL::Transcript object but got a $ref object back. Check your ID"]) if $ref ne 'Bio::EnsEMBL::Transcript';
-  my $mappings = $self->_map_transcript_coords($c, $transcript, $region, 'cdna2genomic');
+  
+  #optional parameter to include original region coordinate mappings, cdna coordinates in this case
+  my $include_original_region = $c->request()->param('include_original_region') || 0;
+  my $mappings = $self->_map_transcript_coords($c, $transcript, $region, 'cdna2genomic', 'cdna', $include_original_region);
+  
   $self->status_ok( $c, entity => { mappings => $mappings } );
 }
 
@@ -59,19 +64,24 @@ sub cds: Chained('/') Args(2) PathPart('map/cds') ActionClass('REST') {
   my $transcript = $c->model('Lookup')->find_object_by_stable_id($id);
   my $ref = ref($transcript);
   $c->go('ReturnError', 'custom', ["Expected a Bio::EnsEMBL::Transcript object but got a $ref object back. Check your ID"]) if $ref ne 'Bio::EnsEMBL::Transcript';
-  my $mappings = $self->_map_transcript_coords($c, $transcript, $region, 'cds2genomic');
+  
+  #optional parameter to include original region coordinate mappings, cds coordinates in this case  
+  my $include_original_region = $c->request()->param('include_original_region') || 0;
+  my $mappings = $self->_map_transcript_coords($c, $transcript, $region, 'cds2genomic','cds', $include_original_region);
+
   $self->status_ok( $c, entity => { mappings => $mappings } );
 }
 
 sub _map_transcript_coords {
-  my ($self, $c, $transcript, $region, $method) = @_;
+  my ($self, $c, $transcript, $region, $method,$type, $include_original_region) = @_;
   my ($start, $end) = $region =~ /^(\d+) (?:\.{2} | -) (\d+)$/xms;
+  
   if(!$start) {
     $c->go('ReturnError', 'custom', ["Region did not correctly parse. Please check documentation"]);
   }
   $start ||= $end;
-  my $mapped = [$transcript->get_TranscriptMapper()->$method($start, $end)];
-  return $self->map_mappings($c, $mapped, $transcript);
+  my $mapped = [$transcript->get_TranscriptMapper()->$method($start, $end, $include_original_region)];
+  return $self->map_mappings($c, $mapped, $transcript, $type, $include_original_region);
 }
 
 ## Create a slice object based on the location string provided
@@ -154,34 +164,78 @@ sub map_data : Private {
 }
 
 sub map_mappings {
-  my ($self, $c, $mapped, $transcript) = @_;
+  my ($self, $c, $mapped, $transcript,$type,$include_original_region) = @_;
+  
   my @r;
   my $seq_region_name = $transcript->seq_region_name();
   my $coord_system = $transcript->coord_system_name();
   my $assembly_name = $transcript->slice->coord_system->version();
+  
   foreach my $m (@{$mapped}) {
-    my $strand = 0;
-    my $gap = 0;
-    if($m->isa('Bio::EnsEMBL::Mapper::Gap')) {
-      $gap = 1;
+    if($include_original_region){
+      my $paired_mapping = map_mappings_include_original_region($m, $seq_region_name, $coord_system, $assembly_name, $type);
+      push(@r, $paired_mapping);
+    }else{
+      my $m_mapped_mappings = _get_mapped_coords($m, $seq_region_name, $coord_system, $assembly_name);
+      push(@r,$m_mapped_mappings);
     }
-    else {
-      $strand = $m->strand();
-    }
-    push(@r, {
-      start => $m->start() * 1,
-      end => $m->end() * 1,
-      strand => $strand,
-      rank => $m->rank(),
-      gap => $gap,
-      seq_region_name => $seq_region_name,
-      coord_system => $coord_system,
-      assembly_name => $assembly_name,
-    });
+   	
   }
   return \@r;
+  
 }
 
+sub map_mappings_include_original_region{
+	
+  my ($m, $seq_region_name, $coord_system, $assembly_name, $type) = @_;
+	
+  my $m_mapped = $m->{'mapped'};
+  my $m_ori = $m->{'original'};
+  	
+  my $m_mapped_mappings = {};
+  my $m_ori_mappings = {};
+	
+  if($m->{'mapped'}){
+    $m_mapped_mappings = _get_mapped_coords($m->{'mapped'}, $seq_region_name, $coord_system, $assembly_name);
+  }
+	
+  #seq_region_name and assembly_name is not applicable for the original region and type (eg: cds or cdna) is assigned to the coordinate_system
+  if($m->{'original'}){
+  	$coord_system = $type;
+	$m_ori_mappings = _get_mapped_coords($m->{'original'}, undef, $coord_system, undef);
+   }
+	
+  my $paired_mappings = { 'original' => $m_ori_mappings, 'mapped' => $m_mapped_mappings };
+  return $paired_mappings;
+
+}
+
+
+sub _get_mapped_coords {
+  my ($m, $seq_region_name, $coord_system, $assembly_name) = @_;
+  my $strand = 0;
+  my $gap = 0;
+  if($m->isa('Bio::EnsEMBL::Mapper::Gap')) {
+    $gap = 1;
+  }
+  else {
+    $strand = $m->strand();
+  }
+  my $mapped_coords =  {
+    start => $m->start() * 1,
+    end => $m->end() * 1,
+    strand => $strand,
+    rank => $m->rank(),
+    gap => $gap,
+    };
+    
+  $mapped_coords->{'seq_region_name'} = $seq_region_name if defined($seq_region_name);
+  $mapped_coords->{'coord_system'} = $coord_system if defined($coord_system);
+  $mapped_coords->{'assembly_name'} = $assembly_name if defined($assembly_name);
+  return $mapped_coords; 
+}
+
+
 __PACKAGE__->meta->make_immutable;
 
 1;