Updated fetch_all_by_Transcript method to optionally filter by feature_type...

Updated fetch_all_by_Transcript method to optionally filter by feature_type (dna_align or protein_align features)

modules/Bio/EnsEMBL/DBSQL/TranscriptSupportingFeatureAdaptor.pm

@@ -75,14 +75,19 @@ use vars qw(@ISA);
 =cut
 
 sub fetch_all_by_Transcript {
-  my ( $self, $transcript )  = @_;
+  my ( $self, $transcript, $feature_type )  = @_;
 
   my $out = [];
+  my $out_feature_type = {};
 
   unless($transcript->dbID) {
     warning("Cannot retrieve evidence for transcript without dbID");
     return [];
   }
+  
+  if(defined $feature_type && $feature_type !~ /(dna)|(protein)_align_feature/) {
+    throw("feature type must be dna_align_feature or protein_align_feature");
+  }
 
   my $sth = $self->prepare("SELECT tsf.feature_type, tsf.feature_id
                             FROM   transcript_supporting_feature tsf
@@ -99,23 +104,34 @@ sub fetch_all_by_Transcript {
   while(my ($type, $feature_id) = $sth->fetchrow){
     if($type eq 'protein_align_feature'){
       $feature = $prot_adp->fetch_by_dbID($feature_id);
-    } elsif($type eq 'dna_align_feature'){
+     } elsif($type eq 'dna_align_feature'){
       $feature = $dna_adp->fetch_by_dbID($feature_id);
     } else {
       warning("Unknown feature type [$type]\n");
     }
-
+    
     if(!$feature) {
       warning("Supporting feature $type $feature_id does not exist in DB");
     } else {
       my $new_feature = $feature->transfer($transcript->slice());
-      push @$out, $new_feature if( $new_feature );
+ 
+      push @{$out_feature_type->{$type}}, $new_feature if ($new_feature);
     }
   }
-
-  $sth->finish();
-
-  return $out;
+	  $sth->finish();
+
+   
+   if(defined $feature_type){
+   	return $out_feature_type->{$feature_type};
+   }else{
+   
+  	while(my ($feature_type, $new_features) = each(%$out_feature_type)){
+  		push @$out, @{$new_features};
+  	}
+  	
+  }
+  
+   return $out;
 }
 
 

modules/t/test-genome-DBs/homo_sapiens/core/transcript.txt

@@ -23,4 +23,4 @@
 21738	18273	1282	469283	31166507	31196939	1	97759	ensembl	protein_coding	KNOWN	\N	1	21738	ENST00000217347	1	2004-12-06 12:00:00	2004-12-06 12:00:00
 21739	18274	1282	469283	31210077	31225346	1	0	ensembl	protein_coding	NOVEL	\N	1	21739	ENST00000300425	1	2004-12-06 12:00:00	2004-12-06 12:00:00
 21740	18275	1282	965899	10060	10405	1	0	ensembl	protein_coding	NOVEL	\N	1	21740	ENST00000355555	1	2004-12-06 12:00:00	2004-12-06 12:00:00
-21741	18276	1282	469290	1	150	1	\N	ensembl	protein_coding	NOVEL	weird	1	21741	ENST00000111111	1	2014-12-11 14:00:00	2014-12-11 14:00:00
+21741	18276	1282	317101	20000	21000	1	\N	ensembl	protein_coding	NOVEL	weird	1	21741	ENST00000111111	1	2014-12-11 14:00:00	2014-12-11 14:00:00
\ No newline at end of file

modules/t/test-genome-DBs/homo_sapiens/core/transcript_supporting_feature.txt

+21741	dna_align_feature	1449321
+21741	dna_align_feature	11290104
+21741	protein_align_feature	813252
+21741	protein_align_feature	813424
+21741	protein_align_feature	813184
\ No newline at end of file

modules/t/transcriptSupportingFeatureAdaptor.t

+# Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
+# Copyright [2016] EMBL-European Bioinformatics Institute
+# 
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+# 
+#      http://www.apache.org/licenses/LICENSE-2.0
+# 
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+use strict;
+use Test::More;
+use Test::Warnings;
+use Bio::EnsEMBL::Test::MultiTestDB;
+
+use Bio::EnsEMBL::DnaDnaAlignFeature;
+use Bio::EnsEMBL::Test::TestUtils;
+use Data::Dumper;
+
+our $verbose = 0;
+
+my $multi = Bio::EnsEMBL::Test::MultiTestDB->new();
+ok(1);
+
+
+#Fetch Transcript by stable_id and ensure it has a slice
+my $db = $multi->get_DBAdaptor('core');
+my $ta = $db->get_TranscriptAdaptor();
+my $tr = $ta->fetch_by_stable_id( "ENST00000111111" );
+ok($tr, "Fetched the Transcript by stable_id");
+ok($tr->slice(), "Transcript has slice");
+
+
+#Get TranscriptSupportingFeatureAdaptor
+my $tsf_adaptor = $db->get_TranscriptSupportingFeatureAdaptor;
+
+
+#Fetch all transcript supporting features
+my $supporting_features = $tsf_adaptor->fetch_all_by_Transcript($tr);
+isa_ok( $supporting_features, 'ARRAY' );
+ok(5 == scalar(@$supporting_features), "Fetched all transcript supporting features");
+
+
+#Fetch all transcript supporting features of type 'protein_align_feature'
+my $supporting_features_proteins = $tsf_adaptor->fetch_all_by_Transcript($tr, "protein_align_feature");
+isa_ok( $supporting_features_proteins, 'ARRAY' );
+ok(3 == scalar(@$supporting_features_proteins), "Fetched all transcript supporting features (protein_align_features) ");
+
+
+foreach my $supporting_feature(@$supporting_features_proteins){
+	ok('Bio::EnsEMBL::DnaPepAlignFeature' eq ref $supporting_feature, "Got back the right ref type: Bio::EnsEMBL::DnaPepAlignFeature");
+}
+
+#Fetch all transcript supporting features of type 'dna_align_feature'
+my $supporting_features_dnas = $tsf_adaptor->fetch_all_by_Transcript($tr, "dna_align_feature");
+isa_ok( $supporting_features_dnas, 'ARRAY' );
+ok(2 == scalar(@$supporting_features_dnas), "Fetched all transcript supporting features (dna_align_features) ");
+
+
+foreach my $supporting_feature(@$supporting_features_dnas){
+	ok('Bio::EnsEMBL::DnaDnaAlignFeature' eq ref $supporting_feature, "Got back the right ref type: Bio::EnsEMBL::DnaDnaAlignFeature");
+}
+
+
+done_testing();