Merge pull request #147 from Ensembl/ENSCORESW-1884

Updated fetch_all_by_Transcript method to optionally filter by featur…

modules/Bio/EnsEMBL/DBSQL/TranscriptSupportingFeatureAdaptor.pm

@@ -63,26 +63,34 @@ use vars qw(@ISA);
 
   Arg [1]    : Bio::EnsEMBL::Transcript $transcript 
                The transcript to fetch supporting features for
+  Arg [2]    : String (optional)
+               Feature type to filter upon (either 'dna_align_feature' or 'protein_align_feature')
   Example    : @sfs = @{$supporting_feat_adaptor->fetch_all_by_Transcript($transcript)};
+  			   @sfs = @{$supporting_feat_adaptor->fetch_all_by_Transcript($transcript, $feature_type)};	
   Description: Retrieves supporting features (evidence) for a given transcript. 
   Returntype : list of Bio::EnsEMBL::BaseAlignFeatures in the same coordinate
                system as the $transcript argument
   Exceptions : warning if $transcript is not in the database (i.e. dbID not defined)
-               throw if a retrieved supporting feature is of unknown type 
+               throw if a retrieved or requested supporting feature is of unknown type 
   Caller     : Bio::EnsEMBL::Transcript
   Status     : Stable
 
 =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
@@ -97,25 +105,36 @@ sub fetch_all_by_Transcript {
 
   my $feature;
   while(my ($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'){
-      $feature = $dna_adp->fetch_by_dbID($feature_id);
+   if ($type eq 'protein_align_feature') {
+        $feature = $prot_adp-> fetch_by_dbID($feature_id);
+    }
+    elsif($type eq 'dna_align_feature') {
+        $feature = $dna_adp-> fetch_by_dbID($feature_id);
     } else {
-      warning("Unknown feature type [$type]\n");
+        warning("Unknown feature type [$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/intronSupportingEvidence.t

@@ -244,7 +244,7 @@ $assert_ise_vs_intron->(21719, 30326248, 30327734, -1);
   
   $db->restore('core');
   note 'All tables restored';
-  $assert_table_counts->(26,173,0,0);
+  $assert_table_counts->(27,173,0,0);
 }
 
 ############# Feature transformation (asserting what occurs when we try to project to something else)

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

@@ -24,3 +24,4 @@
 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
+21742	18276	1282	317101	20000	21000	1	\N	ensembl	protein_coding	NOVEL	weird	1	21742	ENST00000222222	1	2016-08-15 14:00:00	2016-08-15 17:00:00
\ No newline at end of file

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

+21742	dna_align_feature	1449321
+21742	dna_align_feature	11290104
+21742	protein_align_feature	813252
+21742	protein_align_feature	813424
+21742	protein_align_feature	813184
\ No newline at end of file

modules/t/transcript.t

@@ -270,13 +270,13 @@ is($tr->display_id(), $tr->stable_id(), 'Transcript stable id and display id are
 #
 note("Test fetch_all_by_biotype");
 my @transcripts = @{$ta->fetch_all_by_biotype('protein_coding')};
-is(@transcripts, 26, 'Fetching all protein coding transcript');
+is(@transcripts, 27, 'Fetching all protein coding transcript');
 my $transcriptCount = $ta->count_all_by_biotype('protein_coding');
-is($transcriptCount, 26, 'Counting all protein coding');
+is($transcriptCount, 27, 'Counting all protein coding');
 @transcripts = @{$ta->fetch_all_by_biotype(['protein_coding','pseudogene'])};
-is(@transcripts, 26, 'Got 25 transcript');
+is(@transcripts, 27, 'Got 27 transcript');
 $transcriptCount = $ta->count_all_by_biotype(['protein_coding', 'pseudogene']);
-is($transcriptCount, 26, 'Count by biotype is correct');
+is($transcriptCount, 27, 'Count by biotype is correct');
 
 
 #
@@ -293,9 +293,9 @@ is(@transcripts, $transcriptCount, "Counted as many transcripts as were fetched
 note("Test fetch_all_by_source");
 @transcripts = @{$ta->fetch_all_by_source('ensembl')};
 note "Got ".scalar(@transcripts)." ensembl transcripts\n";
-is(23, scalar(@transcripts));
+is(24, scalar(@transcripts));
 $transcriptCount = $ta->count_all_by_source('ensembl');
-is(23, $transcriptCount);
+is(24, $transcriptCount);
 @transcripts = @{$ta->fetch_all_by_source(['havana','vega'])};
 note "Got ".scalar(@transcripts)." (havana, vega) transcripts\n";
 is(3, scalar(@transcripts));
@@ -307,7 +307,7 @@ is(3, $transcriptCount);
 #
 note("Test fetch_all");
 @transcripts = @{ $ta->fetch_all() };
-is(26, scalar(@transcripts), "Got 26 transcripts");
+is(27, scalar(@transcripts), "Got 27 transcripts");
 
 #
 # test TranscriptAdaptor::fetch_all_by_GOTerm

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::Exception;
+use Test::Warnings;
+use Bio::EnsEMBL::Test::MultiTestDB;
+
+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 = $ta->fetch_by_stable_id( "ENST00000222222" );
+ok($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");
+}
+
+#Test exceptions with unknown feature_types
+dies_ok { $tsf_adaptor->fetch_all_by_Transcript($tr, "unknown_feature_type") } 'fetch_all_by_Transcript dies with unknown feature_type';
+throws_ok {$tsf_adaptor->fetch_all_by_Transcript($tr, "unknown_feature_type") } qr/feature type must be dna_align_feature or protein_align_feature/, 
+           'feature type must be dna_align_feature or protein_align_feature';
+
+
+done_testing();