diff --git a/modules/Bio/EnsEMBL/DBSQL/TranscriptSupportingFeatureAdaptor.pm b/modules/Bio/EnsEMBL/DBSQL/TranscriptSupportingFeatureAdaptor.pm
index 0ab9c3dbcf3c9a0137b33d622a3e194525d45763..95569f01aaa1e7d5e8dfea1c369b47850671de9a 100644
--- a/modules/Bio/EnsEMBL/DBSQL/TranscriptSupportingFeatureAdaptor.pm
+++ b/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;
}
diff --git a/modules/t/intronSupportingEvidence.t b/modules/t/intronSupportingEvidence.t
index 7c9e036d18aa006b47c9a58f6e7397eccd6dcdad..92858ebf006dff494f726728f3487dd6013147fc 100644
--- a/modules/t/intronSupportingEvidence.t
+++ b/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);
+ $assert_table_counts->(27,173,0,0);
}
############# Feature transformation (asserting what occurs when we try to project to something else)
diff --git a/modules/t/test-genome-DBs/homo_sapiens/core/transcript.txt b/modules/t/test-genome-DBs/homo_sapiens/core/transcript.txt
index b590a5f7226ffb4daead1a3f727c0f2dd201bd23..6b93997130dfbee3c5ffb02e70c339f4fb08cbf6 100644
--- a/modules/t/test-genome-DBs/homo_sapiens/core/transcript.txt
+++ b/modules/t/test-genome-DBs/homo_sapiens/core/transcript.txt
@@ -24,3 +24,4 @@
21739 18274 1282 469283 31210077 31225346 1 0 ensembl protein_coding NOVEL \N 1 21739 ENST00000300425 1 2004-12-06 12:00:00 2004-12-06 12:00:00
21740 18275 1282 965899 10060 10405 1 0 ensembl protein_coding NOVEL \N 1 21740 ENST00000355555 1 2004-12-06 12:00:00 2004-12-06 12:00:00
21741 18276 1282 469290 1 150 1 \N ensembl protein_coding NOVEL weird 1 21741 ENST00000111111 1 2014-12-11 14:00:00 2014-12-11 14:00:00
+21742 18276 1282 317101 20000 21000 1 \N ensembl protein_coding NOVEL weird 1 21742 ENST00000222222 1 2016-08-15 14:00:00 2016-08-15 17:00:00
\ No newline at end of file
diff --git a/modules/t/test-genome-DBs/homo_sapiens/core/transcript_supporting_feature.txt b/modules/t/test-genome-DBs/homo_sapiens/core/transcript_supporting_feature.txt
new file mode 100644
index 0000000000000000000000000000000000000000..ba54133daf016314c839cb1078a694c1484f0f5a
--- /dev/null
+++ b/modules/t/test-genome-DBs/homo_sapiens/core/transcript_supporting_feature.txt
@@ -0,0 +1,5 @@
+21742 dna_align_feature 1449321
+21742 dna_align_feature 11290104
+21742 protein_align_feature 813252
+21742 protein_align_feature 813424
+21742 protein_align_feature 813184
\ No newline at end of file
diff --git a/modules/t/transcript.t b/modules/t/transcript.t
index 3e267f9f57f68609f9829294a256da28d45a4ea5..7d5bc6c0327bae0584cbebebd0f14d8e7341c9a3 100644
--- a/modules/t/transcript.t
+++ b/modules/t/transcript.t
@@ -270,13 +270,13 @@ is($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
diff --git a/modules/t/transcriptSupportingFeatureAdaptor.t b/modules/t/transcriptSupportingFeatureAdaptor.t
new file mode 100644
index 0000000000000000000000000000000000000000..9292f39d16d5104cd69cd2a44ae4fe00b4d2abb5
--- /dev/null
+++ b/modules/t/transcriptSupportingFeatureAdaptor.t
@@ -0,0 +1,72 @@
+# 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();