From aaf15a2193b1d4e58c71d0c0a6eff2d2ae09cee8 Mon Sep 17 00:00:00 2001
From: Magali Ruffier <mr6@ebi.ac.uk>
Date: Tue, 4 Aug 2015 11:33:05 +0100
Subject: [PATCH] ENSCORESW-1393: fetch by misc set method added
---
.../Bio/EnsEMBL/DBSQL/MiscFeatureAdaptor.pm | 84 +++++++++++++++++++
modules/Bio/EnsEMBL/DBSQL/SliceAdaptor.pm | 39 +++++++++
modules/t/miscFeatureAdaptor.t | 17 ++++
modules/t/sliceAdaptor.t | 9 ++
4 files changed, 149 insertions(+)
diff --git a/modules/Bio/EnsEMBL/DBSQL/MiscFeatureAdaptor.pm b/modules/Bio/EnsEMBL/DBSQL/MiscFeatureAdaptor.pm
index f1e89f369a..8357fc9878 100644
--- a/modules/Bio/EnsEMBL/DBSQL/MiscFeatureAdaptor.pm
+++ b/modules/Bio/EnsEMBL/DBSQL/MiscFeatureAdaptor.pm
@@ -226,6 +226,90 @@ sub fetch_all_by_attribute_type_value {
} ## end sub fetch_all_by_attribute_type_value
+=head2 fetch_by_attribute_set_value
+
+ Arg [1] : string $attrib_type_code
+ The code of the attribute type to fetch features for
+ Arg [2] : (optional) string $attrib_value
+ The value of the attribute to fetch features for
+ Arg [3] : (optional) string $misc_set
+ The name of the set to which the feature belongs
+ Example :
+ $feat = $mfa->fetch_by_attribute_set_value('clone', 'RP11-411G9', 'tilepath');
+ # Get the clone belonging to the tilepath
+ Description: Retrieves MiscFeatures which have a particular attribute.
+ If the attribute value argument is also provided only
+ features which have the attribute AND a particular value
+ are returned. The features are returned in their native
+ coordinate system (i.e. the coordinate system that they
+ are stored in).
+ Returntype : listref of Bio::EnsEMBL::MiscFeatures
+ Exceptions : throw if attrib_type code arg is not provided
+ Caller : general
+ Status : Stable
+
+=cut
+
+sub fetch_by_attribute_set_value {
+ my $self = shift;
+ my $attrib_type_code = shift;
+ my $attrib_value = shift;
+ my $misc_set = shift;
+
+ throw("Attrib type code argument is required.")
+ if ( !$attrib_type_code );
+
+ # Need to do 2 queries so that all of the ids come back with the
+ # features. The problem with adding attrib constraints to filter the
+ # misc_features which come back is that not all of the attributes will
+ # come back
+
+ my $sql = qq(
+ SELECT DISTINCT
+ ma.misc_feature_id
+ FROM misc_attrib ma,
+ attrib_type at,
+ misc_feature mf,
+ misc_feature_misc_set mfs,
+ misc_set ms,
+ seq_region sr,
+ coord_system cs
+ WHERE ma.attrib_type_id = at.attrib_type_id
+ AND at.code = ?
+ AND ma.misc_feature_id = mf.misc_feature_id
+ AND mf.misc_feature_id = mfs.misc_feature_id
+ AND mfs.misc_set_id = ms.misc_set_id
+ AND mf.seq_region_id = sr.seq_region_id
+ AND sr.coord_system_id = cs.coord_system_id
+ AND ma.value = ?
+ AND ms.code = ?
+ AND cs.species_id = ?);
+
+ my $sth = $self->prepare($sql);
+
+ $sth->bind_param( 1, $attrib_type_code, SQL_VARCHAR );
+ $sth->bind_param( 2, $attrib_value, SQL_VARCHAR );
+ $sth->bind_param( 3, $misc_set, SQL_VARCHAR );
+ $sth->bind_param( 4, $self->species_id(), SQL_INTEGER );
+
+ $sth->execute();
+
+ my ($id) = $sth->fetchrow_array();
+
+ if (!$id) {
+ return;
+ }
+
+ $sth->finish();
+
+ my $constraint = "mf.misc_feature_id = $id";
+
+ my ($result) = @{$self->generic_fetch($constraint)};
+
+ return $result;
+} ## end sub fetch_by_attribute_set_value
+
+
#_tables
#
# Arg [1] : none
diff --git a/modules/Bio/EnsEMBL/DBSQL/SliceAdaptor.pm b/modules/Bio/EnsEMBL/DBSQL/SliceAdaptor.pm
index 761c59c8cc..37c2ff4802 100644
--- a/modules/Bio/EnsEMBL/DBSQL/SliceAdaptor.pm
+++ b/modules/Bio/EnsEMBL/DBSQL/SliceAdaptor.pm
@@ -1838,6 +1838,45 @@ sub fetch_by_misc_feature_attribute {
return $self->fetch_by_Feature($feat, $size);
}
+=head2 fetch_by_misc_feature_set
+
+ Arg [1] : string $attribute_type
+ The code of the attribute type
+ Arg [2] : (optional) string $attribute_value
+ The value of the attribute to fetch by
+ Arg [3] : (optional) the name of the set
+ Arg [4] : (optional) int $size
+ The amount of flanking region around the misc feature desired.
+ Example : $slice = $sa->fetch_by_misc_feature_set('clone',
+ 'RP11-411G9'
+ 'tilepath');
+ Description: Fetches a slice around a MiscFeature with a particular
+ attribute type, value and set. If no value is specified then
+ the feature with the particular attribute is used.
+ A size can be specified to include flanking region
+ If no size is specified then 0 is used.
+ Returntype : Bio::EnsEMBL::Slice
+ Exceptions : Throw if no feature with the specified attribute type, value and set
+ exists in the database
+ Warning if multiple features with the specified attribute type, set
+ and value exist in the database.
+ Caller : webcode
+ Status : Stable
+
+=cut
+
+sub fetch_by_misc_feature_set {
+ my ($self, $attrib_type_code, $attrib_value, $misc_set, $size) = @_;
+
+ my $mfa = $self->db()->get_MiscFeatureAdaptor();
+
+ my $feat = $mfa->fetch_by_attribute_set_value($attrib_type_code,
+ $attrib_value,
+ $misc_set);
+
+ return $self->fetch_by_Feature($feat, $size);
+}
+
=head2 fetch_normalized_slice_projection
Arg [1] : Bio::EnsEMBL::Slice $slice
diff --git a/modules/t/miscFeatureAdaptor.t b/modules/t/miscFeatureAdaptor.t
index ec0732c226..3eeef570c4 100644
--- a/modules/t/miscFeatureAdaptor.t
+++ b/modules/t/miscFeatureAdaptor.t
@@ -94,6 +94,23 @@ $features = $mfa->fetch_all_by_attribute_type_value('embl_acc');
ok(@$features == 1);
print_features($features);
+#
+# Test fetch_by_attribute_set_value method
+#
+my $feature = $mfa->fetch_by_attribute_set_value('embl_acc', 'AL000001', 'ntctgs');
+debug('--- fetch_by_attribute_set_value ---');
+ok($feature->dbID() == 2);
+print_features([$feature]);
+
+$feature = $mfa->fetch_by_attribute_set_value('embl_acc', 'rubbish', 'ntctgs');
+ok(!defined $feature);
+
+$feature = $mfa->fetch_by_attribute_set_value('embl_acc', 'AL000001', 'rubbish');
+ok(!defined $feature);
+
+$feature = $mfa->fetch_by_attribute_set_value('rubbish', 'AL000001', 'ntctgs');
+ok(!defined $feature);
+
$multi->hide('core', 'misc_feature', 'misc_feature_misc_set', 'meta_coord',
'misc_attrib', 'attrib_type', 'misc_set');
diff --git a/modules/t/sliceAdaptor.t b/modules/t/sliceAdaptor.t
index c0daefa8e3..fc7e906139 100644
--- a/modules/t/sliceAdaptor.t
+++ b/modules/t/sliceAdaptor.t
@@ -169,6 +169,15 @@ ok($slice->seq_region_name eq '20');
ok($slice->start == 59707812 - $flanking);
ok($slice->end == 60855021 + $flanking);
+#
+# fetch_by_misc_feature_set
+#
+$slice = $slice_adaptor->fetch_by_misc_feature_set('superctg', 'NT_030871', 'tilepath');
+
+ok($slice->seq_region_name eq '20');
+ok($slice->start == 59707812);
+ok($slice->end == 60855021);
+
#
# normalized projected slice
--
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