From 20ae012021f00da1b007917775bde1875b78b977 Mon Sep 17 00:00:00 2001
From: Patrick Meidl <pm2@sanger.ac.uk>
Date: Fri, 28 Jul 2006 11:23:14 +0000
Subject: [PATCH] added list_seq_region_ids()
---
.../Bio/EnsEMBL/DBSQL/BaseFeatureAdaptor.pm | 34 ++++++++++++++++++-
modules/Bio/EnsEMBL/DBSQL/GeneAdaptor.pm | 7 ++++
2 files changed, 40 insertions(+), 1 deletion(-)
diff --git a/modules/Bio/EnsEMBL/DBSQL/BaseFeatureAdaptor.pm b/modules/Bio/EnsEMBL/DBSQL/BaseFeatureAdaptor.pm
index 261bd60e56..2f24b32baa 100644
--- a/modules/Bio/EnsEMBL/DBSQL/BaseFeatureAdaptor.pm
+++ b/modules/Bio/EnsEMBL/DBSQL/BaseFeatureAdaptor.pm
@@ -85,6 +85,11 @@ sub new {
which are on the Slice defined by $slice. If $logic_name is
defined only features with an analysis of type $logic_name
will be returned.
+ NOTE: only features that are entirely on the slice's seq_region
+ will be returned (i.e. if they hang off the start/end of a
+ seq_region they will be discarded). Features can extend over the
+ slice boundaries though (in cases where you have a slice that
+ doesn't span the whole seq_region).
Returntype : listref of Bio::EnsEMBL::SeqFeatures in Slice coordinates
Exceptions : none
Caller : Bio::EnsEMBL::Slice
@@ -564,7 +569,7 @@ sub _remap {
$strand = $f->strand();
$seq_region = $f->slice->seq_region_name();
}
-
+
# maps to region outside desired area
next if ($start > $slice_end) || ($end < $slice_start) ||
($slice_seq_region ne $seq_region);
@@ -761,6 +766,33 @@ sub _max_feature_length {
}
+#
+# Lists all seq_region_ids that a particular feature type is found on.
+# Useful e.g. for finding out which seq_regions have genes.
+# Returns a listref of seq_region_ids.
+#
+sub _list_seq_region_ids {
+ my ($self, $table) = @_;
+
+ my @out;
+
+ my $sql = qq(
+ SELECT distinct(sr.seq_region_id)
+ FROM seq_region sr, $table a
+ WHERE sr.seq_region_id = a.seq_region_id
+ );
+ my $sth = $self->prepare($sql);
+ $sth->execute;
+
+ while (my ($id) = $sth->fetchrow) {
+ push(@out, $id);
+ }
+
+ $sth->finish;
+
+ return \@out;
+}
+
=head1 DEPRECATED METHODS
diff --git a/modules/Bio/EnsEMBL/DBSQL/GeneAdaptor.pm b/modules/Bio/EnsEMBL/DBSQL/GeneAdaptor.pm
index d9b73fb383..93a7fc6102 100644
--- a/modules/Bio/EnsEMBL/DBSQL/GeneAdaptor.pm
+++ b/modules/Bio/EnsEMBL/DBSQL/GeneAdaptor.pm
@@ -145,6 +145,13 @@ sub list_stable_ids {
}
+sub list_seq_region_ids {
+ my $self = shift;
+
+ return $self->_list_seq_region_ids('gene');
+}
+
+
=head2 fetch_by_display_label
Arg [1] : String $label - display label of gene to fetch
--
GitLab