From f55f4be417965ef25104337075dfdddeaf4963f2 Mon Sep 17 00:00:00 2001
From: Magali Ruffier <mr6@ebi.ac.uk>
Date: Thu, 28 Aug 2014 12:06:07 +0100
Subject: [PATCH] add not_dna flag to avoid storing sequence if it is not a dna
database
---
modules/Bio/EnsEMBL/DBSQL/SliceAdaptor.pm | 5 +++--
1 file changed, 3 insertions(+), 2 deletions(-)
diff --git a/modules/Bio/EnsEMBL/DBSQL/SliceAdaptor.pm b/modules/Bio/EnsEMBL/DBSQL/SliceAdaptor.pm
index d767823097..320f693289 100644
--- a/modules/Bio/EnsEMBL/DBSQL/SliceAdaptor.pm
+++ b/modules/Bio/EnsEMBL/DBSQL/SliceAdaptor.pm
@@ -1953,6 +1953,7 @@ sub store {
my $self = shift;
my $slice = shift;
my $seqref = shift;
+ my $not_dna = shift;
#
# Get all of the sanity checks out of the way before storing anything
@@ -1985,7 +1986,7 @@ sub store {
throw("Slice must have valid seq region name.");
}
- if($cs->is_sequence_level()) {
+ if($cs->is_sequence_level() && !$not_dna) {
if(!$seqref) {
throw("Must provide sequence for sequence level coord system.");
}
@@ -2022,7 +2023,7 @@ sub store {
throw("Database seq_region insertion failed.");
}
- if($cs->is_sequence_level()) {
+ if($cs->is_sequence_level() && !$not_dna) {
#store sequence if it was provided
my $seq_adaptor = $db->get_SequenceAdaptor();
$seq_adaptor->store($seq_region_id, $$seqref);
--
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