From 7cf91f59f5ecf326dc0f5d0bce50f8c1d57be3f1 Mon Sep 17 00:00:00 2001
From: Andrew Yates <ayates@ebi.ac.uk>
Date: Fri, 28 Sep 2012 12:54:20 +0000
Subject: [PATCH] [ENSCORESW-264] Can now handle odd sequence region names
involving . - _ now. The supercontig names seemed to be a good source of
these
---
modules/Bio/EnsEMBL/DBSQL/SliceAdaptor.pm | 2 +-
modules/t/sliceAdaptor.t | 9 +++++++++
2 files changed, 10 insertions(+), 1 deletion(-)
diff --git a/modules/Bio/EnsEMBL/DBSQL/SliceAdaptor.pm b/modules/Bio/EnsEMBL/DBSQL/SliceAdaptor.pm
index 8faa1c6306..5f2dc2227c 100644
--- a/modules/Bio/EnsEMBL/DBSQL/SliceAdaptor.pm
+++ b/modules/Bio/EnsEMBL/DBSQL/SliceAdaptor.pm
@@ -531,7 +531,7 @@ sub parse_location_to_values {
my $number_regex = qr/[0-9,_ E]+/xms;
my $strand_regex = qr/[+-1]|-1/xms;
- my $regex = qr/^(\w+) \s* :? \s* ($number_regex)? $separator_regex ($number_regex)? $separator_regex ($strand_regex)? $/xms;
+ my $regex = qr/^((?:\w|\.|_|-)+) \s* :? \s* ($number_regex)? $separator_regex ($number_regex)? $separator_regex ($strand_regex)? $/xms;
my ($seq_region_name, $start, $end, $strand);
if(($seq_region_name, $start, $end, $strand) = $location =~ $regex) {
diff --git a/modules/t/sliceAdaptor.t b/modules/t/sliceAdaptor.t
index 92d2f6ecc7..05061da103 100644
--- a/modules/t/sliceAdaptor.t
+++ b/modules/t/sliceAdaptor.t
@@ -482,6 +482,15 @@ dies_ok { $slice_adaptor->fetch_by_toplevel_location('1:1_000_000_000..100', 1);
ok(!defined $slice_adaptor->fetch_by_toplevel_location('wibble', 1), 'Checking with a bogus region returns undef');
ok(!defined $slice_adaptor->fetch_by_toplevel_location('1:-100--50', 1), 'Checking with a bogus region with negative coords returns undef');
+{
+ #Non standard name check
+ my ($name, $start, $end, $strand) = $slice_adaptor->parse_location_to_values('GL21446.1');
+ is($name, 'GL21446.1', 'Name parses out');
+ ok(!defined $start, 'Start is undefined');
+ ok(!defined $end, 'End is undefined');
+ ok(!defined $strand, 'Strand is undefined');
+}
+
sub test_toplevel_location {
my ($location, $cs_name, $seq_region_name, $start, $end, $strand) = @_;
$strand ||= 1;
--
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