From a5f81269ef020e08384c9744c6dcab2ab23cbec0 Mon Sep 17 00:00:00 2001
From: Andrew Yates <ayates@ebi.ac.uk>
Date: Mon, 27 Feb 2012 16:22:08 +0000
Subject: [PATCH] We were way too generous with the _ cleanup. Applied to
numbers only
---
modules/Bio/EnsEMBL/DBSQL/SliceAdaptor.pm | 7 ++++++-
1 file changed, 6 insertions(+), 1 deletion(-)
diff --git a/modules/Bio/EnsEMBL/DBSQL/SliceAdaptor.pm b/modules/Bio/EnsEMBL/DBSQL/SliceAdaptor.pm
index 66dc9e76b4..359932d7f3 100644
--- a/modules/Bio/EnsEMBL/DBSQL/SliceAdaptor.pm
+++ b/modules/Bio/EnsEMBL/DBSQL/SliceAdaptor.pm
@@ -468,7 +468,7 @@ sub fetch_by_toplevel_location {
throw 'You must specify a location' if ! $location;
my $regex = qr/^(\w+) :? (\d+)? (?:-|[.]{2})? (\d+)?$/xms;
- $location =~ s/\s+|,|_//g; #cleanup any nomenclature like 1_000 or 1 000 or 1,000
+ my $number_seps_regex = qr/\s+|,|_/;
if(my ($seq_region_name, $start, $end) = $location =~ $regex) {
if(defined $start && $start < 1) {
@@ -480,6 +480,11 @@ sub fetch_by_toplevel_location {
}
my $coord_system_name = 'toplevel';
+
+ #cleanup any nomenclature like 1_000 or 1 000 or 1,000
+ $start =~ s/$number_seps_regex//g;
+ $end =~ s/$number_seps_regex//g;
+
my $slice = $self->fetch_by_region($coord_system_name, $seq_region_name, $start, $end, undef, undef, 0);
return unless $slice;
--
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