From ca5289e0bdae0561f57cbcd20b8ff3c060b55ff1 Mon Sep 17 00:00:00 2001
From: Chris Fields <cjfields@bioperl.org>
Date: Thu, 7 Apr 2011 14:25:00 -0500
Subject: [PATCH] comment out overzealous error checking, which caused some
 EMBL files to not parse, fixes #3158

---
 Bio/SeqIO/embl.pm | 9 ++++++---
 1 file changed, 6 insertions(+), 3 deletions(-)

diff --git a/Bio/SeqIO/embl.pm b/Bio/SeqIO/embl.pm
index cb1531b4f..a89ec4cda 100644
--- a/Bio/SeqIO/embl.pm
+++ b/Bio/SeqIO/embl.pm
@@ -1171,9 +1171,12 @@ sub _read_EMBL_Species {
     foreach my $i (0..$#class) {
         my $name = $class[$i];
         $names{$name}++;
-        if ($names{$name} > 1 && $name ne $class[$i - 1]) {
-            $self->throw("$acc seems to have an invalid species classification.");
-        }
+        # this code breaks examples like: Xenopus (Silurana) tropicalis
+        # commenting out, see bug 3158
+        
+        #if ($names{$name} > 1 && ($name ne $class[$i - 1])) {
+        #    $self->warn("$acc seems to have an invalid species classification:$name ne $class[$i - 1]");
+        #}
     }
     my $make = Bio::Species->new();
     $make->scientific_name($sci_name);
-- 
2.11.4.GIT