From 2b31bf771192c996cd57889d1cfea9320366a535 Mon Sep 17 00:00:00 2001
From: Dan Sheppard <ds23@sanger.ac.uk>
Date: Mon, 9 Jan 2012 12:32:33 +0000
Subject: [PATCH] Fix erroneous warning of unmarked selenoprotein when marked
selenoprotein also has unrelated remark beginning with string "selenocysteine
". Found to be the case in OTTDART00000030742 for Dec 19th 2011 Havana
data-freeze of Zebra fish.
---
.../Bio/EnsEMBL/Utils/VegaCuration/Translation.pm | 13 ++++++++-----
1 file changed, 8 insertions(+), 5 deletions(-)
diff --git a/modules/Bio/EnsEMBL/Utils/VegaCuration/Translation.pm b/modules/Bio/EnsEMBL/Utils/VegaCuration/Translation.pm
index ece2a5e2ee..3ff9f7919b 100644
--- a/modules/Bio/EnsEMBL/Utils/VegaCuration/Translation.pm
+++ b/modules/Bio/EnsEMBL/Utils/VegaCuration/Translation.pm
@@ -339,7 +339,13 @@ sub check_for_stops {
$annot_stops=$1;
}
elsif ($text =~ /^$alabel2(.*)/) {
- $annot_stops=$1;
+ my $maybe = $1;
+ if($maybe =~ /^\s*\d+(\s+\d+)*\s*$/) {
+ $annot_stops=$maybe;
+ } else {
+ $log_object->_save_log('log', '', $gene->stable_id, '', $tsi, '', "Maybe annotated stop in incorrect format, maybe just a remark that happens to begin '$alabel2'".
+ " -- might need to investigate: '$alabel2$maybe' [$mod_date]");
+ }
}
}
}
@@ -349,11 +355,8 @@ sub check_for_stops {
if ($annot_stops){
my $i = 0;
foreach my $offset (split(/\s+/, $annot_stops)) {
- if ($offset !~ /^\d+$/) {
- $log_object->_save_log('log', '', $gene->stable_id, '', $tsi, '', "Annotated stop for transcript tsi ($tname) is not an integer \"$offset\" - might need to investigate [$mod_date]");
- }
#OK if it matches a known stop
- elsif (
+ if (
defined($found_stops[$i]) && defined($found_stops[$i]->[1]) && ($found_stops[$i]->[1] == $offset)) {
push @annotated_stops, $offset;
}
--
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