From c2b5775f84134ef767cb55e376ff747d8413f5db Mon Sep 17 00:00:00 2001
From: Steve Trevanion <st3@sanger.ac.uk>
Date: Fri, 10 May 2013 16:36:10 +0000
Subject: [PATCH] skip transcripts that have a ribosomal_frameshift as well as
those having the specific '_rib_frameshift' attribute
---
modules/Bio/EnsEMBL/Utils/VegaCuration/Translation.pm | 6 ++++++
1 file changed, 6 insertions(+)
diff --git a/modules/Bio/EnsEMBL/Utils/VegaCuration/Translation.pm b/modules/Bio/EnsEMBL/Utils/VegaCuration/Translation.pm
index 2a3dada6c9..31d958276e 100644
--- a/modules/Bio/EnsEMBL/Utils/VegaCuration/Translation.pm
+++ b/modules/Bio/EnsEMBL/Utils/VegaCuration/Translation.pm
@@ -255,6 +255,12 @@ sub check_for_stops {
next TRANS;
}
}
+ foreach my $attrib (@{$trans->get_all_Attributes('hidden_remark')}) {
+ if ($attrib->value eq 'ribosomal_frameshift') {
+ $log_object->_save_log('log', '', $gsi, '', $tsi, '', "Skipping $tsi ($tname) since it has a ribosomal frameshift hidden_remark");
+ next TRANS;
+ }
+ }
#$support->log_verbose("Studying transcript $tsi ($tname, $tID)\n",1);
$log_object->_save_log('log_verbose', '', $gsi, '', $tsi, '', "Studying transcript $tsi ($tname, $tID)");
--
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