From b2a78f42aab54864bb6e65d7f7aff4f8fffe8357 Mon Sep 17 00:00:00 2001
From: tcarver <tjc>
Date: Tue, 5 Nov 2013 14:35:13 +0000
Subject: [PATCH] test for selenocysteine qualifier
---
uk/ac/sanger/artemis/io/GFFStreamFeature.java | 30 +++++++++++++++++++
uk/ac/sanger/artemis/io/ValidateFeature.java | 3 ++
2 files changed, 33 insertions(+)
diff --git a/uk/ac/sanger/artemis/io/GFFStreamFeature.java b/uk/ac/sanger/artemis/io/GFFStreamFeature.java
index 9fa2cc0cf..3d4923b22 100644
--- a/uk/ac/sanger/artemis/io/GFFStreamFeature.java
+++ b/uk/ac/sanger/artemis/io/GFFStreamFeature.java
@@ -1320,6 +1320,36 @@ public class GFFStreamFeature extends SimpleDocumentFeature
return false;
}
+ /**
+ * Test if this is feature is marked as having a stop codon
+ * redefined as selenocysteine
+ * @param f
+ * @return
+ */
+ public static boolean isSelenocysteine(Feature f)
+ {
+ if(!(f instanceof GFFStreamFeature))
+ return false;
+ try
+ {
+ ChadoCanonicalGene gffGene = ((GFFStreamFeature)f).getChadoGene();
+ if(gffGene == null)
+ return false;
+ String transcript = gffGene.getTranscriptFromName(
+ GeneUtils.getUniqueName(f));
+ if(transcript == null)
+ return false;
+ Feature pep = gffGene.getProteinOfTranscript(transcript);
+ if(pep == null)
+ return false;
+ if(pep.getQualifierByName("stop_codon_redefined_as_selenocysteine") != null)
+ return true;
+ }
+ catch (Exception e){}
+
+ return false;
+ }
+
public static void main(String args[])
{
Key key = new Key("region");
diff --git a/uk/ac/sanger/artemis/io/ValidateFeature.java b/uk/ac/sanger/artemis/io/ValidateFeature.java
index d1dc8836d..f62ed79db 100644
--- a/uk/ac/sanger/artemis/io/ValidateFeature.java
+++ b/uk/ac/sanger/artemis/io/ValidateFeature.java
@@ -677,6 +677,9 @@ public class ValidateFeature
if(!cds_predicate.testPredicate (f))
return false;
+ if(feature instanceof GFFStreamFeature && GFFStreamFeature.isSelenocysteine(feature))
+ return false;
+
final AminoAcidSequence aa = f.getTranslation ();
return aa.containsStopCodon ();
}
--
GitLab