From a040adb1323383d8dd7fab307ab37352f991f21d Mon Sep 17 00:00:00 2001
From: Eric Coissac <eric.coissac@metabarcoding.org>
Date: Tue, 20 Nov 2018 15:59:57 +0100
Subject: [PATCH] Check the translation for stop codon and add a pseudogene
 qualifier if present.

Former-commit-id: 11b612fcdfa1fdd2a2614148b5b1772954e62e70
Former-commit-id: 02c87c99e5ece530640e521a577867e74ed1541e
---
 detectors/cds/lib/toEmbl.awk | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/detectors/cds/lib/toEmbl.awk b/detectors/cds/lib/toEmbl.awk
index 624f19c..a75b3df 100644
--- a/detectors/cds/lib/toEmbl.awk
+++ b/detectors/cds/lib/toEmbl.awk
@@ -181,6 +181,10 @@ function Unk(s) {
 	QQualifier("product", Product)
 	QQualifier("inference", "similar to DNA sequence:" Simil)
 	QQualifier("inference", "org.annot -- detect pass:" PassType ":" PassInfo)
+	if (match(Translat,/\*/)>0) {
+		QQualifier("pseudogene","unknown")
+		QQualifier("note","nonfunctional due to stop codon")
+	}
 	if (FrameShift==0)
 		QQualifier("translation", Translat)