From 616d5d084b1535d7e169de1ebf048922c924a6af Mon Sep 17 00:00:00 2001
From: Eric Coissac <eric.coissac@metabarcoding.org>
Date: Fri, 5 Nov 2021 09:29:57 +0100
Subject: [PATCH] change tRNA and CDS annotations

Former-commit-id: 12b6c5605f57940e215643b80c93ffbb48d5406e
Former-commit-id: 18663d59e90e6d35b029d9087b66723487b8db1d
---
 detectors/cds/bin/do_rps12.sh          |  2 +-
 detectors/cds/lib/toEmbl.awk           | 12 ++++++------
 detectors/trna/lib/aragorn_wrapper.awk |  2 +-
 3 files changed, 8 insertions(+), 8 deletions(-)

diff --git a/detectors/cds/bin/do_rps12.sh b/detectors/cds/bin/do_rps12.sh
index 882341e..e07a412 100755
--- a/detectors/cds/bin/do_rps12.sh
+++ b/detectors/cds/bin/do_rps12.sh
@@ -371,7 +371,7 @@ blastx \
                  n = split($0,parts,",")
                  j = 1
                  for (i = 1; i <= n; i++) {
-                     if (length(line) + length(parts[i]) > 79) {
+                     if (length(line) + length(parts[i]) > 78) {
                          print line ","
                          line = "FT                   "
                          j = i
diff --git a/detectors/cds/lib/toEmbl.awk b/detectors/cds/lib/toEmbl.awk
index 3484699..73983ff 100644
--- a/detectors/cds/lib/toEmbl.awk
+++ b/detectors/cds/lib/toEmbl.awk
@@ -160,11 +160,11 @@ function Unk(s) {
 	gname = (Ngene == 1 ? GeneName : GeneName "_" ++Igene)
 	locus = ""
 	  
-	Feature("gene", GeneLocation())
-	QQualifier("gene", gname)
-	QQualifier("locus_tag", locus)
-	if (FrameShift)
-		QQualifier("pseudogene","unknown")
+	# Feature("gene", GeneLocation())
+	#QQualifier("gene", gname)
+	#QQualifier("locus_tag", locus)
+	#if (FrameShift)
+	#	QQualifier("pseudogene","unknown")
 		  
 	Feature("CDS", CdsLocation())
 	SQualifier("codon_start", 1)
@@ -180,7 +180,7 @@ function Unk(s) {
 		}
 	QQualifier("product", Product)
 	QQualifier("inference", "similar to DNA sequence:" Simil)
-	QQualifier("inference", "org.annot -- detect pass:" PassType ":" PassInfo)
+	# QQualifier("inference", "org.annot -- detect pass:" PassType ":" PassInfo)
 	if (FrameShift==0) {
 		if (match(Translat,/\*/)>0) {
 			QQualifier("pseudogene","unknown")
diff --git a/detectors/trna/lib/aragorn_wrapper.awk b/detectors/trna/lib/aragorn_wrapper.awk
index 29fa5cc..cdda0ca 100755
--- a/detectors/trna/lib/aragorn_wrapper.awk
+++ b/detectors/trna/lib/aragorn_wrapper.awk
@@ -168,7 +168,7 @@ function emblTRNA(geneid,trna,loc,anti,intron,notes,seq) {
 	   print "FT                   /gene=\""trna"\"";
 	   print "FT                   /anticodon=\""anti"\"";	   
 	   print "FT                   /product=\""product"("anti")\"";
-	   print "FT                   /inference=\"Aragorn-1.2.38\"";
+#	   print "FT                   /inference=\"Aragorn-1.2.38\"";
 	   if (notes!="-")
 		   print "FT                   /note=\""notes"\"";