From 90b3ee9b04bf5c15bf4537427a275e1df862b5de Mon Sep 17 00:00:00 2001
From: Eric Coissac <eric.coissac@metabarcoding.org>
Date: Mon, 14 Feb 2022 15:29:02 +0100
Subject: [PATCH] Do correct renaming of RPS12 genes if several

Former-commit-id: 8ddbfaea302c440aa0992f3443632cf026b0d3a9
Former-commit-id: 2559779ab79d1b52d5193e1a60b443f6290dda48
---
 detectors/cds/bin/do_rps12.sh | 16 +++++++++++++---
 1 file changed, 13 insertions(+), 3 deletions(-)

diff --git a/detectors/cds/bin/do_rps12.sh b/detectors/cds/bin/do_rps12.sh
index 39239b7..d5a3186 100755
--- a/detectors/cds/bin/do_rps12.sh
+++ b/detectors/cds/bin/do_rps12.sh
@@ -263,12 +263,13 @@ blastx \
     #
         export PASS1_SPEEDUP=0
         cp $DBROOT/Annot.lst RPS12
-
+        nbseq = 0
         for fasta in rps12_fragments_*.fasta ; do
             tcsh -f ${PROG_DIR}/do_exonerate.csh \
                 $fasta \
                 "RPS12/rps12.fasta" \
                 $DBROOT/../models $(pwd)
+            ((nbseq=nbseq+1))
         done
 
     #
@@ -276,8 +277,9 @@ blastx \
     # fragment to the chloroplaste genome coordinates 
     #
 
-
+        n=0
         for f in *.res ; do
+            ((n=n+1))
             mv $f $f.ori
             if [[ -z "$TEMP" ]] ; then
                 dest="/dev/stdout"
@@ -382,9 +384,17 @@ blastx \
                  $0 = line
               }
           {print $0}
+        ' | \
+        $AwkCmd -v n=$n -v nbseq=$nbseq '
+            /^FT +\/gene="rps12"/ && (nbseq > 1) {
+                sub(/rps12/,"rps12_" n,$0)
+            }
+            {
+                print $0
+            }       
         ' > $dest
         done
-        
+         
     
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