From 3d9be22e1d35c3448af27c9642686a28b200e6ea Mon Sep 17 00:00:00 2001
From: Eric Coissac <eric.coissac@metabarcoding.org>
Date: Thu, 11 May 2023 14:29:43 +0200
Subject: [PATCH] Small changes

Former-commit-id: bf83f19efe2590803c089697858590aee4720089
Former-commit-id: e7d0bae099d6449b97c431f7ba82568f45bcc005
---
 config/guess_port  |  1 +
 summarize_annot.sh | 37 +++++++++++++++++++++++++++----------
 2 files changed, 28 insertions(+), 10 deletions(-)

diff --git a/config/guess_port b/config/guess_port
index ee97cb5..3fbed87 100755
--- a/config/guess_port
+++ b/config/guess_port
@@ -26,6 +26,7 @@ case ${mach}:${syst}:${rels} in
     x*86*:Linux:*    )  echo i386-linux;;
     i*86:Darwin:*    )  echo i386-darwin;;
     x*86*:Darwin:*   )  echo i386-darwin;;
+    arm64:Darwin:*   )  echo arm64-darwin;;
     IP*:IRIX*:*      )  echo mips-irix;;
     i*86:MINGW32*:*  )  echo x86-mingw32;;
     
diff --git a/summarize_annot.sh b/summarize_annot.sh
index ab8101f..880defc 100755
--- a/summarize_annot.sh
+++ b/summarize_annot.sh
@@ -1,12 +1,29 @@
 #!/bin/bash
 
-egrep "^FT   (CDS|rRNA|tRNA) |/gene=" $1 \
-  | awk '
-        /\/gene=/ && (gene!=1) {
-            print $0; 
-            gene=1
-            } 
-        /^FT   (CDS|rRNA|tRNA)/ {
-            print $0;
-            gene=0
-            }' 
\ No newline at end of file
+resume_ft() {
+    local input=$1
+    grep -E "^FT   (CDS|rRNA|tRNA) |/gene=" ${input} \
+    | awk '
+            /\/gene=/ && (gene!=1) {
+                print $0; 
+                gene=1
+                } 
+            /^FT   (CDS|rRNA|tRNA)/ {
+                print $0;
+                gene=0
+                }' 
+}
+
+count_tRNA() {
+    local input=$1
+
+    resume_ft $input \
+    | grep '^FT   tRNA' \
+    | wc -l
+}
+
+
+
+
+printf "tRNA genes : %d\n" "$(count_tRNA $1)"
+