From 8c35a32f7e701a2f547cfedc53f6a008d3fdd4ad Mon Sep 17 00:00:00 2001
From: peguerin <pierre-edouard.guerin@cefe.cnrs.fr>
Date: Thu, 21 Nov 2019 17:06:40 +0100
Subject: [PATCH] first contact with this script lol
---
03_dereplication/derep_tally.sh | 4 ++--
1 file changed, 2 insertions(+), 2 deletions(-)
diff --git a/03_dereplication/derep_tally.sh b/03_dereplication/derep_tally.sh
index 0a04669..b16784b 100644
--- a/03_dereplication/derep_tally.sh
+++ b/03_dereplication/derep_tally.sh
@@ -77,9 +77,9 @@ for sample in `ls $main_dir/"$pref"_sample_*.fasta`;
do
sample_sh="${sample/.fasta/_cmd.sh}"
echo "bash "$sample_sh >> $all_samples_parallel_cmd_sh
-# D�r�plication des reads en s�quences uniques
+# Dereplicate sequences with tally
dereplicated_sample="${sample/.fasta/.uniq.fasta}"
-echo "/usr/bin/time $tally -i "$sample" --fasta-in --fasta-out -o "$dereplicated_sample > $sample_sh;
+echo "$tally -i "$sample" --fasta-in --fasta-out -o "$dereplicated_sample > $sample_sh;
# On garde les s�quences de plus de 20pb sans bases ambigues
good_sequence_sample="${dereplicated_sample/.fasta/.l20.fasta}"
echo "$obigrep -s '^[ACGT]+$' -l 20 "$dereplicated_sample" > "$good_sequence_sample >> $sample_sh
--
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