From 50892e18eeb082b9deb977bf003d772397dd9fa2 Mon Sep 17 00:00:00 2001
From: peguerin <pierre-edouard.guerin@cefe.cnrs.fr>
Date: Mon, 11 Jan 2021 14:56:34 +0100
Subject: [PATCH] bash command entrez

---
 usage_entrez.sh | 7 +++++++
 1 file changed, 7 insertions(+)
 create mode 100644 usage_entrez.sh

diff --git a/usage_entrez.sh b/usage_entrez.sh
new file mode 100644
index 0000000..495c214
--- /dev/null
+++ b/usage_entrez.sh
@@ -0,0 +1,7 @@
+# dans un terminal bash
+
+## search Rana temporaria entreies in "Nucleotide" database from NCBI
+## and then keep only entries with the "complete genome" mention
+esearch -db Nucleotide -query "rana temporaria mitochondrion" | efilter -query "complete genome"
+## download reference Rana temporaria mitochondrion FASTA file
+efetch -format fasta -id NC_042226.1 -db Nucleotide > mitogenome/NC_042226.1.fas
-- 
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