From 88d81f853cf04b7f28681dd9cdee775b0422f252 Mon Sep 17 00:00:00 2001
From: Peter Amstutz
Date: Tue, 21 Apr 2020 12:53:19 -0400
Subject: Working on NCBI import

Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curii.com>
---
 scripts/foreach.sh | 18 ++++++++++++++++++
 1 file changed, 18 insertions(+)
 create mode 100755 scripts/foreach.sh

(limited to 'scripts/foreach.sh')

diff --git a/scripts/foreach.sh b/scripts/foreach.sh
new file mode 100755
index 0000000..35b07b8
--- /dev/null
+++ b/scripts/foreach.sh
@@ -0,0 +1,18 @@
+#!/bin/sh
+rm -rf validated fasta_and_yaml_*
+mkdir -p validated
+./from_genbank_to_fasta_and_yaml.py
+fasta_files=$(find fasta_and_yaml_20200421/ -name "*.fasta")
+for f in $fasta_files ; do
+    yaml=$(echo $f | rev | cut -c7- | rev).yaml
+    echo $f
+    echo $yaml
+    if bh20-seq-uploader --validate $f $yaml ; then
+	sz=$(stat --format=%s $f)
+	if test $sz -gt 20000 ; then
+	    mv $f $yaml validated
+	else
+	    echo "Fasta file too small"
+	fi
+    fi
+done
-- 
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