Merge branch 'master' of https://github.com/arvados/bh20-seq-resource

1 files changed, 18 insertions, 0 deletions

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