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#!/bin/sh
rm -rf validated fasta_and_yaml_*
mkdir -p validated
./from_genbank_to_fasta_and_yaml.py
fasta_files=$(find fasta_and_yaml/ -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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