#!/bin/bash

test "$AUTOPKGTEST_TMP" = "" && AUTOPKGTEST_TMP=$(mktemp --directory)
cd "$AUTOPKGTEST_TMP"

STATUS=1

# H_new_fliC_protein_database.fasta does not have GIs, thus synthetic ones are added here
perl -lne 'if( /^>/ ) { print ">gi|$.|ref|$.| hypothetical protein" } else { print $_ }' /usr/share/seqsero/database/H_new_fliC_protein_database.fasta | tr -d '*' > fliC.fasta

head -n  2 fliC.fasta > input.fasta
tail -n +3 fliC.fasta | sponge fliC.fasta

makeblastdb -in fliC.fasta -parse_seqids -dbtype prot -out fliC
rm fliC.fasta

cat > input.var <<END
D44E
D44H
D44L
END

provean -q input.fasta -v input.var --psiblast psiblast --cdhit cdhit --blastdbcmd blastdbcmd -d fliC && STATUS=0

exit $STATUS
