#!/usr/bin/env bash
# SPAAN's original command file uses legacy line endings. This POSIX-compatible
# wrapper preserves its intended sequence of operations.
set -euo pipefail

printf 'standardization going on...\n'
cp query.dat query.fasta
./standard query.fasta
mv query.std query.ext

printf 'filteration going on...\n'
./filter query.ext
./annotate query.flt '1gi|'
rm -f query.ext query.fasta

printf 'recognition going on...\n'
(
  cd AAcompo
  ./AAcompo ../query.ant query.NN1in
  ./recognize spec.reco
)
(
  cd charge
  ./charge ../query.ant query.NN1in
  ./recognize spec.reco
)
(
  cd hdr
  ./hdr ../query.ant query.NN1in
  ./recognize spec.reco
)
(
  cd multiplets
  ./multiplets ../query.ant query.NN1in
  ./recognize spec.reco
)
(
  cd dipep
  ./querydipep ../query.ant query.NN1in
  ./recognize spec.reco
)

./finalp1 \
  AAcompo/query.NN2in \
  charge/query.NN2in \
  hdr/query.NN2in \
  multiplets/query.NN2in \
  dipep/query.NN2in \
  query.flt \
  query.out

rm -f query.ant query.flt