#!/usr/bin/env bash
#
# orthologer - Pipeline for deducing orthology from fasta files.
# Copyright (C) 2005-2023 E. Zdobnov lab: F. Tegenfeldt
# <fredrik.tegenfeldt@unige.ch> based on code by E. Kriventseva
#
# This file is part of orthologer.
#
# orthologer is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
#
# orthologer is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
# GNU General Public License for more details.
#
# You should have received a copy of the GNU General Public License
# along with orthologer.  If not, see <http://www.gnu.org/licenses/>.
#
#--- check if environment is ok -----------------
[[ "${LOADED_COMMON_PIPELINE_SH+1}" == "" ]] && echo "ERROR $0 : main config has not been loaded" 1>&2 && exit 255
#------------------------------------------------
set -u

[[ $# -eq 1 ]] || fatal_msg "usage: $0 <todo>"

todo="$1"
err=0
first=0
titlestr=""

for tf in $(cat $todo); do

    ff="${DIR_PROJECT_SEQUENCES}/${tf}.${EXT_FASTA}"

    [[ $first -eq 0 ]] && titlestr="--title"
    ${DIR_ORTHOLOGER_BIN}/check_fasta.py $titlestr --stats -f $ff
    ec=$?
    if [[ $ec -ne 0 ]]; then
	    error_msg "$0: check_fasta.py script failed with ec = $ec"
	    exit 1
    fi
    first=1
    titlestr=""
done

exit $err
