#!/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/>.
#
#
# Run given cluster algorithm.
# The command line format is
#   run_cluster.sh <fasta1> <fasta2> ...
#
#--- check if environment is ok -----------------
[[ "${LOADED_COMMON_PIPELINE_SH+1}" == "" ]] && echo "ERROR $0 : main config has not been loaded" 1>&2 && exit 255
#------------------------------------------------
[[ $# -eq 1 ]] || fatal_msg "usage: $0 <cluster file>,<brh file>,<output>"
args=( $(tokenize "," $1) )
[[ ${#args[@]} -eq 3 ]] || fatal_msg "got wrong nr of tokens in argument (${#args[@]} ${args[@]})"

clfile="${args[0]}"
brhfile="${args[1]}"
output="${args[2]}"

cmd=$DIR_BRHCLUS/statclus
[[ -x "$cmd" ]] || fatal_msg "statclus command not found : $cmd"

###$DIR_BRHCLUS/statclus -C $clfile -P $brhfile > $output
$DIR_BRHCLUS/statclus -C $clfile > $output

