binding

#!/bin/bash
# ======================================================== #
# |                    *** Usage ***                     | #
# ======================================================== #
usage(){
cat << EOF
    evaluate-network v1.0
    
    binding command for evaluating network with binding data
    binding [options]
    
    GENERAL arguments
    --p_in_net                : path of file for input network, three-columns tab separated file for regulators, targets and edge scores. No header for this file (mandatory).
    --nbr_top_edges           : number of top (TF, target) edges that will be evaluated (optional, default 50)
    --nbr_edges_per_threshold : number of (TF, target) edges evaluated in the first threshold (optional, default 5)
    --p_binding_event         : path of binding file, two-columns tab separated file for regulators and targets. These are the edges that have evidence of direct binding by experiments of binding such as ChIP-Chip (mandatory)
    --conda_env               : conda environment that will be used (neteval) (mandatory, if flag_singularity is OFF)
    --p_out_eval              :  path of output file for evaluation (mandatory)
    --flag_debug              : ON or OFF, if ON the bash command is printed
    
    SINGULARITY arguments
    --flag_singularity        : ON or OFF, for singularity run (optional, default ON)
    --p_singularity_bindpath  : path of mounted directory to singularity container (optional)
    --p_singularity_img       : path of directory for singularity containerr image provided in github page (mandatory, if flag_singularity is ON)  
   
    SLURM arguments
    --flag_slurm              : ON or OFF, for SLURM run (optional, default OFF)
    --p_out_logs              : path of directory for SLURM log files (mandatory, only if flag_slurm is ON)
    
EOF
}

# ======================================================== #
# |         *** Define Default Arguments ***             | #
# ======================================================== #
nbr_top_edges=50
nbr_edges_per_threshold=5
p_src_code="$(cd "$( dirname "${BASH_SOURCE[0]}" )" &> /dev/null && pwd)/"
conda_env=neteval
p_binding_event=NONE
flag_slurm=OFF
flag_singularity=ON
p_singularity_bindpath=/home/
p_singularity_img=NONE
flag_debug=OFF
data=""

# ======================================================== #
# |               *** Parse Arguments ***                | #
# ======================================================== #
while getopts ":h-:" OPTION
do
    case "${OPTION}" in
        h)
            usage
            exit 2
            ;;
        -)
            case "${OPTARG}" in
                 # input
                 p_in_net)
                     p_in_net="${!OPTIND}"; OPTIND=$(( ${OPTIND} + 1 ))
                     ;;
                 nbr_top_edges)
                     nbr_top_edges="${!OPTIND}"; OPTIND=$(( ${OPTIND} + 1 ))
                     ;;
                 nbr_edges_per_threshold)
                     nbr_edges_per_threshold="${!OPTIND}"; OPTIND=$(( ${OPTIND} + 1 ))
                     ;;
                 conda_env)
                     conda_env="${!OPTIND}"; OPTIND=$(( ${OPTIND} + 1 ))
                     ;;
                 p_binding_event)
                     p_binding_event="${!OPTIND}"; OPTIND=$(( ${OPTIND} + 1 ))
                     ;;
                 flag_debug)
                     flag_debug="${!OPTIND}"; OPTIND=$(( ${OPTIND} + 1 ))
                     ;;
                 data)
                     data="${!OPTIND}"; OPTIND=$(( ${OPTIND} + 1 ))
                     ;;
                     
                 # output    
                 p_out_eval)
                     p_out_eval="${!OPTIND}"; OPTIND=$(( ${OPTIND} + 1 ))
                     ;;
                     
                 # SLURM arguments
                 flag_slurm)
                     flag_slurm="${!OPTIND}"; OPTIND=$(( ${OPTIND} + 1 ))
                     ;;
                 p_out_logs)
                     p_out_logs="${!OPTIND}"; OPTIND=$(( ${OPTIND} + 1 ))
                     ;;
                 
                 # SINGULARITY arguments
                 flag_singularity)
                     flag_singularity="${!OPTIND}"; OPTIND=$(( ${OPTIND} + 1 ))
                     ;;
                 p_singularity_bindpath)
                     p_singularity_bindpath="${!OPTIND}"; OPTIND=$(( ${OPTIND} + 1 ))
                     ;;
                 p_singularity_img)
                     p_singularity_img="${!OPTIND}"; OPTIND=$(( ${OPTIND} + 1 ))
                     ;;
            esac;;
    esac
done

# ======================================================== #
# |              *** Define Command ***                  | #
# ======================================================== #

command=""

if [ ${flag_slurm} == "ON" ]
then
    mkdir -p ${p_out_logs}
    command+="sbatch 
            -o ${p_out_logs}eval_binding_%J.out \
            -e ${p_out_logs}eval_binding_%J.err \
            -J eval_with_binding_${data} "
fi

if [ ${p_binding_event} == "NONE" ]
then
    p_binding_event=${p_src_code}metadata/yeast/reg_target_cc_exo_chip_exclusive.txt
fi

command+="${p_src_code}wrapper/binding.sh \
            --p_in_net ${p_in_net} \
            --p_out_eval ${p_out_eval} \
            --nbr_top_edges ${nbr_top_edges} \
            --nbr_edges_per_threshold ${nbr_edges_per_threshold} \
            --p_src_code ${p_src_code} \
            --flag_slurm ${flag_slurm} \
            --conda_env ${conda_env} \
            --p_binding_event ${p_binding_event} \
            --flag_singularity ${flag_singularity} \
            --p_singularity_bindpath ${p_singularity_bindpath} \
            --p_singularity_img ${p_singularity_img} \
            --flag_debug ${flag_debug}"

# ======================================================== #
# |                *** Run Command ***                   | #
# ======================================================== #
if [ ${flag_debug} == "ON" ]
then
    echo "${command}"
fi
eval ${command}