np2

#!/bin/bash

# ========================================================================= #
# |                    **** USAGE OF NETPROPHET 2.1 ****                  | #      
# ========================================================================= #
usage(){
cat << EOF
    netprophet2.1 [options]
    
    INPUT arguments:
    --p_in_target            : input file for list of target genes
    --p_in_reg               : input file for list of regulators
    --p_in_sample            : input file for list of sample (condition) ids
    --p_in_expr_target       : input file for expression of target genes (target x sample)
    --p_in_net_de            : input file for network of differential expression
    --p_in_binding_event     : input file for binding events |REGULATOR|TARGET|
    
    NETPROPHET1 arguments:
    --fname_net_np1          : name of generated network for netprophet1 (optional)
    
    NETPROPHET2 arguments:
    --fname_net_bart         : name of generated network for bart (optional)
    --fname_net_np2          : name of generated network for netprophet2 (optional)
    --p_in_dbd_pids          : path of folder for DBD_PIDS
    --p_in_promoter          : path of file for promoters
    
    OUTPUT arguments:
    --p_out_dir              : path of output directory for results

    SLURM arguments:
    --p_out_logs             : output director for log files (.out & .err) for slurm runs
EOF
}


# ========================================================================= #
# |                  **** END USAGE OF NETPROPHET 2.1 ****                | #      
# ========================================================================= #

# general input
data=""
seed=747

<<<<<<< HEAD
# LASSO
flag_microarray="ON"
lasso_nbr_fold=10
flag_global_shrinkage="OFF"
flag_local_shrinkage="ON"
# LASSO SLURM
lasso_slurm_mem=10GB
lasso_slurm_nodes=1
lasso_slurm_ntasks=10

# BART SLURM
bart_slurm_mem=20GB
bart_slurm_nodes=1
bart_slurm_ntasks=20

# PWM
=======
# lasso
flag_global_shrinkage="OFF"
flag_local_shrinkage="ON"
flag_microarray="MICROARRAY"
lasso_nbr_fold=10

# bart
bart_nbr_rmpi_slave=2

# pwm
>>>>>>> e78cf4fb5e7d9a5729830a717ed8451f16430db8
p_in_promoter="NONE"
# PWM SLURM
pwm_slurm_nodes=1
pwm_slurm_ntasks=10


# smoothing
p_in_dbd_pids="NONE"

# LOGISTICS
p_src_code="$(cd "$( dirname "${BASH_SOURCE[0]}" )" &> /dev/null && pwd)/"

# SLURM arguments
mail_type=FAIL
mail_user="NONE"
flag_slurm="OFF"

# SINGULARITY arguments
flag_singularity="ON"
p_singularity_img="NONE"
p_singularity_bindpath="NONE"


# initialize flags for specific components runs
flag_run_np1="OFF"  # -n
flag_run_bart="OFF"  # -b bart
flag_run_combine="OFF"  # -c combine
flag_run_combine_np1bart_pwm="OFF" # -k combine
flag_run_pwm="OFF" # -m pwm
flag_run_all="ON"  # -a to run all components



# ========================================================================= #
# |                         **** PARSE ARGUMENTS ****                     | #      
# ========================================================================= #

while getopts ":hpnbvwcismkya-:" OPTION
do
    case "${OPTION}" in
    n)
        flag_run_np1="ON"
        flag_run_all="OFF"
        ;;
    b)
        flag_run_bart="ON"
        flag_run_all="OFF"
        ;;
    c)
        flag_run_combine="ON"
        flag_run_all="OFF"
        ;;
    m)
        flag_run_pwm="ON"
        flag_run_all="OFF"
        ;;
    k)
        flag_run_combine_np1bart_pwm="ON"
        flag_run_all="OFF"
        ;;
    a)
        flag_run_all="ON"
        ;;
    h)
        usage
        exit 2
        ;;
    -)
        case "${OPTARG}" in
            # Input general param
            p_in_expr_target)
                p_in_expr_target="${!OPTIND}"; OPTIND=$(( $OPTIND + 1 ))
                ;;
            p_in_expr_reg)
                p_in_expr_reg="${!OPTIND}"; OPTIND=$(( $OPTIND + 1 ))
                ;;
            
            # LASSO
            flag_global_shrinkage)
                flag_global_shrinkage="${!OPTIND}"; OPTIND=$(( $OPTIND + 1 ))
                ;;
            flag_local_shrinkage)
                flag_local_shrinkage="${!OPTIND}"; OPTIND=$(( $OPTIND + 1 ))
                ;;
            lasso_nbr_fold)
                lasso_nbr_fold="${!OPTIND}"; OPTIND=$(( $OPTIND + 1 ))
                ;;
            flag_microarray)
                flag_microarray="${!OPTIND}"; OPTIND=$(( $OPTIND + 1 ))
                ;;
            p_in_net_de)
                p_in_net_de="${!OPTIND}"; OPTIND=$(( $OPTIND + 1 ))
                ;;
            p_in_binding_event)
                p_in_binding_event="${!OPTIND}"; OPTIND=$(( $OPTIND + 1 ))
                ;;
<<<<<<< HEAD
            # LASSO SLURM
            lasso_slurm_mem)
                lasso_slurm_mem="${!OPTIND}"; OPTIND=$(( $OPTIND + 1 ))
                ;;
            lasso_slurm_nodes)
                lasso_slurm_nodes="${!OPTIND}"; OPTIND=$(( $OPTIND + 1 ))
                ;;
            lasso_slurm_ntasks)
                lasso_slurm_ntasks="${!OPTIND}"; OPTIND=$(( $OPTIND + 1 ))
                ;;
                
            # BART SLURM
            bart_slurm_mem)
                bart_slurm_mem="${!OPTIND}"; OPTIND=$(( $OPTIND + 1 ))
                ;;
            bart_slurm_nodes)
                bart_slurm_nodes="${!OPTIND}"; OPTIND=$(( $OPTIND + 1 ))
                ;;
            bart_slurm_ntasks)
                bart_slurm_ntasks="${!OPTIND}"; OPTIND=$(( $OPTIND + 1 ))
                ;;
                
=======
            # bart
            bart_nbr_rmpi_slave)
		bart_nbr_rmpi_slave="${!OPTIND}"; OPTIND=$(( $OPTIND + 1 ))
                ;;
>>>>>>> e78cf4fb5e7d9a5729830a717ed8451f16430db8
            # smoothing
            p_in_dbd_pids)
                p_in_dbd_pids="${!OPTIND}"; OPTIND=$(( $OPTIND + 1 ))
                ;;
                
            # PWM
            p_in_promoter)
                p_in_promoter="${!OPTIND}"; OPTIND=$(( $OPTIND + 1 ))
                ;;
            pwm_slurm_ntasks)
                pwm_slurm_ntasks="${!OPTIND}"; OPTIND=$(( $OPTIND + 1 ))
                ;;
            pwm_slurm_nodes)
                pwm_slurm_nodes="${!OPTIND}"; OPTIND=$(( $OPTIND + 1 ))
                ;;
                
            # Logistics
            p_src_code)
                p_src_code="${!OPTIND}"; OPTIND=$(( $OPTIND + 1 ))
                ;;
            seed)
                seed="${!OPTIND}"; OPTIND=$(( $OPTIND + 1 ))
                ;;
            data)
                data="${!OPTIND}"; OPTIND=$(( $OPTIND + 1 ))
                ;;
                
            # Output
            p_out_dir)
                p_out_dir="${!OPTIND}"; OPTIND=$(( $OPTIND + 1 ))
                ;;
                
            # SLURM
            flag_slurm)
                flag_slurm="${!OPTIND}"; OPTIND=$(( $OPTIND + 1 ))
                ;;
            mail_type)
                mail_type="${!OPTIND}"; OPTIND=$(( $OPTIND + 1 ))
                ;;
            mail_user)
                mail_user="${!OPTIND}"; OPTIND=$(( $OPTIND + 1 ))
                ;;
            p_out_dir_logs)
                p_out_dir_logs="${!OPTIND}"; OPTIND=$(( $OPTIND + 1 ))
                ;;
                  
            # Singularity
            flag_singularity)
                    flag_singularity="${!OPTIND}"; OPTIND=$(( $OPTIND + 1 ))
                  ;;
            p_singularity_img)
                p_singularity_img="${!OPTIND}"; OPTIND=$(( $OPTIND + 1 ))
              ;;
            p_singularity_bindpath)
                p_singularity_bindpath="${!OPTIND}"; OPTIND=$(( $OPTIND + 1 ))
              ;;
            
        esac;;
    esac

done

# ========================================================================= #
# |                       **** END PARSE ARGUMENTS ****                   | #      
# ========================================================================= #


mkdir -p ${p_out_dir}

# ========================================================== #
# |                **** Run NETPROPHET1 ***                | #
# ========================================================== #
job_id_np1=1    
if [ ${flag_run_np1} == "ON" ] || [ ${flag_run_all} == "ON" ]
then
    cmd_run_np1=""
    if [ ${flag_slurm} == "ON" ]
    then
        mkdir -p ${p_out_dir_logs}tmp/
        cmd_run_np1+="sbatch \
                       -o ${p_out_dir_logs}build_np1_%J.out \
                       -e ${p_out_dir_logs}build_np1_%J.err \
                       -J ${data}_np1 \
                       --mail-type=${mail_type} \
                       --mail-user=${mail_user} \
                       -D ${p_out_dir_logs}tmp/ \
                       --nodes=1-${lasso_slurm_nodes} \
                       --ntasks=${lasso_slurm_ntasks} \
                       --mem=${lasso_slurm_mem} \
                       --cpus-per-task=3 "
    fi
    cmd_run_np1+="${p_src_code}src/build_np1/workflow/build_net_np1_and_smooth.sh \
                    --p_in_expr_target ${p_in_expr_target} \
                    --p_in_expr_reg ${p_in_expr_reg} \
                    --flag_global_shrinkage ${flag_global_shrinkage} \
                    --flag_local_shrinkage ${flag_local_shrinkage} \
                    --lasso_nbr_fold ${lasso_nbr_fold} \
                    --flag_microarray ${flag_microarray} \
                    --p_in_dbd_pids ${p_in_dbd_pids} \
                    --p_in_net_de ${p_in_net_de} \
                    --seed ${seed} \
                    --p_out_dir ${p_out_dir} \
                    --f_out_name_lasso net_lasso.tsv \
                    --f_out_name_np1 net_np1.tsv \
                    --f_out_name_np1_smoothed net_np1_smoothed.tsv \
                    --p_src_code ${p_src_code} \
                    --flag_slurm ${flag_slurm} \
                    --flag_singularity ${flag_singularity} \
                    --p_singularity_img ${p_singularity_img} \
                    --p_singularity_bindpath ${p_singularity_bindpath}" 
    
    echo "run NP1.."
    job_id_np1=$(echo $(eval ${cmd_run_np1}) | awk '{split($0, a, " "); print a[4]}')
fi

# ========================================================== #
# |                    **** Run BART ****                  | #
# ========================================================== #
job_id_bart=1
if [ ${flag_run_bart} == "ON" ] || [ ${flag_run_all} == "ON" ]
then
    cmd_run_bart=""
    if [ ${flag_slurm} == "ON" ]; then
        bart_nbr_rmpi_slave=20
        mkdir -p ${p_out_dir_logs}tmp/
        cmd_run_bart+="sbatch \
                       -o ${p_out_dir_logs}build_bart_%J.out \
                       -e ${p_out_dir_logs}build_bart_%J.err \
                       -J ${data}_bart \
                       --mail-type=${mail_type} \
                       --mail-user=${mail_user} \
<<<<<<< HEAD
                       --nodes=1-${bart_slurm_nodes} \
                       --ntasks=${bart_slurm_ntasks} \
=======
                       -n ${bart_nbr_rmpi_slave} \
                       -N 1 \
>>>>>>> e78cf4fb5e7d9a5729830a717ed8451f16430db8
                       -D ${p_out_dir_logs}tmp/ \
                       --mem=${bart_slurm_mem} "
    fi
    cmd_run_bart+="${p_src_code}src/build_bart/workflow/build_net_bart_and_smooth.sh \
                    --p_in_expr_target ${p_in_expr_target} \
                    --p_in_expr_reg ${p_in_expr_reg} \
                    --nbr_rmpi_slaves ${bart_slurm_ntasks} \
                    --p_in_dbd_pids ${p_in_dbd_pids} \
                    --seed ${seed} \
                    --p_out_dir ${p_out_dir} \
                    --f_out_name_bart net_bart.tsv \
                    --f_out_name_bart_smoothed net_bart_smoothed.tsv \
                    --bart_nbr_rmpi_slave ${bart_nbr_rmpi_slave} \
                    --p_src_code ${p_src_code} \
                    --flag_slurm ${flag_slurm} \
                    --flag_singularity ${flag_singularity} \
                    --p_singularity_img ${p_singularity_img} \
                    --p_singularity_bindpath ${p_singularity_bindpath}" 
    
    echo "run BART.."
    job_id_bart=$(echo $(eval ${cmd_run_bart}) | awk '{split($0, a, " "); print a[4]}')
fi


# ========================================================== #
# |              **** Combine NP1 & BART ****              | #
# ========================================================== #
job_id_combine=1
if [ ${flag_run_combine} == "ON" ] || [ ${flag_run_all} == "ON" ]
then
    if [ ${p_in_dbd_pids} != "NONE" ]; then
        p_net_bart=${p_out_dir}net_bart_smoothed.tsv
        p_net_np1=${p_out_dir}net_np1_smoothed.tsv
    else
        p_net_bart=${p_out_dir}net_bart.tsv
        p_net_np1=${p_out_dir}net_np1.tsv
    fi
    
    # combine np1 & bart
    cmd_run_combine=""
    if [ ${flag_slurm} == "ON" ]; then
        mkdir -p ${p_out_dir_logs}tmp/
        cmd_run_combine+="sbatch \
                          -o ${p_out_dir_logs}combine_np1_bart_%J.out \
                          -e ${p_out_dir_logs}combine_np1_bart_%J.err \
                          --dependency=afterok:${job_id_np1}:${job_id_bart} \
                          -J ${data}_combine_np1_bart \
                          --mail-type=${mail_type} \
                          --mail-user=${mail_user} \
                          --mem=10GB "
    fi
    cmd_run_combine+="${p_src_code}src/combine_networks/wrapper/quantile_combine_networks.sh \
                          ${p_net_np1} \
                          ${p_net_bart} \
                          ${p_out_dir}net_np1_bart.tsv \
                          ${p_src_code} \
                          ${flag_slurm} \
                          ${flag_singularity} \
                          ${p_singularity_img} \
                          ${p_singularity_bindpath}"
                 
    echo "run combine NP1 & BART.."
    job_id_combine=$(echo $(eval ${cmd_run_combine}) | awk '{split($0, a, " "); print a[4]}')
    
fi


# ========================================================== #
# |                    **** Run PWM ****                   | #
# ========================================================== #
job_id_pwm=1
if [ ${flag_run_pwm} == "ON" ] || [ ${flag_run_all} == "ON" ]
then
    nbr_job_pwm=${nbr_job}
    if [ ${flag_slurm} == "ON" ]; then
        mkdir -p ${p_out_dir_logs}tmp/
        nbr_job_pwm=40
        cmd_run_pwm+="sbatch \
                      -o ${p_out_dir_logs}build_pwm_%J.out \
                      -e ${p_out_dir_logs}build_pwm_%J.err \
                      -J ${data}_pwm \
                      --mail-type=${mail_type} \
                      --mail-user=${mail_user} \
                      --nodes=1-${pwm_slurm_nodes} \
                      --ntasks=${pwm_slurm_ntasks} \
                      --cpus-per-task=2 \
                      -D ${p_out_dir_logs}tmp/ \
                      --dependency=afterok:${job_id_combine} "
    fi
    cmd_run_pwm+="${p_src_code}src/build_pwm/workflow/build_net_pwm.sh \
                 --p_in_net ${p_out_dir}net_np1_bart.tsv \
                 --p_in_promoter ${p_in_promoter} \
                 --p_out_dir ${p_out_dir} \
                 --f_out_name net_pwm.tsv \
                 --flag_slurm ${flag_slurm} \
                 --flag_singularity ${flag_singularity} \
                 --p_singularity_img ${p_singularity_img} \
                 --p_singularity_bindpath ${p_singularity_bindpath} \
                 --p_src_code ${p_src_code} \
                 --nbr_job ${nbr_job_pwm}"
                 
    echo "run PWM.."             
    job_id_pwm=$(echo $(eval ${cmd_run_pwm}) | awk '{split($0, a, " "); print a[4]}')
fi

job_id_combine=1
if [ ${flag_run_combine_np1bart_pwm} == "ON" ] || [ ${flag_run_all} == "ON" ]
then    
    # combine np1_bart & pwm
    if [ -f ${p_out_dir}"net_pwm.tsv" ] || [ ${flag_run_pwm} == "ON" ] || [ ${flag_run_all} == "ON" ]
    then
        cmd_run_combine=""
        if [ ${flag_slurm} == "ON" ]; then
            mkdir -p ${p_out_dir_logs}tmp/
            cmd_run_combine+="sbatch \
                              -o ${p_out_dir_logs}combine_np1bart_pwm_%J.out \
                              -e ${p_out_dir_logs}combine_np1bart_pwm_%J.err \
                              --dependency=afterok:${job_id_pwm} \
                              -J ${data}_combine_np1bart_pwm \
                              --mail-type=${mail_type} \
                              --mail-user=${mail_user} \
                              --mem=150GB "
        fi
        
        cmd_run_combine+="${p_src_code}src/combine_networks/workflow/combine_networks_and_smooth.sh \
                              --p_in_net_np1_bart ${p_out_dir}net_np1_bart.tsv \
                              --p_in_net_pwm ${p_out_dir}net_pwm.tsv \
                              --p_in_dbd_pids ${p_in_dbd_pids} \
                              --p_out_dir ${p_out_dir} \
                              --f_out_name_np2 net_np2.tsv \
                              --f_out_name_np2_smoothed net_np2_smoothed.tsv \
                              --p_src_code ${p_src_code} \
                              --flag_slurm ${flag_slurm} \
                              --flag_singularity ${flag_singularity} \
                              --p_singularity_img ${p_singularity_img} \
                              --p_singularity_bindpath ${p_singularity_bindpath}"
                                                         
        echo "run combine NP1_BART & PWM.."
        job_id_combine=$(echo $(eval ${cmd_run_combine}) | awk '{split($0, a, " "); print a[4]}')
    fi
fi