Gensor-Units

#!/bin/bash

###### Functions ######
function usage()
{
   # Display Help
   echo
   echo "Syntax: Gensor-Units command [options]"
   echo "Commands:"
   echo "   Update   Updates gu-library files"
   echo "   Gensor   Builds Gensor Units of the TFs in the regulatory network"
   echo "   Feedback  Searches for feedback within each GENSOR unit"
   echo
   echo "Options:"
   echo "-h | --help     Print usage."
   echo
}

function GU-help()
{
   # Display Help
   echo
   echo "Syntax: Gensor-Units Gensor -n <path to Network> -o <name of output directory>"
   echo "Commands:"
   echo "   Gensor   Builds Gensor Units of the TFs in the regulatory network"
   echo
   echo "Options:"
   echo "-h     Print this help message."
   echo "-n     Path to Network."
   echo "-o     Name of output directory."
   echo
}

function Feedback-help()
{
   # Display Help
   echo
   echo "Syntax: Gensor-Units Feedback -g <path to GU directory>"
   echo "Commands:"
   echo "   Feedback   Searches for feedback in the Gensor Units provided"
   echo
   echo "Options:"
   echo "-h     Print this help message."
   echo "-g     Path to GU directory."
   echo "-o     Path to output directory."
   echo
}

function update 
{
   echo "Updating GU library files"
   ./bin/update_library.sh
}

function Gensor-units
{  
   Ntw=$1 
   outdir=$2
   ./bin/pipeline_permissive_connectivity.sh $Ntw $outdir
}

function feedback
{
   echo "Calculating feedback"
   GUdir=${1%/}
   outdir=${2%/}
   ./bin/search_feedback.py $GUdir $outdir
}

############################################################
# Main program                                             #
############################################################

# Process options
#
if (( $# < 1 ))
   then
   echo "No commands or arguments provided"
   usage
   exit 0
fi;

while (( $# ))
do
    case "$1" in

         --help | -h)
               usage
               exit 0
         ;;

         Gensor)
            shift
            while getopts ":n:o:h" option; do
               case $option in
                  h) # display Help
                     GU-help
                     exit;;
                  n) # Enter a name
                     Ntw=$OPTARG;;
                  o) #output name
                     out=$OPTARG;;
                  \?) # Invalid option
                     echo "Error: Invalid option"
                     GU-help
                     exit;;
               esac
            done
            
            if [ "$*" == "" ]; then
               echo "No arguments provided"
               GU-help
               exit 1
            fi

            Gensor-units $Ntw $out
            exit 0
         ;;

         Update)
            shift
            update
            exit 0
         ;;

         Feedback)
            shift
            while getopts ":g:o:h" option; do
               case $option in
                  h) # display Help
                     Feedback-help
                     exit;;
                  g) # Enter a name
                     gu=$OPTARG;;
                  o) # Output dir
                     out=$OPTARG;;
                  \?) # Invalid option
                     echo "Error: Invalid option"
                     Feedback-help
                     exit;;
               esac
            done
            
            if [ "$*" == "" ]; then
               echo "No arguments provided"
               Feedback-help
               exit 1
            fi
            feedback $gu $out
            exit 0
         ;;

         *)
            echo "Command not recognized."
            usage
            exit 1
         ;;
    esac
done