probe

#!/usr/bin/perl

use strict;
use Getopt::Long;
use FindBin;
use lib "$FindBin::Bin/Perlib";
use predict;
use tfbs;
use tfen;
use reg;
use net;

my $G_USAGE = "

Program: probe (Predict Regulators Based On Binding site and Expression)
Version: 1.0

Usage:   probe <command> [options]

Commands:
         predict     predict TFs from protein sequences        
         tfbs        generate TFBS set for species 
         tfen        conduct TF enrichment analysis using hypergeometric distribution
         reg         Generate the transcriptional regulatory landscape based on the TFBS
         net         Generate the regulatory network based on TFBS and hub genes  

";

my $command = undef;
if (!defined $ARGV[0] || substr($ARGV[0],0,1) eq '-' || substr($ARGV[0],0,2) eq '--') {
        die($G_USAGE);
}
$command = shift @ARGV; $command = lc $command;

# auto-flush for both stderr and stdout
 select(STDERR);
 $| = 1;
 select(STDOUT);
 $| = 1;

if('predict' eq $command){
         runpredict();
                       }
if ('tfbs' eq $command) {
        runtfbs();
} elsif ('tfen' eq $command) {
         runtfen();
} elsif ('reg' eq $command){
        runreg();
                                                       
} elsif ('net' eq $command) {
         runnet();
} else {
  
    print $G_USAGE;
       }
 
      
  exit 0;
       
















                                                           

##
##      PROBE: Predict Regulators Based on Binding site and Expression
##
##      author: Fei Shen <352363546@qq.com>  
##
## Copyright (c) 2021 Beijing Agro-biotechnology Research Center
##
## Permission is hereby granted, free of charge, to any person obtaining a copy
## of this software and associated documentation files (the "Software"), to deal
## in the Software without restriction, including without limitation the rights
## to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
## copies of the Software, and to permit persons to whom the Software is
## furnished to do so, subject to the following conditions:
## 
## The above copyright notice and this permission notice shall be included in all
## copies or substantial portions of the Software.
## 
## THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
## IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
## FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
## AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
## LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
## OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
## SOFTWARE.