miARma

#!/usr/bin/perl

#########################################################################	
#	miARma, miRNA and RNASeq multiprocess Analysis						#
#																		#
#	Created at Computational Biology and Bioinformatics Group (CbBio)	#
#	Institute of Biomedicine of Seville. IBIS (Spain)					#
#	Modified and Updated at Bioinformatics Unit at IPBLN-CSIC            #
#   Institue for Parasitology and Biomedicine Lopez-Neyra (IPBLN-CSIC)  # 
#   Granada (Spain)                   									#
#   Copyright (c) 2017 IBIS & IPBLN. All rights reserved.              	#
#	mail : miARma-devel@cbbio.es 										#
#########################################################################

use strict;
my $configuration_file;
my $miARmaPath;
my $check_input;

sub help{
	print_header();
my $usage = qq{
Usage:\n 
  perl $0 file.ini [options]
	
Options:

 -check   Instead of running the analysis contained in file.ini, it checks that parameters are correct and then quits.
 -help    Print this help.
	
	
};

			print STDERR $usage;
			exit(1);	
}

sub print_header{
	system("clear");
	print "#########################################################################	
#   miARma, miRNA and RNASeq Multiprocess Analysis			#
#                miARma v 1.7 (Aug-2017)                                #
#               		                              		#
#   Created at Computational Biology and Bioinformatics Group (CbBio)   #
#   Institute of Biomedicine of Seville. IBIS (Spain)                   #
#   Modified and Updated at Bioinformatics Unit at IPBLN-CSIC   	#
#   Institue for Parasitology and Biomedicine Lopez-Neyra (IPBLN-CSIC). #
#   Granada (Spain)             				        #
#   Copyright (c) 2017 IBIS & IPBLN. All rights reserved.               #
#   mail : miARma-devel\@cbbio.es                                        #
#########################################################################\n";
}

BEGIN {
	
	#checking input parameter
	if(@ARGV<1){
		help();
	}
	if($ARGV[0] eq "help" or $ARGV[0] eq "-help" or  $ARGV[0] eq "--help"){
		help();
	}
	# configuration file
	$configuration_file=$ARGV[0];
	$check_input=$ARGV[1];
	my $check=0;
	
	# Searching for needed parameters before start
	open(FILE,$configuration_file) || help();
	while(<FILE>){
		chomp;
		if(lc($_) =~ /miarmapath/){
			$miARmaPath=$_;
			$miARmaPath=~s/.+=(.+)/$1/g;
			$check=1;
		}
	}
	close FILE;
	if($check ==0){
		print STDERR "\nSEVERE ERROR :: $configuration_file is incorrect. Please check the parameter miARmaPath under [General] Section\n\n";
		exit;
	}
}

#loading miARma libraries
use lib "$miARmaPath/lib/";
use lib "$miARmaPath/lib/Perl";
use CbBio::RNASeq::miARma;
run_miARma(
	config=>$configuration_file,
	miARmaPath=>$miARmaPath,
	check=>$check_input,
)