--- a/old_version/optimizer.pl	Wed Jul 22 19:20:30 2020 +0000
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,163 +0,0 @@
-#!/usr/bin/perl -w
-use Cwd;
-
-%arguments=
-(
-"fileR"=>"",		    #file: vcf file of affected individuals
-"fileC"=>"",		    #file: vcf file of unaffected individuals
-"ofile"=>"",		    #name: name of the output files
-"AD"=>"T",
-"XL"=>"F",		    #
-"disease_clinvar"=>[4,6],   #numeric mandadory, multiple values
-"score_AF"=>[2,4],          #numeric mandatory, multiple values
-"score_functional"=>[4,6],  #numeric mandatory, multiple values
-"score_NS"=>[2,4],          #numeric mandatory, multiple values
-"score_nIND"=>[2,4],        #numeric mandatory, multiple values
-"scoreeQTL"=>[2,4],         #numeric mandatory, multiple values
-"scoreG"=>[3,5],            #numeric  mandatory, multiple values
-"scoreI"=>[1..3],
-"disease"=>"",          #name   optional
-"similarD"=>"",         #file optional
-"lgenes"=>"",           #file optional
-"leQTL"=>"qfile",       #file   mandatory, but default value
-"keywords"=>"kfile",    #file   mandatory, but default value
-"effects"=>"efile",     #file   mandatory, but default value
-"ifile"=>"inter_Hs.file"
-"nind"=>5,
-"AF"=>0.0001
-);
-
-@arguments=@ARGV;
-for ($i=0;$i<=$#ARGV;$i+=2)
-{
-        $act=$ARGV[$i];
-        $act=~s/-//g;
-        $val=$ARGV[$i+1];
-        if (exists $arguments{$act})
-        {
-		unless ($val=~/\:/)
-		{
-                	$arguments{$act}=$val;
-		}else{
-			($s,$e)=(split(/\:/,$val));
-			@vls=();
-			print "$s $e\n";
-			for ($I=$s;$I<=$e;$I++)
-			{
-				push(@vls,$I);
-			}
-			print "@vls\n";
-			$arguments{$act}=\@vls;
-		}
-        }else{
-                warn("$act: unknown argument\n");
-                @valid=keys %arguments;
-                warn("Valid arguments are @valid\n");
-                die("All those moments will be lost in time, like tears in rain.\n Time to die!\n");
-        }
-        #print "$act $val\n";
-}
-
-%compose_ARG=
-(
-        "disease"=>1,          #name   optional
-        "similarD"=>1,         #file optional
-        "lgenes"=>1,           #file optional
-        "leQTL"=>1,       #file   mandatory, but default value
-        "keywords"=>1,    #file   mandatory, but default value
-        "effects"=>1,     #file
-	"AF"=>1,
-	"nind"=>1,
-	"AD"=>1,
-	"XL"=>1,
-	"ifile"=>1
-
-);
-
-$dir=getcwd();
-print "$dir\n";
-$add_string=" ";
-
-foreach $a (keys %compose_ARG)
-{
-	$add_string.="-$a $arguments{$a} " if $arguments{$a} ne "";
-}
-
-#print "$add_string";
-
-
-@DC=@{$arguments{"disease_clinvar"}};	#=>[2..8],   #numeric mandadory, but default value
-@AF=@{$arguments{"score_AF"}};          #numeric mandatory, but default value
-@FUN=@{$arguments{"score_functional"}};	#=>[2..8],  #numeric mandatory, but default value
-@NS=@{$arguments{"score_NS"}};		#=>[2..8],          #numeric mandatory, but default value
-@NI=@{$arguments{"score_nIND"}};	#=>[2..8],        #numeric mandatory, but default value
-@Q=@{$arguments{"scoreeQTL"}};        	#numeric mandatory, but default value
-@G=@{$arguments{"scoreG"}};		#=>[1..3],            #numeric  mandatory, but default value
-@I=@{$arguments{"scoreI"}};
-
-$Rfile=$arguments{"fileR"};
-$Tfile=$arguments{"fileC"};
-$Ofile=$arguments{"ofile"};
-open(O,">$Ofile");
-print O "disease_clinvar\tscore_AF\tscore_functional\tscore_NS\tscore_nIND\tscoreeQTL\tscoreG\tCut_off\tPosD\tPosH\tPvalue\tFold_change\n";
-$commandR="perl $dir/score_complete_alt_M.pl -vcf $dir/$Rfile -ofile $dir/R.csv  -ovcfile $dir/R.vcf  $add_string";
-$commandT="perl $dir/score_complete_alt_M.pl -vcf $dir/$Tfile -ofile $dir/T.csv  -ovcfile $dir/T.vcf  $add_string";
-
-
-foreach $dc (@DC)
-{
-
-	foreach $af (@AF)
-	{
-
-		foreach $fun (@FUN)
-		{
-
-			foreach $ns (@NS)
-			{
-
-				foreach $ni (@NI)
-				{
-					
-
-					foreach $Q (@Q)
-					{
-						foreach $G (@G)
-						{
-							foreach $I (@I)
-							{
-							$commandR.="-score_AF $af ";
-                					$commandT.="-score_AF $af ";
-							$commandR.="-score_functional $fun ";
-                        				$commandT.="-score_functional $fun ";
-							$commandR.="-score_NS $ns ";
-                                			$commandT.="-score_NS $ns ";
-							$commandR.="-score_nIND $ni ";
-                                        		$commandT.="-score_nIND $ni ";
-							$commandR.="-scoreeQTL $Q ";
-                                                	$commandT.="-scoreeQTL $Q ";
-							$commandR.="-disease_clinvar $dc ";
-        						$commandT.="-disease_clinvar $dc ";
-							$commandR.="-scoreG $G ";
-                                        		$commandT.="-scoreG $G ";
-							$commandR.="-scoreI $I ";
-                                                        $commandT.="-scoreI $I ";
-
-							#print "$commandR\n$commandT\n";
-							system($commandR)==0||die("Non giro Rfile");
-							system($commandT)==0||die("Non giro Tfile");
-							$commandR="perl $dir/score_complete_alt_M.pl -vcf $dir/$Rfile -ofile $dir/R.csv  -ovcfile $dir/R.vcf  $add_string";
-							$commandT="perl $dir/score_complete_alt_M.pl -vcf $dir/$Tfile -ofile $dir/T.csv  -ovcfile $dir/T.vcf  $add_string";
-
-							$r=`Rscript --vanilla $dir/survival_optM.R $dir/R.csv $dir/T.csv`;
-							
-							print O "$dc\t$af\t$fun\t$ns\t$ni\t$Q\t$G\t$r\n";
-							}
-							#die();
-						}
-					}
-				}
-			}
-		}
-	}
-}