--- a/genetic/optimizer_genetic.pl	Wed Jul 22 19:20:30 2020 +0000
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,110 +0,0 @@
-#!/usr/bin/perl -w
-use Cwd;
-use strict;
-#scoreN=c("-disease_clinvar","-score_AF","-score_functional",
-#                 "-score_NS","-score_nIND","-scoreeQTL",
-#                 "-scoreG","-scoreT","-scoreM",
-#                 "-scoreR","-scoreSP","-scoreGW")
-
-
-my %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"=>[1,10],   #numeric mandadory, multiple values
-"score_AF"=>[1,10],          #numeric mandatory, multiple values
-"score_functional"=>[1,10],  #numeric mandatory, multiple values
-"score_NS"=>[1,10],          #numeric mandatory, multiple values
-"score_nIND"=>[1,10],        #numeric mandatory, multiple values
-"scoreeQTL"=>[1,10],         #numeric mandatory, multiple values
-"scoreG"=>[1,10],            #numeric  mandatory, multiple values
-"scoreT"=>[1,10],
-"scoreM"=>[1,10],
-"scoreR"=>[1,10],
-"scoreSP"=>[1,10],
-"scoreGW"=>[1,10],
-"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
-"nind"=>5,
-"AF"=>0.0001
-);
-
-my @arguments=@ARGV;
-for (my $i=0;$i<=$#ARGV;$i+=2)
-{
-        my $act=$ARGV[$i];
-        $act=~s/-//g;
-        my $val=$ARGV[$i+1];
-        if (exists $arguments{$act})
-        {
-		unless ($val=~/\:/)
-		{
-                	$arguments{$act}=$val;
-		}else{
-			my ($s,$e)=(split(/\:/,$val));
-			$arguments{$act}=[$s,$e];
-		}
-        }else{
-                warn("$act: unknown argument\n");
-                my @valid=keys %arguments;
-                warn("Valid arguments are @valid\n");
-                die("All those moments will be lost in time, like tears in rain.\n Time to die!\n");
-        }
-        #print "$act $val\n";
-}
-
-my %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,
-);
-
-my $dir=getcwd();
-my $add_string=" ";
-
-foreach my $a (keys %compose_ARG)
-{
-	$add_string.="-$a $arguments{$a} " if $arguments{$a} ne "";
-}
-
-
-my @DC=@{$arguments{"disease_clinvar"}};#=>[2..8],   #numeric mandadory, but default value
-my @AF=@{$arguments{"score_AF"}};       #numeric mandatory, but default value
-my @FUN=@{$arguments{"score_functional"}};#=>[2..8],  #numeric mandatory, but default value
-my @NS=@{$arguments{"score_NS"}};#=>[2..8],          #numeric mandatory, but default value
-my @NI=@{$arguments{"score_nIND"}};#=>[2..8],        #numeric mandatory, but default value
-my @Q=@{$arguments{"scoreeQTL"}};        #numeric mandatory, but default value
-my @G=@{$arguments{"scoreG"}};	#=>[1..3],        #numeric  mandatory, but default value
-my @T=@{$arguments{"scoreT"}};
-my @M=@{$arguments{"scoreM"}};
-my @R=@{$arguments{"scoreR"}};
-my @SP=@{$arguments{"scoreSP"}};
-my @GW=@{$arguments{"scoreGW"}};
-
-my $Rfile=$arguments{"fileR"};
-my $Cfile=$arguments{"fileC"};
-my $Ofile=$arguments{"ofile"};
-
-my $minVals="$DC[0] $AF[0] $FUN[0] $NS[0] $NI[0] $Q[0] $G[0] $T[0] $M[0] $R[0] $SP[0] $GW[0]";
-my $maxVals="$DC[1] $AF[1] $FUN[1] $NS[1] $NI[1] $Q[1] $G[1] $T[1] $M[1] $R[1] $SP[1] $GW[1]";
-
-system("Rscript --vanilla $dir/GENEO_VINYL.R $Rfile $Cfile \"$add_string\" \"$minVals\" \"$maxVals\" $dir/$Ofile.tmp")==0||die("no optimization");
-
-system("sort -nk 19 -r $dir/$Ofile.tmp > $dir/$Ofile")==0||die("no sort");
-system("rm $dir/$Ofile.tmp")==0||die("no rm tmp file");
-