diff optimizer_genetic.pl @ 0:4c6529d120c3 draft

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/optimizer_genetic.pl	Tue Jun 09 16:07:19 2020 +0000
@@ -0,0 +1,109 @@
+#!/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\" $Ofile.tmp")==0||die("no optimization");
+
+system("(head -n 1 $Ofile.tmp && tail -n +1 $Ofile.tmp | sort -nk 19 -r) > $Ofile")==0||die("no sort");
+