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1 #!/usr/bin/perl -w
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2 use Cwd;
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3 use strict;
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4 #scoreN=c("-disease_clinvar","-score_AF","-score_functional",
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5 # "-score_NS","-score_nIND","-scoreeQTL",
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6 # "-scoreG","-scoreT","-scoreM",
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7 # "-scoreR","-scoreSP","-scoreGW")
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8
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9
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10 my %arguments=
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11 (
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12 "fileR"=>"", #file: vcf file of affected individuals
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13 "fileC"=>"", #file: vcf file of unaffected individuals
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14 "ofile"=>"", #name: name of the output files
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15 "AD"=>"T",
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16 "XL"=>"F", #
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17 "disease_clinvar"=>[1,10], #numeric mandadory, multiple values
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18 "score_AF"=>[1,10], #numeric mandatory, multiple values
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19 "score_functional"=>[1,10], #numeric mandatory, multiple values
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20 "score_NS"=>[1,10], #numeric mandatory, multiple values
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21 "score_nIND"=>[1,10], #numeric mandatory, multiple values
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22 "scoreeQTL"=>[1,10], #numeric mandatory, multiple values
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23 "scoreG"=>[1,10], #numeric mandatory, multiple values
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24 "scoreT"=>[1,10],
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25 "scoreM"=>[1,10],
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26 "scoreR"=>[1,10],
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27 "scoreSP"=>[1,10],
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28 "scoreGW"=>[1,10],
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29 "disease"=>"", #name optional
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30 "similarD"=>"", #file optional
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31 "lgenes"=>"", #file optional
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32 "leQTL"=>"qfile", #file mandatory, but default value
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33 "keywords"=>"kfile", #file mandatory, but default value
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34 "effects"=>"efile", #file mandatory, but default value
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35 "nind"=>5,
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36 "AF"=>0.0001
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37 );
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38
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39 my @arguments=@ARGV;
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40 for (my $i=0;$i<=$#ARGV;$i+=2)
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41 {
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42 my $act=$ARGV[$i];
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43 $act=~s/-//g;
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44 my $val=$ARGV[$i+1];
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45 if (exists $arguments{$act})
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46 {
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47 unless ($val=~/\:/)
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48 {
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49 $arguments{$act}=$val;
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50 }else{
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51 my ($s,$e)=(split(/\:/,$val));
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52 $arguments{$act}=[$s,$e];
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53 }
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54 }else{
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55 warn("$act: unknown argument\n");
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56 my @valid=keys %arguments;
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57 warn("Valid arguments are @valid\n");
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58 die("All those moments will be lost in time, like tears in rain.\n Time to die!\n");
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59 }
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60 #print "$act $val\n";
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61 }
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62
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63 my %compose_ARG=
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64 (
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65 "disease"=>1, #name optional
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66 "similarD"=>1, #file optional
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67 "lgenes"=>1, #file optional
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68 "leQTL"=>1, #file mandatory, but default value
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69 "keywords"=>1, #file mandatory, but default value
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70 "effects"=>1, #file
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71 "AF"=>1,
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72 "nind"=>1,
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73 "AD"=>1,
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74 "XL"=>1,
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75 );
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76
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77 my $dir=getcwd();
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78 my $add_string=" ";
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79
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80 foreach my $a (keys %compose_ARG)
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81 {
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82 $add_string.="-$a $arguments{$a} " if $arguments{$a} ne "";
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83 }
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84
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85
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86 my @DC=@{$arguments{"disease_clinvar"}};#=>[2..8], #numeric mandadory, but default value
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87 my @AF=@{$arguments{"score_AF"}}; #numeric mandatory, but default value
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88 my @FUN=@{$arguments{"score_functional"}};#=>[2..8], #numeric mandatory, but default value
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89 my @NS=@{$arguments{"score_NS"}};#=>[2..8], #numeric mandatory, but default value
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90 my @NI=@{$arguments{"score_nIND"}};#=>[2..8], #numeric mandatory, but default value
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91 my @Q=@{$arguments{"scoreeQTL"}}; #numeric mandatory, but default value
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92 my @G=@{$arguments{"scoreG"}}; #=>[1..3], #numeric mandatory, but default value
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93 my @T=@{$arguments{"scoreT"}};
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94 my @M=@{$arguments{"scoreM"}};
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95 my @R=@{$arguments{"scoreR"}};
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96 my @SP=@{$arguments{"scoreSP"}};
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97 my @GW=@{$arguments{"scoreGW"}};
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98
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99 my $Rfile=$arguments{"fileR"};
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100 my $Cfile=$arguments{"fileC"};
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101 my $Ofile=$arguments{"ofile"};
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102
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103 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]";
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104 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]";
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105
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106 system("Rscript --vanilla $dir/GENEO_VINYL.R $Rfile $Cfile \"$add_string\" \"$minVals\" \"$maxVals\" $Ofile.tmp")==0||die("no optimization");
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107
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108 system("(head -n 1 $Ofile.tmp && tail -n +1 $Ofile.tmp | sort -nk 19 -r) > $Ofile")==0||die("no sort");
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109
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