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1 #!/usr/bin/perl -w
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2 use Cwd;
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3
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4 %arguments=
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5 (
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6 "fileR"=>"", #file: vcf file of affected individuals
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7 "fileC"=>"", #file: vcf file of unaffected individuals
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8 "ofile"=>"", #name: name of the output files
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9 "AD"=>"T",
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10 "XL"=>"F", #
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11 "disease_clinvar"=>[4,6], #numeric mandadory, multiple values
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12 "score_AF"=>[2,4], #numeric mandatory, multiple values
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13 "score_functional"=>[4,6], #numeric mandatory, multiple values
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14 "score_NS"=>[2,4], #numeric mandatory, multiple values
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15 "score_nIND"=>[2,4], #numeric mandatory, multiple values
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16 "scoreeQTL"=>[2,4], #numeric mandatory, multiple values
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17 "scoreG"=>[3,5], #numeric mandatory, multiple values
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18 "scoreI"=>[1..3],
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19 "disease"=>"", #name optional
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20 "similarD"=>"", #file optional
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21 "lgenes"=>"", #file optional
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22 "leQTL"=>"qfile", #file mandatory, but default value
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23 "keywords"=>"kfile", #file mandatory, but default value
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24 "effects"=>"efile", #file mandatory, but default value
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25 "ifile"=>"inter_Hs.file"
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26 "nind"=>5,
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27 "AF"=>0.0001
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28 );
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29
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30 @arguments=@ARGV;
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31 for ($i=0;$i<=$#ARGV;$i+=2)
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32 {
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33 $act=$ARGV[$i];
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34 $act=~s/-//g;
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35 $val=$ARGV[$i+1];
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36 if (exists $arguments{$act})
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37 {
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38 unless ($val=~/\:/)
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39 {
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40 $arguments{$act}=$val;
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41 }else{
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42 ($s,$e)=(split(/\:/,$val));
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43 @vls=();
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44 print "$s $e\n";
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45 for ($I=$s;$I<=$e;$I++)
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46 {
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47 push(@vls,$I);
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48 }
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49 print "@vls\n";
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50 $arguments{$act}=\@vls;
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51 }
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52 }else{
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53 warn("$act: unknown argument\n");
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54 @valid=keys %arguments;
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55 warn("Valid arguments are @valid\n");
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56 die("All those moments will be lost in time, like tears in rain.\n Time to die!\n");
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57 }
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58 #print "$act $val\n";
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59 }
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60
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61 %compose_ARG=
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62 (
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63 "disease"=>1, #name optional
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64 "similarD"=>1, #file optional
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65 "lgenes"=>1, #file optional
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66 "leQTL"=>1, #file mandatory, but default value
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67 "keywords"=>1, #file mandatory, but default value
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68 "effects"=>1, #file
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69 "AF"=>1,
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70 "nind"=>1,
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71 "AD"=>1,
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72 "XL"=>1,
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73 "ifile"=>1
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74
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75 );
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76
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77 $dir=getcwd();
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78 print "$dir\n";
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79 $add_string=" ";
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80
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81 foreach $a (keys %compose_ARG)
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82 {
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83 $add_string.="-$a $arguments{$a} " if $arguments{$a} ne "";
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84 }
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85
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86 #print "$add_string";
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87
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88
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89 @DC=@{$arguments{"disease_clinvar"}}; #=>[2..8], #numeric mandadory, but default value
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90 @AF=@{$arguments{"score_AF"}}; #numeric mandatory, but default value
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91 @FUN=@{$arguments{"score_functional"}}; #=>[2..8], #numeric mandatory, but default value
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92 @NS=@{$arguments{"score_NS"}}; #=>[2..8], #numeric mandatory, but default value
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93 @NI=@{$arguments{"score_nIND"}}; #=>[2..8], #numeric mandatory, but default value
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94 @Q=@{$arguments{"scoreeQTL"}}; #numeric mandatory, but default value
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95 @G=@{$arguments{"scoreG"}}; #=>[1..3], #numeric mandatory, but default value
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96 @I=@{$arguments{"scoreI"}};
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97
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98 $Rfile=$arguments{"fileR"};
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99 $Tfile=$arguments{"fileC"};
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100 $Ofile=$arguments{"ofile"};
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101 open(O,">$Ofile");
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102 print O "disease_clinvar\tscore_AF\tscore_functional\tscore_NS\tscore_nIND\tscoreeQTL\tscoreG\tCut_off\tPosD\tPosH\tPvalue\tFold_change\n";
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103 $commandR="perl $dir/score_complete_alt_M.pl -vcf $dir/$Rfile -ofile $dir/R.csv -ovcfile $dir/R.vcf $add_string";
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104 $commandT="perl $dir/score_complete_alt_M.pl -vcf $dir/$Tfile -ofile $dir/T.csv -ovcfile $dir/T.vcf $add_string";
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105
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106
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107 foreach $dc (@DC)
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108 {
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109
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110 foreach $af (@AF)
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111 {
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112
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113 foreach $fun (@FUN)
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114 {
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115
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116 foreach $ns (@NS)
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117 {
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118
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119 foreach $ni (@NI)
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120 {
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121
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122
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123 foreach $Q (@Q)
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124 {
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125 foreach $G (@G)
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126 {
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127 foreach $I (@I)
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128 {
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129 $commandR.="-score_AF $af ";
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130 $commandT.="-score_AF $af ";
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131 $commandR.="-score_functional $fun ";
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132 $commandT.="-score_functional $fun ";
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133 $commandR.="-score_NS $ns ";
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134 $commandT.="-score_NS $ns ";
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135 $commandR.="-score_nIND $ni ";
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136 $commandT.="-score_nIND $ni ";
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137 $commandR.="-scoreeQTL $Q ";
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138 $commandT.="-scoreeQTL $Q ";
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139 $commandR.="-disease_clinvar $dc ";
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140 $commandT.="-disease_clinvar $dc ";
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141 $commandR.="-scoreG $G ";
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142 $commandT.="-scoreG $G ";
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143 $commandR.="-scoreI $I ";
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144 $commandT.="-scoreI $I ";
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145
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146 #print "$commandR\n$commandT\n";
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147 system($commandR)==0||die("Non giro Rfile");
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148 system($commandT)==0||die("Non giro Tfile");
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149 $commandR="perl $dir/score_complete_alt_M.pl -vcf $dir/$Rfile -ofile $dir/R.csv -ovcfile $dir/R.vcf $add_string";
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150 $commandT="perl $dir/score_complete_alt_M.pl -vcf $dir/$Tfile -ofile $dir/T.csv -ovcfile $dir/T.vcf $add_string";
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151
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152 $r=`Rscript --vanilla $dir/survival_optM.R $dir/R.csv $dir/T.csv`;
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153
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154 print O "$dc\t$af\t$fun\t$ns\t$ni\t$Q\t$G\t$r\n";
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155 }
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156 #die();
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157 }
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158 }
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159 }
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160 }
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161 }
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162 }
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163 }
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