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1 #!/usr/bin/perl
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2
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3 # 17/12/2013
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4
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5 if($#ARGV==0){
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6 print "This program takes the Saint Output File and produces two matrices.\n";
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7 print "One has average spectral counts and the other FDR scores,\n";
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8 print "\nusage:\n $0\n-i [csv saint output file]\n-s [FDR cutoff, default=0.01]\n\n";
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9 die;
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10 }
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11 else{
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12 $i=0;
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13 $cutoff=0.01;
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14 $spec_cutoff=0;
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15 while($i<=$#ARGV){
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16 if($ARGV[$i] eq '-i'){
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17 $i++;
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18 $ifile=$ARGV[$i];
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19 }
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20 elsif($ARGV[$i] eq '-s'){
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21 $i++;
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22 if($ARGV[$i]>1 || $ARGV[$i]<0){
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23 die "\nFDR cutoff must be between 0 and 1 \n\n";
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24 }
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25 $cutoff=$ARGV[$i];
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26 }
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27 elsif($ARGV[$i] eq '-x'){
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28 $i++;
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29 if($ARGV[$i]<0){
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30 die "\nAvgSpec cutoff must be > 0 \n\n";
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31 }
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32 $spec_cutoff=$ARGV[$i];
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33 }
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34 else{
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35 die "\Incorrect program usage\n\n";
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36 }
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37 $i++;
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38 }
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39 }
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40
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41 $baitn=0, $bait[0]=xxxx, $sig_preysn=0;
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42 $file='';
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43 open(IFILE,"<$ifile") || die "$ifile can't be opened: $!";
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44 { local $/=undef; $file=<IFILE>; }
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45 @lines=split /[\r\n]+/, $file;
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46 foreach $line (@lines) {
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47 if($line =~ /^Bait/){
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48 }
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49 elsif($line =~ /^([^\t]+)\t[^\t]+\t([^\t]+)\t[^\t]+\t[\d]+\t([\d\.]+)\t[\d]+\t[^\t]+\t[^\t]+\t[^\t]+\t[^\t]+\t[^\t]+\t([^\t]+)\t[^\t]+\t([^\t]+)\t/){
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50 if($1 ne $bait[$baitn]){
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51 $baitn++;
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52 $bait[$baitn]=$1;
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53 $preyn[$baitn]=0;
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54 }
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55 $preyn[$baitn]++;
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56 $preys[$baitn][$preyn[$baitn]]=$2;
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57 $avgspec[$baitn][$preyn[$baitn]]=$3;
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58 $saint[$baitn][$preyn[$baitn]]=$4;
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59 $fdr[$baitn][$preyn[$baitn]]=$5;
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60 if($5 <= $cutoff && $3 >= $spec_cutoff){
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61 $check_prey=0;
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62 for($i=1; $i<=$sig_preysn; $i++){
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63 if($sig_preys[$i] eq $2){
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64 $check_prey=1;
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65 }
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66 }
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67 if($check_prey==0){
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68 $sig_preysn++;
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69 $sig_preys[$sig_preysn]=$2;
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70 }
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71 }
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72 }
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73 else{
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74 }
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75 }
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76 close(IFILE);
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77
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78 open(SC_FILE, ">SC_data.txt");
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79 open(FDR_FILE, ">FDR_data.txt");
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80
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81 for($i=1; $i<=$baitn; $i++){
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82 print SC_FILE "\t$bait[$i]";
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83 print FDR_FILE "\t$bait[$i]";
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84 }
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85 print SC_FILE "\n";
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86 print FDR_FILE "\n";
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87 for($i=1; $i<=$sig_preysn; $i++){
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88 print SC_FILE "$sig_preys[$i]";
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89 print FDR_FILE "$sig_preys[$i]";
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90 for($j=1; $j<=$baitn; $j++){
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91 $krem=0;
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92 for($k=1; $k<=$preyn[$j]; $k++){;
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93 if($preys[$j][$k] eq $sig_preys[$i]){
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94 $krem=$k;
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95 last;
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96 }
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97 }
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98 if($krem != 0){
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99 print SC_FILE "\t$avgspec[$j][$krem]";
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100 print FDR_FILE "\t$fdr[$j][$krem]";
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101 }
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102 else{
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103 print SC_FILE "\t0";
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104 print FDR_FILE "\t1";
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105 }
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106 }
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107 print SC_FILE "\n";
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108 print FDR_FILE "\n";
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109 }
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110 close(SC_FILE);
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111 close(FDR_FILE);
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112
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