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1 #this is a script to automate data workup following Fishers exact test association analyses
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2 # This script takes the R_result and the names file and then generates
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3 #4 4xls spreadsheets
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4 # 3 images
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5 @name;
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6 @sub_name;
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7 @result;
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8 @sub_result;
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9 $count = 0;
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10 unless (-d "results/Assoc") {
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11 mkdir("results/Assoc");
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12 }
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13 open OUT1, "> results/Assoc/Associations.xls";
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14 open OUT2, "> results/Assoc/Ann_cis_list.txt";
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15 open OUT3, "> results/Assoc/Ann_cis_table.xls";
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16 print OUT3 "Event1\tEvent2\tFET Pvalue\tBonferroni Significance\tBH 20%FDR Significancei\n";
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17 open OUT4, "> results/Assoc/Cis_cis_list.txt";
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18 open OUT5, "> results/Assoc/Cis_cis_table.xls";
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19 print OUT5 "Event1\tEvent2\tFET Pvalue\tBonferroni Significance\tBH 20%FDR Significance\n";
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20 open OUT6, "> results/Assoc/Ann_ann_list.txt";
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21 open OUT7, "> results/Assoc/Ann_Ann_table.xls";
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22 print OUT7 "Event1\tEvent2\tFET Pvalue\tBonferroni Significance\tBH 20%FDR Significance\n";
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23 open SOURCE, "< results/Assoc/R_result.txt";
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24 @tableAnnCis;
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25 @tableAnnAnn;
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26 @tableCisCis;
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27 while (defined($line = <SOURCE>)) {
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28 $count++;
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29 chomp $line;
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30 @result= split(/\t/, $line);
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31 @sub_result= split(/\s=\s|\s<\s/, $result[1]);
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32 print $sub_result[1];
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33 $pval[$count]= $sub_result[1];
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34 }
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35 $count = 0;
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36 open SOURCE, "< results/Assoc/Fisher_pre_named.txt";
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37 while (defined($line = <SOURCE>)) {
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38 $count++;
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39 chomp $line;
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40 @name= split(/\t/, $line);
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41 @sub_name= split(/__/, $name[0]);
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42 print OUT1 "$line\t$pval[$count]\n";
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43 if (($sub_name[1] =~m/descriptor/) and ($sub_name[0] !~ m/descriptor/)) {
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44 $viewpval= -(log($pval[$count])/log(10));
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45 print OUT2 "$sub_name[1]\t$sub_name[0]\t$viewpval\n";
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46 if ($pval[$count] < 0.05) {
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47 $data4table = "$sub_name[1]\t$sub_name[0]\t$pval[$count]\n";
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48 push(@tableAnnCis, $data4table);
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49 }
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50 }
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51
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52
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53 if (($sub_name[1] !~m/descriptor/) and ($sub_name[0] !~ m/descriptor/)) {
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54 $viewpval= -log($pval[$count]);
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55 print OUT4 "$sub_name[1]\t$sub_name[0]\t$viewpval\n";
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56 print OUT4 "$sub_name[0]\t$sub_name[1]\t$viewpval\n";
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57 if ($pval[$count] < 0.05) {
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58 $data4table = "$sub_name[1]\t$sub_name[0]\t$pval[$count]\n";
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59 push(@tableCisCis, $data4table);
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60 }
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61 }
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62
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63 if (($sub_name[1] =~m/descriptor/) and ($sub_name[0] =~ m/descriptor/)) {
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64 $viewpval= -log($pval[$count]);
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65 print OUT6 "$sub_name[1]\t$sub_name[0]\t$viewpval\n";
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66 print OUT6 "$sub_name[0]\t$sub_name[1]\t$viewpval\n";
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67 if ($pval[$count] < 0.05) {
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68 $data4table = "$sub_name[1]\t$sub_name[0]\t$pval[$count]\n";
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69 push(@tableAnnAnn, $data4table);
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70 }
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71 }
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72
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73
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74 }
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75 @sortedAnnCis = sort { (split '\t', $a)[2] <=> (split '\t', $b)[2] } @tableAnnCis;
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76 @sortedCisCis = sort { (split '\t', $a)[2] <=> (split '\t', $b)[2] } @tableCisCis;
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77 @sortedAnnAnn = sort { (split '\t', $a)[2] <=> (split '\t', $b)[2] } @tableAnnAnn;
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78
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79 open SOURCE, "< FISH/multi_test.txt";
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80 while (defined($line = <SOURCE>)) {
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81 chomp $line;
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82 @name=split(/\t/, $line);
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83 $corrAnnCis = $name[2];
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84 $corrCisCis = $name[3];
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85 $corrAnnAnn = $name[4];
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86 }
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87
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88 $pos = 1;
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89 foreach (@sortedAnnCis) {
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90 $bonf = 0.05/$corrAnnCis;
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91 $fdr = ($pos/$corrAnnCis)*0.20;
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92 $pos++;
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93 chomp $_;
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94 print OUT3 "$_\t$bonf\t$fdr\n";
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95 }
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96 $pos = 1;
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97
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98 foreach (@sortedCisCis) {
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99 $bonf = 0.05/$corrCisCis;
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100 $fdr = ($pos/$corrCisCis)*0.20;
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101 $pos++;
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102 chomp $_;
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103 print OUT5 "$_\t$bonf\t$fdr\n";
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104 }
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105 $pos =1;
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106 foreach (@sortedAnnAnn) {
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107 $bonf = 0.05/$corrAnnAnn;
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108 $fdr = ($pos/$corrAnnAnn)*0.20;
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109 $pos++;
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110 chomp $_;
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111 print OUT7 "$_\t$bonf\t$fdr\n";
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112 }
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113
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114
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115 close OUT7;
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116 close OUT6;
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117 close OUT5;
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118 close OUT4;
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119 close OUT3;
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120 close OUT2;
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121 close OUT1;
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122 system ("perl lib/list2tab.pl 1 2 3 0 results/Assoc/Ann_cis_list.txt > results/Assoc/Ann_cis_matrix.txt");
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123 system ("perl lib/list2tab.pl 1 2 3 0 results/Assoc/Cis_cis_list.txt > results/Assoc/Cis_cis_matrix.txt");
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124 system ("perl lib/list2tab.pl 1 2 3 0 results/Assoc/Ann_ann_list.txt > results/Assoc/Ann_ann_matrix.txt");
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