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1 #!/usr/bin/perl -w
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2
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3 # The program takes as input a set of categories, such that each category contains many elements.
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4 # It also takes a table relating elements with criteria, such that each element is assigned a number
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5 # representing the number of times the element satisfies a certain criterion.
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6 # The first input is a TABULAR format file, such that the left column represents the name of categories and,
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7 # all other columns represent the names of elements.
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8 # The second input is a TABULAR format file relating elements with criteria, such that the first line
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9 # represents the names of criteria and the left column represents the names of elements.
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10 # The output is a TABULAR format file relating catergories with criteria, such that each categoy is
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11 # assigned a number representing the total number of times its elements satisfies a certain criterion.
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12 # Each category is assigned as many numbers as criteria.
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13
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14 use strict;
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15 use warnings;
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16
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17 #variables to handle information of the categories input file
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18 my @categoryElementsArray = ();
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19 my @categoriesArray = ();
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20 my $categoryMemberNames;
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21 my $categoryName;
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22 my %categoryMembersHash = ();
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23 my $memberNumber = 0;
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24 my $totalMembersNumber = 0;
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25 my $totalCategoriesNumber = 0;
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26 my @categoryCountersTwoDimArray = ();
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27 my $lineCounter1 = 0;
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28
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29 #variables to handle information of the criteria and elements data input file
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30 my $elementLine;
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31 my @elementDataArray = ();
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32 my $elementName;
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33 my @criteriaArray = ();
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34 my $criteriaNumber = 0;
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35 my $totalCriteriaNumber = 0;
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36 my $lineCounter2 = 0;
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37
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38 #variable representing the row and column indices used to store results into a two-dimensional array
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39 my $row = 0;
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40 my $column = 0;
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41
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42 # check to make sure having correct files
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43 my $usage = "usage: categorize_motifs_significance.pl [TABULAR.in] [TABULAR.in] [TABULAR.out] \n";
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44 die $usage unless @ARGV == 3;
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45
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46 #get the categories input file
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47 my $categories_inputFile = $ARGV[0];
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48
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49 #get the criteria and data input file
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50 my $elements_data_inputFile = $ARGV[1];
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51
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52 #get the output file
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53 my $categorized_data_outputFile = $ARGV[2];
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54
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55 #open the input and output files
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56 open (INPUT1, "<", $categories_inputFile) || die("Could not open file $categories_inputFile \n");
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57 open (INPUT2, "<", $elements_data_inputFile ) || die("Could not open file $elements_data_inputFile \n");
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58 open (OUTPUT, ">", $categorized_data_outputFile) || die("Could not open file $categorized_data_outputFile \n");
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59
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60 #store the first input file into an array
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61 my @categoriesData = <INPUT1>;
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62
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63 #reset the value of $lineCounter1 to 0
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64 $lineCounter1 = 0;
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65
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66 #iterate through the first input file to get the names of categories and their corresponding elements
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67 foreach $categoryMemberNames (@categoriesData){
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68 chomp ($categoryMemberNames);
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69
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70 @categoryElementsArray = split(/\t/, $categoryMemberNames);
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71
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72 #store the name of the current category into an array
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73 $categoriesArray [$lineCounter1] = $categoryElementsArray[0];
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74
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75 #store the name of the current category into a two-dimensional array
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76 $categoryCountersTwoDimArray [$lineCounter1] [0] = $categoryElementsArray[0];
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77
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78 #get the total number of elements in the current category
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79 $totalMembersNumber = @categoryElementsArray;
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80
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81 #store the names of categories and their corresponding elements into a hash
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82 for ($memberNumber = 1; $memberNumber < $totalMembersNumber; $memberNumber++) {
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83
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84 $categoryMembersHash{$categoryElementsArray[$memberNumber]} = $categoriesArray[$lineCounter1];
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85 }
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86
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87 $lineCounter1++;
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88 }
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89
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90 #store the second input file into an array
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91 my @elementsData = <INPUT2>;
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92
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93 #reset the value of $lineCounter2 to 0
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94 $lineCounter2 = 0;
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95
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96 #iterate through the second input file in order to count the number of elements
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97 #in each category that satisfy each criterion
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98 foreach $elementLine (@elementsData){
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99 chomp ($elementLine);
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100
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101 $lineCounter2++;
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102
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103 @elementDataArray = split(/\t/, $elementLine);
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104
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105 #if at the first line, get the total number of criteria and the total
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106 #number of catergories and initialize the two-dimensional array
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107 if ($lineCounter2 == 1){
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108 @criteriaArray = @elementDataArray;
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109 $totalCriteriaNumber = @elementDataArray;
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110
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111 $totalCategoriesNumber = @categoriesArray;
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112
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113 #initialize the two-dimensional array
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114 for ($row = 0; $row < $totalCategoriesNumber; $row++) {
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115
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116 for ($column = 1; $column <= $totalCriteriaNumber; $column++) {
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117
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118 $categoryCountersTwoDimArray [$row][$column] = 0;
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119 }
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120 }
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121 }
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122 else{
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123 #get the element data
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124 $elementName = $elementDataArray[0];
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125
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126 #do the counting and store the result in the two-dimensional array
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127 for ($criteriaNumber = 0; $criteriaNumber < $totalCriteriaNumber; $criteriaNumber++) {
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128
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129 if ($elementDataArray[$criteriaNumber + 1] > 0){
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130
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131 $categoryName = $categoryMembersHash{$elementName};
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132
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133 my ($categoryIndex) = grep $categoriesArray[$_] eq $categoryName, 0 .. $#categoriesArray;
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134
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135 $categoryCountersTwoDimArray [$categoryIndex] [$criteriaNumber + 1] = $categoryCountersTwoDimArray [$categoryIndex] [$criteriaNumber + 1] + $elementDataArray[$criteriaNumber + 1];
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136 }
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137 }
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138 }
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139 }
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140
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141 print OUTPUT "\t";
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142
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143 #store the criteria names into the output file
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144 for ($column = 1; $column <= $totalCriteriaNumber; $column++) {
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145
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146 if ($column < $totalCriteriaNumber){
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147 print OUTPUT $criteriaArray[$column - 1] . "\t";
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148 }
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149 else{
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150 print OUTPUT $criteriaArray[$column - 1] . "\n";
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151 }
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152 }
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153
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154 #store the category names and their corresponding number of elements satisfying criteria into the output file
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155 for ($row = 0; $row < $totalCategoriesNumber; $row++) {
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156
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157 for ($column = 0; $column <= $totalCriteriaNumber; $column++) {
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158
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159 if ($column < $totalCriteriaNumber){
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160 print OUTPUT $categoryCountersTwoDimArray [$row][$column] . "\t";
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161 }
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162 else{
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163 print OUTPUT $categoryCountersTwoDimArray [$row][$column] . "\n";
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164 }
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165 }
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166 }
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167
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168 #close the input and output file
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169 close(OUTPUT);
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170 close(INPUT2);
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171 close(INPUT1);
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172
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