root/galaxy-central/tools/regVariation/categorize_elements_satisfying_criteria.pl

#!/usr/bin/perl -w

# The program takes as input a set of categories, such that each category contains many elements.
# It also takes a table relating elements with criteria, such that each element is assigned a number
# representing the number of times the element satisfies a certain criterion. 
# The first input is a TABULAR format file, such that the left column represents the name of categories and, 
# all other columns represent the names of elements.
# The second input is a TABULAR format file relating elements with criteria, such that the first line
# represents the names of criteria and the left column represents the names of elements.
# The output is a TABULAR format file relating catergories with criteria, such that each categoy is 
# assigned a number representing the total number of times its elements satisfies a certain criterion.
# Each category is assigned as many numbers as criteria.

use strict;
use warnings;

#variables to handle information of the categories input file
my @categoryElementsArray = ();
my @categoriesArray = ();
my $categoryMemberNames;
my $categoryName;
my %categoryMembersHash = ();
my $memberNumber = 0;
my $totalMembersNumber = 0;
my $totalCategoriesNumber = 0;
my @categoryCountersTwoDimArray = ();
my $lineCounter1 = 0;

#variables to handle information of the criteria and elements data input file
my $elementLine;
my @elementDataArray = ();
my $elementName;
my @criteriaArray = ();
my $criteriaNumber = 0;
my $totalCriteriaNumber = 0;
my $lineCounter2 = 0;

#variable representing the row and column indices used to store results into a two-dimensional array
my $row = 0;
my $column = 0;

# check to make sure having correct files
my $usage = "usage: categorize_motifs_significance.pl [TABULAR.in] [TABULAR.in] [TABULAR.out] \n";
die $usage unless @ARGV == 3;

#get the categories input file
my $categories_inputFile = $ARGV[0];

#get the criteria and data input file
my $elements_data_inputFile = $ARGV[1];

#get the output file
my $categorized_data_outputFile = $ARGV[2];

#open the input and output files
open (INPUT1, "<", $categories_inputFile) || die("Could not open file $categories_inputFile \n");
open (INPUT2, "<", $elements_data_inputFile ) || die("Could not open file $elements_data_inputFile  \n");
open (OUTPUT, ">", $categorized_data_outputFile) || die("Could not open file $categorized_data_outputFile \n"); 

#store the first input file into an array
my @categoriesData = <INPUT1>;

#reset the value of $lineCounter1 to 0 
$lineCounter1 = 0;

#iterate through the first input file to get the names of categories and their corresponding elements   
foreach $categoryMemberNames (@categoriesData){
        chomp ($categoryMemberNames);
                
        @categoryElementsArray = split(/\t/, $categoryMemberNames);
        
        #store the name of the current category into an array
        $categoriesArray [$lineCounter1] = $categoryElementsArray[0];
        
        #store the name of the current category into a two-dimensional array
        $categoryCountersTwoDimArray [$lineCounter1] [0] = $categoryElementsArray[0];
                
        #get the total number of elements in the current category
        $totalMembersNumber = @categoryElementsArray;
        
        #store the names of categories and their corresponding elements into a hash
        for ($memberNumber = 1; $memberNumber < $totalMembersNumber; $memberNumber++) {
                        
                $categoryMembersHash{$categoryElementsArray[$memberNumber]} = $categoriesArray[$lineCounter1];
        }
        
        $lineCounter1++;
}

#store the second input file into an array
my @elementsData = <INPUT2>;

#reset the value of $lineCounter2 to 0 
$lineCounter2 = 0;

#iterate through the second input file in order to count the number of elements
#in each category that satisfy each criterion   
foreach $elementLine (@elementsData){
        chomp ($elementLine);
                
        $lineCounter2++;
        
        @elementDataArray = split(/\t/, $elementLine);
        
        #if at the first line, get the total number of criteria and the total  
        #number of catergories and initialize the two-dimensional array
        if ($lineCounter2 == 1){
                @criteriaArray = @elementDataArray;     
                $totalCriteriaNumber = @elementDataArray;
                
                $totalCategoriesNumber = @categoriesArray;
                
                #initialize the two-dimensional array
                for ($row = 0; $row < $totalCategoriesNumber; $row++) {
        
                        for ($column = 1; $column <= $totalCriteriaNumber; $column++) {
                                
                                $categoryCountersTwoDimArray [$row][$column] = 0;
                        }
                }
        }
        else{
                #get the element data
                $elementName = $elementDataArray[0];
                
                #do the counting and store the result in the two-dimensional array
                for ($criteriaNumber = 0; $criteriaNumber < $totalCriteriaNumber; $criteriaNumber++) {
                        
                        if ($elementDataArray[$criteriaNumber + 1] > 0){
                                
                                $categoryName = $categoryMembersHash{$elementName};
                                
                                my ($categoryIndex) = grep $categoriesArray[$_] eq $categoryName, 0 .. $#categoriesArray;
                                
                                $categoryCountersTwoDimArray [$categoryIndex] [$criteriaNumber + 1] = $categoryCountersTwoDimArray [$categoryIndex] [$criteriaNumber + 1] + $elementDataArray[$criteriaNumber + 1];
                        }
                }
        }
}

print OUTPUT "\t";

#store the criteria names into the output file  
for ($column = 1; $column <= $totalCriteriaNumber; $column++) {
                
        if ($column < $totalCriteriaNumber){
                print OUTPUT $criteriaArray[$column - 1] . "\t";
        }
        else{
                print OUTPUT $criteriaArray[$column - 1] . "\n";
        }
}
        
#store the category names and their corresponding number of elements satisfying criteria into the output file
for ($row = 0; $row < $totalCategoriesNumber; $row++) {
        
        for ($column = 0; $column <= $totalCriteriaNumber; $column++) {
                
                if ($column < $totalCriteriaNumber){
                        print OUTPUT $categoryCountersTwoDimArray [$row][$column] . "\t";
                }
                else{
                        print OUTPUT $categoryCountersTwoDimArray [$row][$column] . "\n";
                }
        }
}

#close the input and output file
close(OUTPUT);
close(INPUT2);
close(INPUT1);