--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/regVariation/compute_motif_frequencies_for_all_motifs.pl	Fri Mar 09 19:37:19 2012 -0500
@@ -0,0 +1,153 @@
+#!/usr/bin/perl -w
+
+# a program to compute the frequencies of each motif at a window size, determined by the user, in both 
+# upstream and downstream sequences flanking indels in all chromosomes.
+# the first input is a TABULAR format file containing the motif names and sequences, such that the file 
+# consists of two columns: the left column represents the motif names and the right column represents 
+# the motif sequence, one line per motif.
+# the second input is a TABULAR format file containing the windows into which both upstream and downstream 
+# sequences flanking indels have been divided.
+# the fourth input is an integer number representing the number of windows to be considered in both 
+# upstream and downstream flanking sequences.
+# the output is a TABULAR format file consisting of three columns: the left column represents the motif 
+# name, the middle column represents the motif frequency in the window of the upstream sequence flanking 
+# an indel, and the the right column represents the motif frequency in the window of the downstream 
+# sequence flanking an indel, one line per indel.
+# The total number of lines in the output file = number of motifs x number of indels.
+
+use strict;
+use warnings;
+
+#variable to handle the window information
+my $window = "";
+my $windowNumber = 0;
+my $totalWindowsNumber = 0;
+my $upstreamAndDownstreamFlankingSequencesWindows = "";
+
+#variable to handle the motif information
+my $motif = "";
+my $motifName = "";
+my $motifSequence = "";
+my $motifNumber = 0;
+my $totalMotifsNumber = 0;
+my $upstreamMotifFrequencyCounter = 0;
+my $downstreamMotifFrequencyCounter = 0;
+
+#arrays to sotre window and motif data
+my @windowsArray = ();
+my @motifNamesArray = ();
+my @motifSequencesArray = ();
+
+#variable to handle the indel information
+my $indelIndex = 0;
+
+#variable to store line counter value
+my $lineCounter = 0;
+
+# check to make sure having correct files
+my $usage = "usage: compute_motif_frequencies_for_all_motifs.pl [TABULAR.in] [TABULAR.in] [windowSize] [TABULAR.out] \n";
+die $usage unless @ARGV == 4;
+
+#get the input arguments
+my $motifsInputFile = $ARGV[0];
+my $indelFlankingSequencesWindowsInputFile = $ARGV[1];
+my $numberOfConsideredWindows = $ARGV[2];
+my $motifFrequenciesOutputFile = $ARGV[3];
+
+#open the input files
+open (INPUT1, "<", $motifsInputFile) || die("Could not open file $motifsInputFile \n"); 
+open (INPUT2, "<", $indelFlankingSequencesWindowsInputFile) || die("Could not open file indelFlankingSequencesWindowsInputFile \n");   
+open (OUTPUT, ">", $motifFrequenciesOutputFile) || die("Could not open file $motifFrequenciesOutputFile \n");   
+
+#store the motifs input file in the array @motifsData
+my @motifsData = <INPUT1>;
+
+#iterated through the motifs (lines) of the motifs input file
+foreach $motif (@motifsData){
+	chomp ($motif);
+	#print ($motif . "\n");
+	
+	#split the motif data into its name and its sequence
+	my @motifNameAndSequenceArray = split(/\t/, $motif);
+	
+	#store the name of the motif into the array @motifNamesArray
+	push @motifNamesArray, $motifNameAndSequenceArray[0];
+	
+	#store the sequence of the motif into the array @motifSequencesArray
+	push @motifSequencesArray, $motifNameAndSequenceArray[1];
+}
+
+#compute the size of the motif names array 
+$totalMotifsNumber = @motifNamesArray;
+
+
+#store the first output file containing the windows of both upstream and downstream flanking sequences in the array @windowsData
+my @windowsData = <INPUT2>;
+
+#check if the number of considered window entered by the user is 0 or negative, if so make it equal to 1
+if ($numberOfConsideredWindows <= 0){
+	$numberOfConsideredWindows = 1;
+}
+
+#iterated through the motif sequences to check their occurrences in the considered windows
+#and store the count of their occurrences in the corresponding ouput file
+for ($motifNumber = 0; $motifNumber < $totalMotifsNumber; $motifNumber++){
+	
+	#get the motif name
+	$motifName = $motifNamesArray[$motifNumber];
+	
+	#get the motif sequence
+    $motifSequence = $motifSequencesArray[$motifNumber];
+		        	
+	#iterated through the lines of the second input file. Each line represents   
+	#the windows of the upstream and downstream flanking sequences of an indel
+	foreach $upstreamAndDownstreamFlankingSequencesWindows (@windowsData){
+		
+		chomp ($upstreamAndDownstreamFlankingSequencesWindows);
+		$lineCounter++;
+		
+		#split both upstream and downstream flanking sequences into their windows
+		my @windowsArray = split(/\t/, $upstreamAndDownstreamFlankingSequencesWindows);
+		
+		if ($lineCounter == 1){
+			$totalWindowsNumber = @windowsArray;
+			$indelIndex = ($totalWindowsNumber - 1)/2;		
+		}
+		
+		#reset the motif frequency counters
+		$upstreamMotifFrequencyCounter = 0;
+		$downstreamMotifFrequencyCounter = 0;
+		
+		#iterate through the considered windows of the upstream flanking sequence and increment the motif frequency counter
+		for ($windowNumber = $indelIndex - 1; $windowNumber > $indelIndex - $numberOfConsideredWindows - 1; $windowNumber--){
+			
+			#get the window
+			$window = $windowsArray[$windowNumber];
+			
+			#if the motif is found in the window, then increment its corresponding counter
+			if ($window =~ m/$motifSequence/i){
+	        	$upstreamMotifFrequencyCounter++;
+	        }  
+		}
+		
+		#iterate through the considered windows of the upstream flanking sequence and increment the motif frequency counter
+		for ($windowNumber = $indelIndex + 1; $windowNumber < $indelIndex + $numberOfConsideredWindows + 1; $windowNumber++){
+			
+			#get the window
+		    $window = $windowsArray[$windowNumber];
+		 
+		    #if the motif is found in the window, then increment its corresponding counter
+			if ($window =~ m/$motifSequence/i){
+	        	$downstreamMotifFrequencyCounter++;
+	        }  
+		}
+		
+		#store the result into the output file of the motif
+		print OUTPUT $motifName . "\t" . $upstreamMotifFrequencyCounter . "\t" . $downstreamMotifFrequencyCounter . "\n";
+	}
+}
+	
+#close the input and output files
+close(OUTPUT);
+close(INPUT2);
+close(INPUT1);
\ No newline at end of file