--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/generate_matrix_for_pca_lda.pl	Mon Jul 28 11:30:18 2014 -0400
@@ -0,0 +1,147 @@
+#!/usr/bin/perl -w
+
+use strict;
+use warnings;
+
+my $Input_Matrix = $ARGV[0];
+my $Input_Label = $ARGV[1];
+
+my %Hash_X = ();
+my %Hash_Y = ();
+my $My_Num_X = 0;
+my $My_Num_Y = 0;
+
+open (OUT, "> $ARGV[2]");
+
+open (LABEL, "< $Input_Label")     ||
+	die "Sorry, I couldn't open the escape.txt for clone: $!\n";
+
+my $Label_Index = 0;
+my $X_Label;
+my $input_Label;
+while (defined($input_Label = <LABEL>)){
+	chomp($input_Label);
+	my @cArray_Label = $input_Label =~ /(\S+)\s*/g;
+	if ($input_Label =~ /\w/){
+		if ($Label_Index == 0){
+			$Hash_X{$cArray_Label[0]} = $cArray_Label[1];
+			$X_Label = $cArray_Label[1];
+			$Label_Index = 1;
+		}else{
+			if ($cArray_Label[1] eq $X_Label){
+				$Hash_X{$cArray_Label[0]} = $cArray_Label[1];
+			}else{
+				$Hash_Y{$cArray_Label[0]} = $cArray_Label[1];
+			}
+		}
+	}
+}
+close(LABEL);
+
+open (MATRIX, "< $Input_Matrix")     ||
+	die "Sorry, I couldn't open the escape.txt for clone: $!\n";
+
+my %Hash_Matrix = ();
+my %Hash_Features = ();
+my @cArray_Features = ();
+
+my %Hash_Sum = ();
+my $Matrix_Index = 0;
+my $input_Matrix;
+while (defined($input_Matrix = <MATRIX>)){
+	chomp($input_Matrix);
+	my @cArray_Matrix = $input_Matrix =~ /(\S+)\s*/g;
+	if ($input_Matrix =~ /\w/){
+		if ($Matrix_Index == 0){
+			@cArray_Features = @cArray_Matrix;
+			my $Temp_Num_Array = scalar(@cArray_Matrix);
+			my $Temp_Index = 0;
+			for(;$Temp_Index < $Temp_Num_Array; $Temp_Index++){
+				$Hash_Features{$cArray_Matrix[$Temp_Index]} = "BOL";	
+				$Hash_Sum{$cArray_Matrix[$Temp_Index]} = 0;	
+			}
+			$Matrix_Index = 1;
+		}else{
+			$Hash_Matrix{$cArray_Matrix[0]} = $input_Matrix;
+		}
+	}
+}
+close(MATRIX);	
+
+my $Trace_Key;
+
+foreach $Trace_Key (sort {$a cmp $b} keys %Hash_X){
+	my @cArray_Trace_X = $Hash_Matrix{$Trace_Key} =~ /(\S+)\s*/g;
+	my $Num_Array_Feature_X = scalar(@cArray_Features);
+	my $Index_Feature_X = 0;
+	for(;$Index_Feature_X < $Num_Array_Feature_X; $Index_Feature_X++){
+		if ($Hash_Features{$cArray_Features[$Index_Feature_X]} eq "BOL"){
+			$Hash_Features{$cArray_Features[$Index_Feature_X]} = $cArray_Trace_X[$Index_Feature_X + 1];
+		}else{
+			$Hash_Features{$cArray_Features[$Index_Feature_X]} = $Hash_Features{$cArray_Features[$Index_Feature_X]} . "\t" . $cArray_Trace_X[$Index_Feature_X + 1];
+		}
+
+		$Hash_Sum{$cArray_Features[$Index_Feature_X]} += $cArray_Trace_X[$Index_Feature_X + 1];
+	} 		
+	$My_Num_X ++;
+}
+
+my $Append_Key;
+foreach $Append_Key (keys %Hash_Features){
+	$Hash_Features{$Append_Key} = $Hash_Features{$Append_Key} . "\t" . $Hash_Sum{$Append_Key};
+	$Hash_Sum{$Append_Key} = 0;
+}
+
+foreach $Trace_Key (sort {$a cmp $b} keys %Hash_Y){
+	my @cArray_Trace_Y = $Hash_Matrix{$Trace_Key} =~ /(\S+)\s*/g;
+	my $Num_Array_Feature_Y = scalar(@cArray_Features);
+	my $Index_Feature_Y = 0;
+	for(;$Index_Feature_Y < $Num_Array_Feature_Y; $Index_Feature_Y++){
+		if ($Hash_Features{$cArray_Features[$Index_Feature_Y]} eq "BOL"){
+			$Hash_Features{$cArray_Features[$Index_Feature_Y]} = $cArray_Trace_Y[$Index_Feature_Y + 1];
+		}else{
+			$Hash_Features{$cArray_Features[$Index_Feature_Y]} = $Hash_Features{$cArray_Features[$Index_Feature_Y]} . "\t" . $cArray_Trace_Y[$Index_Feature_Y + 1];
+		}
+
+		$Hash_Sum{$cArray_Features[$Index_Feature_Y]} += $cArray_Trace_Y[$Index_Feature_Y + 1];
+	} 		
+	$My_Num_Y ++;
+}
+
+foreach $Append_Key (keys %Hash_Features){
+	$Hash_Features{$Append_Key} = $Hash_Features{$Append_Key} . "\t" . $Hash_Sum{$Append_Key} . "\t" . "EOL";
+}
+
+my $Prt_Key;
+print OUT " \t";
+foreach $Prt_Key (sort {$a cmp $b} keys %Hash_X){
+	print OUT "$Prt_Key \t";
+}
+print OUT "X(SUM) \t";
+
+foreach $Prt_Key (sort {$a cmp $b} keys %Hash_Y){
+	print OUT "$Prt_Key \t";
+}
+print OUT "Y(SUM) \t";
+print OUT "\n";
+
+my $Prt_Index = 0;
+my $Prt_Array_Num = scalar (@cArray_Features);
+for(;$Prt_Index < $Prt_Array_Num; $Prt_Index++){
+	print OUT "$cArray_Features[$Prt_Index] \t$Hash_Features{$cArray_Features[$Prt_Index]}\n";
+}
+
+print OUT " \t";
+my $My_Label_Index = 0;
+for(;$My_Label_Index < $My_Num_X; $My_Label_Index++){
+	print OUT "X \t";
+}
+print OUT " \t";
+
+$My_Label_Index = 0;
+for(;$My_Label_Index < $My_Num_Y; $My_Label_Index++){
+	print OUT "Y \t";
+}
+print OUT " \t\n";
+
+close(OUT);