changeset 0:04cdbd00dcec draft default tip

Imported from capsule None
author devteam
date Mon, 28 Jul 2014 11:56:05 -0400
parents
children
files first_matrix_generator_example_file.png generate_matrix_for_pca_lda.pl generate_matrix_for_pca_lda.xml second_matrix_generator_example_file.png test-data/matrix_generator_for_pc_and_lda_input_1.tabular test-data/matrix_generator_for_pc_and_lda_input_2.tabular test-data/matrix_generator_for_pc_and_lda_output.tabular
diffstat 7 files changed, 458 insertions(+), 0 deletions(-) [+]
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line diff
Binary file first_matrix_generator_example_file.png has changed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/generate_matrix_for_pca_lda.pl	Mon Jul 28 11:56:05 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);
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/generate_matrix_for_pca_lda.xml	Mon Jul 28 11:56:05 2014 -0400
@@ -0,0 +1,48 @@
+<tool id="generate_matrix_for_pca_and_lda1" name="Generate A Matrix" version="1.0.0">
+    <description>for using PC and LDA</description>
+    <command interpreter="perl">generate_matrix_for_pca_lda.pl $input_1 $input_2 $output</command>
+
+    <inputs>
+        <param format="tabular" name="input_1" type="data" label="Source file First: a matrix (samples/observations in rows and variables/features in columns)"> </param>
+        <param format="tabular" name="input_2" type="data" label="Source file Second: a table (samples/observations with response/class label)"> </param>
+    </inputs>
+
+    <outputs>
+        <data format="tabular" name="output" />
+    </outputs>
+
+    <tests>
+        <test>
+            <param name="input_1" value="matrix_generator_for_pc_and_lda_input_1.tabular"/>
+            <param name="input_2" value="matrix_generator_for_pc_and_lda_input_2.tabular"/>
+            <output name="output" file="matrix_generator_for_pc_and_lda_output.tabular"/>
+        </test>
+    </tests>
+
+    <help>
+
+.. class:: infomark
+
+**What it does**
+
+This tool consists of a module to generate a matrix to be used for running the Linear Discriminant Analysis as described in Carrel et al., 2006 (PMID: 17009873)
+
+*Carrel L, Park C, Tyekucheva S, Dunn J, Chiaromonte F, et al. (2006) Genomic Environment Predicts Expression Patterns on the Human     Inactive X Chromosome. PLoS Genet 2(9): e151. doi:10.1371/journal.pgen.0020151*
+
+-----
+
+**Example**
+
+- Input file (Source file First)
+
+.. image:: tools/lda/first_matrix_generator_example_file.png
+
+
+- Input file (Source file Second)
+
+.. image:: tools/lda/second_matrix_generator_example_file.png
+
+
+</help>
+
+</tool>
Binary file second_matrix_generator_example_file.png has changed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/matrix_generator_for_pc_and_lda_input_1.tabular	Mon Jul 28 11:56:05 2014 -0400
@@ -0,0 +1,88 @@
+	CTCAGAAAAAAA 	CCATCCATCCATCCATCC 	AGAGGGAGAGGG 	ATCTGTTGATGG 	AGGGGTGACAGA 	ATCCCATTTACA 	AAGGGTATCAGT 	ATAATATATACA 	TATTATATGTATA 	CATCATCATCATCA 	CCCCATGATCCA 	TGATTCCTTAAAGAA 	AACACTTGGACA 	TATTAATATAATTTATAAA 	ATGTTTATTTTA 	TATCCAGGAGAA 	CAATTCTCCTGCC 	ACCATAAAAATGAGAAC 	CTCAGCCATAAAAA 	ATGAGTGAGAATAT 	ACTGTGAGTCAA 	TAAACTAAAGAGCTTCTGCACAGCA 	TCCTTTGGGTATAT 	ATGCTGCTATAAAGACACATGCACAC 	TGCTGGAGAGGATGTGGAGAAATAGGAACACTTTTACACTG 	TCCACAATGGTTGAA 	TTGGCTGCATAAAT 	CAATGGAACAGAACAGAGCCCTCAGAAATAA 	GAACTAGAAATACCATTTGACCCAGC 	TCAAAGATCAGAT 	GACCCATCTCACACCAGTTAGAATG 	CAAAGAGAATAAAATACCTAGGTATTTTATTCTTTTT 	AAAATGGCCATACTGCCCAAG 	AAATTTTTCCAATTCTGTGAAGAAA 	TTCACAATAGCAAAGAC 	TAGGAAGAATCAATA 	CTGGGTATATACCCAGTAATGG 	TTGGAAGTTCTGGCCAGGGCAA 	TGAAGGACCTCTTCAAGGAGAACTACAAACCACTGCTCAA 	CTCTCACCACTCCTATTCAACATA 	ACACACACATAT 	CCATGAGCATGGAATGTTCT 	AACCCAAATGTCC 	TTTACAAGAAAAAAACAAACAACCCCA 	AGTTCTAGATCC 	CTGGAAGCATTCCCTTT 	GATCCCATTTGTC 	GATATGAACAGACA 	TGGGTTTGTCATA 	AGTTTCTTTTGC 	AATTACCCAGTCT 	TCATGTCATCTGCAAACA 	AAAACTCTCAAT 	CAACTTCAGCAA 	ATTGGCTGTGGGTTT 	AATTAGATCCCA 	GACCTAAAACCA 	AGAATCTACAAT 	AAACCAAACACC 	GGAGTTCCAGACCAGCCT 	CCTTGCCCATGCC 	ATCATACTGAAT 	AGGAAGTCAAATT 	AGCAAACCACCA 	AGCATGATTTATA 	GAGAGCCAAATCATGAGTG 	AAAGAGCCAAAT 	AGCAATTGTGAATGG 	CACTATTCACAATTGC 	TCAGGATACAAAATCAATG 	CAATGAACTCAAACAAATT 	TCCAACAAAGGACATGAACTCATC 	AATTGAACAATGAGAACATGTGGTAT 	AACCACAATGAGAACA 	GTGTATATATATACAT 	ACATATATATAT 	GTCAGATGGATA 	TCATCTGACAAAGGGCTAATATCCAG 	TTTGTCAGGTTTGTCAAAG 	TTCTTAATCCAGTCTATCATT 	TTTAATCCATCTTGA 	AAACTACCATCAGAGTGAACAGGCA 	GCCATCAGAGAAAT 	ACAGGCAACCTACA 	GCAACCTACTCA 	TAGAAAACCCCAT 
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+HDX 	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+APOOL 	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	1	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0
+ZNF711 	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+POF1B 	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+CHM 	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+DACH2 	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+KLHL4 	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0
+CPXCR1 	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	1	1	0	0	0	1	1	1	0	0	0	0	1	0	0	0	0	1	1	0	0	1	0	1	0	0	0	0	1	0	0	0	0	0
+PABPC5 	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+DIAPH2 	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+SYTL4 	0	0	1	1	2	0	1	3	0	1	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	5	1	0	0	1	0	1	1	0	0	0	0	0	3	2	0	0	0	1	3	0	0	0	0	1	0	0	2	6	0	1	2	1	0	0	0	1	1	1	1	0	0	2	3	1	0	1	0	0	3	1	2	0
+CSTF2 	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	1	0	1	0	1	1	0	0	0	0	0	1	0	0	0	0	0	1	0	1	0	0	1	1	0	1	1	1	0	0	1	0	2	1	0	0	0	0	0	0	0	0	1	0	0	0	1	0	1
+DRP2 	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
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+BEX5 	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+NXF3 	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+BEX4 	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+TCEAL4 	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+ESX1 	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
+IL1RAPL2 	0	3	2	1	0	0	0	0	0	0	1	0	0	0	0	0	1	0	0	2	3	2	3	0	0	0	0	0	2	0	0	1	1	1	0	0	0	0	0	0	0	1	0	0	1	0	1	0	0	1	0	1	1	1	0	0	0	0	0	1	1	0	0	1	0	0	0	0	0	1	1	1	0	0	0	0	1	0	0	0	0	0	0	0	0	0
+NRK 	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/matrix_generator_for_pc_and_lda_input_2.tabular	Mon Jul 28 11:56:05 2014 -0400
@@ -0,0 +1,87 @@
+ARHGEF9 	XLMR
+KIAA2022 	XLMR
+ZDHHC15 	XLMR
+PGK1 	XLMR
+BRWD3 	XLMR
+PAK3 	XLMR
+AGTR2 	XLMR
+GRIA3 	XLMR
+ZDHHC9 	XLMR
+GPC3 	XLMR
+PHF6 	XLMR
+SOX3 	XLMR
+FMR1 	XLMR
+MTM1 	XLMR
+SHROOM4 	XLMR
+KLF8 	XLMR
+UXT 	XLMR
+PCSK1N 	XLMR
+PAGE1 	XLMR
+PAGE4 	XLMR
+CLCN5 	XLMR
+NUDT10 	XLMR
+NUDT11 	XLMR
+GSPT2 	XLMR
+TMEM29 	XLMR
+GPR173 	XLMR
+HUWE1 	XLMR
+TSR2 	XLMR
+TRO 	XLMR
+MAGEH1 	XLMR
+USP51 	XLMR
+RRAGB 	XLMR
+UBQLN2 	CONTROL
+SPIN3 	CONTROL
+SPIN2A 	CONTROL
+ZXDA 	CONTROL
+SPIN4 	CONTROL
+MTMR8 	CONTROL
+KIAA1166 	CONTROL
+LAS1L 	CONTROL
+MSN 	CONTROL
+HEPH 	CONTROL
+AR 	CONTROL
+STARD8 	CONTROL
+TMEM28 	CONTROL
+EDA 	CONTROL
+SLC7A3 	CONTROL
+CXCR3 	CONTROL
+NAP1L2 	CONTROL
+CHIC1 	CONTROL
+FXYD8 	CONTROL
+RNF12 	CONTROL
+UPRT 	CONTROL
+MAGEE2 	CONTROL
+CXorf26 	CONTROL
+MAGEE1 	CONTROL
+FGF16 	CONTROL
+TAF9B 	CONTROL
+CYSLTR1 	CONTROL
+ZCCHC5 	CONTROL
+GPR23 	CONTROL
+P2RY10 	CONTROL
+ITM2A 	CONTROL
+TBX22 	CONTROL
+NSBP1 	CONTROL
+RPS6KA6 	CONTROL
+HDX 	CONTROL
+APOOL 	CONTROL
+ZNF711 	CONTROL
+POF1B 	CONTROL
+CHM 	CONTROL
+DACH2 	CONTROL
+KLHL4 	CONTROL
+CPXCR1 	CONTROL
+PABPC5 	CONTROL
+DIAPH2 	CONTROL
+SYTL4 	CONTROL
+CSTF2 	CONTROL
+DRP2 	CONTROL
+TCEAL2 	CONTROL
+BEX5 	CONTROL
+NXF3 	CONTROL
+BEX4 	CONTROL
+TCEAL4 	CONTROL
+ESX1 	CONTROL
+IL1RAPL2 	CONTROL
+NRK 	CONTROL
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/matrix_generator_for_pc_and_lda_output.tabular	Mon Jul 28 11:56:05 2014 -0400
@@ -0,0 +1,88 @@
+ 	AGTR2 	ARHGEF9 	BRWD3 	CLCN5 	FMR1 	GPC3 	GPR173 	GRIA3 	GSPT2 	HUWE1 	KIAA2022 	KLF8 	MAGEH1 	MTM1 	NUDT10 	NUDT11 	PAGE1 	PAGE4 	PAK3 	PCSK1N 	PGK1 	PHF6 	RRAGB 	SHROOM4 	SOX3 	TMEM29 	TRO 	TSR2 	USP51 	UXT 	ZDHHC15 	ZDHHC9 	X(SUM) 	APOOL 	AR 	BEX4 	BEX5 	CHIC1 	CHM 	CPXCR1 	CSTF2 	CXCR3 	CXorf26 	CYSLTR1 	DACH2 	DIAPH2 	DRP2 	EDA 	ESX1 	FGF16 	FXYD8 	GPR23 	HDX 	HEPH 	IL1RAPL2 	ITM2A 	KIAA1166 	KLHL4 	LAS1L 	MAGEE1 	MAGEE2 	MSN 	MTMR8 	NAP1L2 	NRK 	NSBP1 	NXF3 	P2RY10 	PABPC5 	POF1B 	RNF12 	RPS6KA6 	SLC7A3 	SPIN2A 	SPIN3 	SPIN4 	STARD8 	SYTL4 	TAF9B 	TBX22 	TCEAL2 	TCEAL4 	TMEM28 	UBQLN2 	UPRT 	ZCCHC5 	ZNF711 	ZXDA 	Y(SUM) 	
+CTCAGAAAAAAA 	0	0	0	0	0	0	0	0	0	0	1	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	4	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	EOL
+CCATCCATCCATCCATCC 	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	0	3	0	0	0	0	0	0	0	0	0	4	3	0	0	0	1	0	3	3	0	0	0	3	2	0	0	0	0	3	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	3	0	0	26	EOL
+AGAGGGAGAGGG 	2	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	5	0	0	0	0	0	0	0	0	0	3	3	0	0	0	3	0	3	4	0	0	1	2	2	0	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	2	0	0	0	0	0	0	4	0	0	30	EOL
+ATCTGTTGATGG 	0	0	0	0	0	0	0	1	0	0	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	4	0	0	0	0	0	0	0	0	0	1	1	0	0	0	2	0	1	0	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	2	0	0	11	EOL
+AGGGGTGACAGA 	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	2	2	0	0	2	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	1	0	0	0	0	0	0	1	0	0	12	EOL
+ATCCCATTTACA 	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	EOL
+AAGGGTATCAGT 	0	0	0	0	0	0	0	1	0	0	0	1	0	1	1	0	0	0	2	0	0	0	0	0	0	0	0	0	0	2	0	0	8	0	0	0	0	0	0	0	0	0	3	2	0	0	0	3	0	3	3	0	0	0	0	2	0	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	2	0	0	22	EOL
+ATAATATATACA 	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	2	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	1	1	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	3	0	0	0	0	0	0	0	0	0	0	8	EOL
+TATTATATGTATA 	0	1	0	0	0	0	0	1	0	0	0	0	0	1	1	0	0	0	0	0	8	0	0	0	0	0	0	0	0	0	0	0	12	0	0	0	0	0	0	0	0	0	1	0	0	0	0	1	0	1	1	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	6	EOL
+CATCATCATCATCA 	0	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	1	0	0	4	EOL
+CCCCATGATCCA 	1	0	1	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	4	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	1	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	0	0	7	EOL
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+ACTGTGAGTCAA 	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	2	0	0	0	0	0	0	0	0	0	3	2	0	0	0	2	0	3	3	0	0	0	3	3	0	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	0	0	0	0	3	0	0	26	EOL
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+TCCACAATGGTTGAA 	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	EOL
+TTGGCTGCATAAAT 	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	3	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	1	0	0	0	0	0	0	1	0	0	6	EOL
+CAATGGAACAGAACAGAGCCCTCAGAAATAA 	0	4	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	5	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	EOL
+GAACTAGAAATACCATTTGACCCAGC 	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	1	0	0	0	0	2	0	0	5	0	0	0	0	0	0	0	0	0	2	2	0	0	0	4	0	2	2	0	0	2	2	2	0	0	0	0	2	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	2	0	0	0	0	0	0	4	0	0	28	EOL
+TCAAAGATCAGAT 	1	0	0	0	0	0	0	1	0	0	1	1	0	2	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	2	0	0	10	0	0	0	0	0	0	0	0	0	2	1	0	0	0	2	0	3	3	0	0	0	0	2	0	0	0	0	3	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	0	0	0	0	2	0	0	20	EOL
+GACCCATCTCACACCAGTTAGAATG 	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	3	EOL
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+AAAATGGCCATACTGCCCAAG 	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	0	0	0	0	0	1	0	0	1	0	0	0	0	0	1	0	0	5	0	0	0	0	0	0	0	0	0	1	1	0	0	0	1	0	1	1	0	0	0	1	1	0	0	0	0	1	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	2	0	0	12	EOL
+AAATTTTTCCAATTCTGTGAAGAAA 	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	2	0	0	5	0	0	0	0	0	0	0	1	0	2	2	0	0	0	1	0	2	4	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	5	1	0	0	0	0	0	0	1	0	0	20	EOL
+TTCACAATAGCAAAGAC 	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	1	0	0	0	2	0	0	0	0	0	0	2	0	0	6	0	0	0	0	0	0	1	0	0	3	1	0	0	0	1	0	2	1	0	0	0	0	2	0	0	0	0	1	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	1	0	0	16	EOL
+TAGGAAGAATCAATA 	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	0	0	7	EOL
+CTGGGTATATACCCAGTAATGG 	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	3	0	0	0	0	0	0	0	0	0	0	1	6	0	0	0	0	0	0	0	0	0	2	1	0	0	0	1	0	0	1	0	0	2	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	0	0	10	EOL
+TTGGAAGTTCTGGCCAGGGCAA 	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	1	0	2	1	0	0	0	0	0	2	0	0	0	0	0	2	0	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	4	0	0	16	EOL
+TGAAGGACCTCTTCAAGGAGAACTACAAACCACTGCTCAA 	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	1	0	0	0	0	0	0	0	0	0	1	1	0	0	0	1	0	0	1	0	0	0	0	1	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	0	0	0	0	1	0	0	9	EOL
+CTCTCACCACTCCTATTCAACATA 	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	2	2	0	0	0	0	0	1	0	0	6	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	1	0	0	0	0	1	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	1	0	0	7	EOL
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+TGGGTTTGTCATA 	1	0	0	0	0	0	0	1	0	0	0	0	0	1	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	0	0	5	0	0	0	0	0	0	0	1	0	2	0	0	0	0	0	0	1	2	0	0	0	0	1	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	9	EOL
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+ATTGGCTGTGGGTTT 	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	1	0	0	2	0	0	0	0	0	0	0	1	0	1	0	0	0	0	1	0	1	2	0	0	0	0	2	0	1	0	0	0	0	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	3	0	0	15	EOL
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+CCTTGCCCATGCC 	0	0	1	0	0	0	0	0	0	0	1	0	0	0	1	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	4	0	0	0	0	0	0	0	1	0	0	1	0	0	0	1	0	0	1	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	1	0	0	0	0	0	0	0	0	0	9	EOL
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+AGGAAGTCAAATT 	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	1	0	2	1	0	0	0	0	0	1	3	0	0	0	0	3	0	0	0	0	3	0	0	0	0	3	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	2	0	0	21	EOL
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+GAGAGCCAAATCATGAGTG 	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	1	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	0	0	0	7	EOL
+AAAGAGCCAAAT 	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	3	EOL
+AGCAATTGTGAATGG 	0	0	0	0	0	0	0	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	3	0	0	0	0	0	0	0	1	0	2	0	0	0	0	0	0	2	2	0	0	0	0	2	0	0	0	0	2	0	0	0	0	4	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	2	0	0	18	EOL
+CACTATTCACAATTGC 	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	1	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	2	0	0	6	EOL
+TCAGGATACAAAATCAATG 	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	1	1	0	0	0	0	0	1	0	0	4	0	0	0	0	0	0	1	2	0	3	1	0	0	0	2	0	3	1	0	0	0	1	3	0	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	2	0	0	0	0	0	0	2	0	0	24	EOL
+CAATGAACTCAAACAAATT 	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	2	0	0	0	0	0	0	1	1	0	1	1	0	0	0	2	0	2	2	0	0	0	1	1	0	0	0	0	0	0	0	0	0	2	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	2	0	0	18	EOL
+TCCAACAAAGGACATGAACTCATC 	0	1	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	3	0	0	0	0	0	0	0	0	0	1	1	0	0	0	1	0	1	1	0	0	0	1	2	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	0	0	0	0	0	1	0	0	12	EOL
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+TCATCTGACAAAGGGCTAATATCCAG 	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	3	EOL
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