# HG changeset patch
# User devteam
# Date 1406562965 14400
# Node ID 04cdbd00dcec128f96c44690955fa2ac7dba026d

Imported from capsule None

diff -r 000000000000 -r 04cdbd00dcec first_matrix_generator_example_file.png
Binary file first_matrix_generator_example_file.png has changed
diff -r 000000000000 -r 04cdbd00dcec generate_matrix_for_pca_lda.pl
--- /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);
diff -r 000000000000 -r 04cdbd00dcec generate_matrix_for_pca_lda.xml
--- /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>
diff -r 000000000000 -r 04cdbd00dcec second_matrix_generator_example_file.png
Binary file second_matrix_generator_example_file.png has changed
diff -r 000000000000 -r 04cdbd00dcec test-data/matrix_generator_for_pc_and_lda_input_1.tabular
--- /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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diff -r 000000000000 -r 04cdbd00dcec test-data/matrix_generator_for_pc_and_lda_input_2.tabular
--- /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
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+FMR1 	XLMR
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+PAGE1 	XLMR
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+NUDT10 	XLMR
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+HUWE1 	XLMR
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+TRO 	XLMR
+MAGEH1 	XLMR
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diff -r 000000000000 -r 04cdbd00dcec test-data/matrix_generator_for_pc_and_lda_output.tabular
--- /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 @@
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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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+AGCATGATTTATA 	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	3	0	0	0	0	0	0	1	1	0	3	1	0	0	0	2	0	2	2	0	0	1	0	0	0	0	0	0	1	0	0	0	0	1	0	0	0	0	0	0	0	0	0	0	0	2	1	0	0	0	0	0	0	1	0	0	19	EOL
+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
+AATTGAACAATGAGAACATGTGGTAT 	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	2	1	0	0	0	0	0	0	0	0	1	1	0	0	0	2	0	0	1	0	0	3	0	0	0	1	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	0	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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