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author aaronpetkau
date Sat, 04 Jul 2015 08:58:07 -0400
parents 44c401ebc424
children 6889442b27dc
files README_ASSEMBLY_STATS assembly_stats_txt.py assembly_stats_txt.xml fasta_summary.pl
diffstat 4 files changed, 0 insertions(+), 972 deletions(-) [+]
line wrap: on
line diff
--- a/README_ASSEMBLY_STATS	Sat Jul 04 08:57:35 2015 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,14 +0,0 @@
-#Created 07/01/2011
-#Konrad Paszkiewicz, University of Exeter
-
-Assembly stats
-
-This series of scripts calculates various metrics on an input FASTA file. Typically this is most useful on either denovo genomic or transcriptomic data.
-
-Prerequisites:
-
-1. The bundled perl script fasta_summary.pl 
-
-Limitations:
-
-Ideally this should output a composite dataset of some sort
--- a/assembly_stats_txt.py	Sat Jul 04 08:57:35 2015 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,122 +0,0 @@
-#!/usr/bin/env python
-#Version 1.01 - bugs kindly corrected by Jan van Haarst
-import pkg_resources
-import logging, os, string, sys, tempfile, glob, shutil, types, urllib
-import shlex, subprocess
-from optparse import OptionParser, OptionGroup
-from stat import *
-
-
-log = logging.getLogger( __name__ )
-
-assert sys.version_info[:2] >= ( 2, 4 )
-
-def stop_err( msg ):
-    sys.stderr.write( "%s\n" % msg )
-    sys.exit()
-
-def __main__():
-    #Parse Command Line
-    s = 'assembly_stats_txt.py:  argv = %s\n' % (sys.argv)
-    argcnt = len(sys.argv)
-    html_file = sys.argv[1]
-    working_dir = sys.argv[2]
-    type = sys.argv[3]
-    bucket = sys.argv[4]
-    input = sys.argv[5]
-    stats = sys.argv[6]
-    sortedcontigs = sys.argv[7]
-    histogrampng = sys.argv[8]
-    summedcontigspng = sys.argv[9]
-    histogramdata = sys.argv[10]
-    summedcontigdata = sys.argv[11]
-    try: # for test - needs this done
-        os.makedirs(working_dir)
-    except Exception, e:
-        stop_err( 'Error running assembly_stats_txt.py ' + str( e ) )
-  
-    
-    cmdline = '%s/fasta_summary.pl -i %s -t %s %s -o %s > /dev/null' % (os.path.dirname(sys.argv[0]),input, type, bucket, working_dir)
-    try:
-        proc = subprocess.Popen( args=cmdline, shell=True, stderr=subprocess.PIPE )
-        returncode = proc.wait()
-        # get stderr, allowing for case where it's very large
-        stderr = ''
-        buffsize = 1048576
-        try:
-            while True:
-                stderr += proc.stderr.read( buffsize )
-                if not stderr or len( stderr ) % buffsize != 0:
-                    break
-        except OverflowError:
-            pass
-        if returncode != 0:
-            raise Exception, stderr
-    except Exception, e:
-        stop_err( 'Error running assembly_stats.py ' + str( e ) )
- 
-    stats_path = os.path.join(working_dir,'stats.txt')
-    sorted_contigs_path = os.path.join(working_dir,'sorted_contigs.fa')
-    histogram_png_path = os.path.join(working_dir,'histogram_bins.dat.png')
-    summed_contigs_path = os.path.join(working_dir,'summed_contig_lengths.dat.png')
-    histogram_data_path =  os.path.join(working_dir,'histogram_bins.dat')
-    summed_contigs_data_path = os.path.join(working_dir,'summed_contig_lengths.dat')
-
-    out = open(stats,'w')
-    for line in open( stats_path ):
-        out.write( "%s" % (line) )
-    out.close()
-
-    out = open(sortedcontigs,'w')
-    for line in open(sorted_contigs_path ):
-        out.write( "%s" % (line) )
-    out.close()
-
-    out = open(histogrampng,'w')
-    for line in open(histogram_png_path ):
-        out.write( "%s" % (line) )
-    out.close()
-
-    out = open(summedcontigspng,'w')
-    for line in open(summed_contigs_path ):
-        out.write( "%s" % (line) )
-    out.close()
-
-
-    out = open(histogramdata,'w')
-    for line in open(histogram_data_path ):
-        out.write( "%s" % (line) )
-    out.close()
-
-    out = open(summedcontigdata,'w')
-    for line in open(summed_contigs_data_path ):
-        out.write( "%s" % (line) )
-    out.close()
-
-
-
-
-
-
-
-
-
-#    rval = ['<html><head><title>Assembly stats Galaxy Composite Dataset </title></head><p/>']
-#    rval.append('<div>%s<p/></div>' % (cmdline) )
-#    rval.append('<div>This composite dataset is composed of the following files:<p/><ul>')
-#    rval.append( '<li><a href="%s" type="text/plain">%s </a>%s</li>' % (stats_path,'stats.txt','stats.txt' ) )
-#    rval.append( '<li><a href="%s" type="text/plain">%s </a>%s</li>' % (sorted_contigs_path,'sorted_contigs.fa','sorted_contigs.fa' ) )
-#    rval.append( '<li><a href="%s" type="image/png">%s </a>%s</li>' % (histogram_png_path,'histogram_bins.dat.png','histogram_bins.dat.png' ) )
-#    rval.append( '<li><a href="%s" type="image/png">%s </a>%s</li>' % (summed_contigs_path,'summed_contig_lengths.dat.png','summed_contig_lengths.dat.png' ) )
-#    rval.append( '<li><a href="%s" type="text/plain">%s </a>%s</li>' % (histogram_data_path,'histogram_bins.dat','histogram_bins.dat' ) )	
-#    rval.append( '<li><a href="%s" type="text/plain">%s </a>%s</li>' % (summed_contigs_data_path,'summed_contig_lengths.dat','summed_contig_lengths.dat' ) )
-
-
-#	
-#    rval.append( '</ul></div></html>' )
-#    f = file(html_file,'w')
-#    f.write("\n".join( rval ))
-#    f.write('\n')
-#    f.close()
-
-if __name__ == "__main__": __main__()
--- a/assembly_stats_txt.xml	Sat Jul 04 08:57:35 2015 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,60 +0,0 @@
-<tool id="assemblystats" name="assemblystats" version="1.0.2">
-    <description>Summarise an assembly (e.g. N50 metrics)</description>
-    <requirements>
-		</requirements>
-    <command interpreter="python">
-	  assembly_stats_txt.py 
-           '$input_type' '$stats.extra_files_path'
-           '$input_type'
-           '$bucket'
-	   '$input'
-   	    '$stats'
-    '$sortedcontigs'
-    '$histogrampng' 
-    '$summedcontigspng'
-    '$histogramdata' 
-    '$summedcontigdata' 
-
-	</command>
-    <inputs>
-        <param help="Is this from an genomic (contig) or transcriptomic assembly (isotig) or are these raw reads (read)" label="Type of read" name="input_type" type="select">
-            <option selected="yes" value="contig">Contig (if from genomic assembly)</option>
-            <option value="isotig">Isotig (if from transcriptomic assembly)</option>
-            <option value="read">Raw reads from sequencer in FASTA format (useful for 454 data)</option>
-        </param>
-        <param falsevalue="" help="Use this to specify whether or not bin sizes of 1 should be used when plotting histograms" label="Output histogram with bin sizes=1" name="bucket" truevalue="-b" type="boolean" />
-        <param format="fasta" label="Source file in FASTA format" name="input" type="data" />
-        <param checked="false" help="If checked, all output files will be displayed. If not checked, only the file 'Assembly Statistics' will be provided." label="Return all output files" name="all_outputs" type="boolean" />
-    </inputs>
-    <outputs>
-        <data format="tabular" label="Assembly statistics - $input.display_name" name="stats" />
-        <data format="fasta" label="Sorted contigs - $input.display_name" name="sortedcontigs">
-            <filter>all_outputs is True</filter>
-        </data>
-        <data format="png" label="Histogram of contig sizes - $input.display_name" name="histogrampng">
-            <filter>all_outputs is True</filter>
-        </data>
-        <data format="png" label="Cumulative sum of contig sizes - $input.display_name" name="summedcontigspng">
-            <filter>all_outputs is True</filter>
-        </data>
-        <data format="tabular" label="Histogram data - $input.display_name" name="histogramdata">
-            <filter>all_outputs is True</filter>
-        </data>
-        <data format="tabular" label="Cumulative sum of contig size data - $input.display_name" name="summedcontigdata">
-            <filter>all_outputs is True</filter>
-        </data>
-    </outputs>
-    <help>
-**Summarise assembly overview** 
-
-This script is used to give summary statistics of an assembly or set of reads. Typically this is run after an assembly to evaluate gross features.
-
-
-# Gives back
-# - N50
-# - num of contigs &gt; 1 kb
-# - num of contigs
-# - Read or Contig Histogram and graphs.
-# - Summed contig length (by number of contigs, in sorted order)
-	</help>
-</tool>
--- a/fasta_summary.pl	Sat Jul 04 08:57:35 2015 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,776 +0,0 @@
-#!/usr/bin/perl
-
-#==============================================================================================
-
-# Script to output statistsics and histograms for reads and contigs/isotigs
-
-
-# Outputs include:
-#    Mean, N50, StdDev or reads or contig lengths,
-#    Mean and Modal read or contig lengths.
-#    Number of reads or contigs > 1 kb in length 
-#    Summed contig length (by number of contigs, in sorted order)
-#    Histogram of read or contig lengths,
-#    Graph of sums of read-lengths
-#    File of reads or contigs sorted by read or contig length
-#    Test for mono/di-nucelotide repeats
-#    Randomly selected reads or contigs
-
-
-# Needs gnuplot installed to create the histograms:
-#   On Fedora/Redhat linux: sudo yum install gnuplot 
-#   On Ubuntu/Debian: sudo apt-get install gnuplot
-
-#  Uses a linux pipe to call gnu-plot directly, rather than as a separate shell script.
-
-# Original written by Sujai Kumar, 2008-09-05 University of Edinburgh
-# Modified by Stephen: 29-Apr-2009:
-# Last changed by Stephen: 9-Aug-2010
-
-
-# Usage: fasta_summary.pl -i infile.fasta  -o process_reads -t read OR contig OR isotig (to use 'read' or 'contig' or 'isotig' in the output table & graphs. Isotig is for 'runAssembly -cdna ...' output file '454Isotigs.fna') [-r 1 to indicate count simple nucleotide repeats] [-n number of random reads to output] [-c cutoff_length] [-l 1 to indicate output the longest read] [-f (s or t or w) for spacer, tab or wiki format table output.]
-
-# Note: The parameters above in the [] are optional.
-
-# eg: fasta_summary.pl -i myfile.fasta  -o process_reads -t read
-# Where:
-#  -i reads or contigs as input, in fasta format.
-#  -o output_dir (created if it doesn't exist)
-#  -t read, contig or isotig
-
-# Gives back
-# - N50
-# - num of contigs > 1 kb
-# - num of contigs
-# - Read or Contig Histogram and graphs.
-# - Summed contig length (by number of contigs, in sorted order)
-
-#==============================================================================================
-
-
-use strict;
-use warnings;
-use Getopt::Long;
-
-my $infile;
-my $output_dir;
-my $type='read'; # Defaults to 'read' at present
-my $repeats=1;
-my $num_random_reads_to_output=0;
-my $cutoff_length=-1; # -1 means won't check this cutoff
-my $longest_read=-1; # -1 mean's don't output the sequence for the longest read.
-my $doCommify=1; # Outputs statistics numbers in format: 9,999,999
-my $format="t";  # "s"=spaces between columns, "t"=tabs between columns, "w"=wiki '||' and '|'.
-my $bucket1=0; # For optional exact length histogram distribution as asked for by JH.
-
-if ($#ARGV==-1) {die "
- Usage:  
-
-    fasta_summary.pl -i infile.fasta  -o output_dir  -t ( read | contig | isotig ) [ -r 0 ] [ -n num_reads ] [ -c cutoff_length ] [ -l 1 ] [ -d 0 ] [ -f (w | t ) ] [ -bucket1 ]
-
- where:
-
-    -i or -infile  infile.fasta  :  input fatsa file of raeds, contigs or isotigs, 
-
-    -o or -output_dir output_directory : directory to put output stats and graphs into.
-
-    -t or -type (read or contig or isotig) : for displaying the graph title, where type is 'read' or 'contig' or 'isotig'.
-
-    -r or -repeats 0 or 1        :  1=count number of reads that contain over 70% simple mono-nucleotide and di-nucleotide repeat bases; 0=don't count.
-
-    -n or -number num_reads      : For outputting specified number of randomly selected reads or contigs.
-
-    -c or -cutoff cutoff_length  : Give a number of reads to do extra analysis (calculating again the number of reads and number of bases in reads above this length)
-
-    -l or -longest 0 or 1        : 1=Output the longest read;  0= don't output the longest read
-
-    -d or -doCommify 0 or 1      : Output numbers formatted with commas to make easier to read: 0=no commas, default=1
-
-    -f or -format w or t         : w=wiki_format (ie. table with || and | for column dividers), t=tabs between column symbols for the wiki pages, default is spaces between columns.
-
-    -b or -bucket1               : To also output histogram file of exact read lengths (ie. bucket size of 1)
-
-
-  eg: For 454 reads:      fasta_summary.pl  -i RawReads.fna -o read_stats -t read
-      For 454 isotigs:    fasta_summary.pl  -i 454Isotigs.fna -o isotig_stats -t isotig
-
-";}
-
-GetOptions (
-	"infile=s"      => \$infile,
-	"output_dir=s"  => \$output_dir,
-	"type=s"        => \$type, ## type is 'read' or 'contig' or 'isotig' - for displaying the graph title
-	"repeats=i"     => \$repeats, # To count simple repeats
-	"number=i"      => \$num_random_reads_to_output, # For outputting specified number of random reads
-	"cutoff=i"      => \$cutoff_length, # Give a number of reads to do extra analysis (calculating again the number of reads and number of bases in reads above this length)
-	"longest=i"     => \$longest_read, # Output the longest read.
-	"doCommify=i"   => \$doCommify, # Output numbers formatted with commas to make easier to read: 0=no commas, default=1
-	"format=s"      => \$format, # "w"=wiki_format (ie. table with || and | for column dividers), "t"=tabs between column symbols for the wiki pages, default is spaces between columns.
-        "bucket1"       => \$bucket1, # To also output histogram file of exact read lengths (ie. bucket size of 1)
-);
-if ($#ARGV>-1) {die "Unused options specified: @ARGV\n";}
-if ( (! defined $infile) || ($infile eq '') ) {die "\nPlease give input fasta file, preceeded by the '-i' option\n\n";}
-if ( (! defined $output_dir) || ($output_dir eq '') ) {die "Please give output_directory, preceeded by the '-o' option\n\n";}
-if ( (! defined $type) || (($type ne 'contig') && ($type ne 'read') && ($type ne 'isotig')) ) {die "ERROR: On commandline: -t type must be 'contig' or 'read' or 'isotig'\n\n";}
-
-
-my ($L,$M,$R, $Lh,$Mh,$Rh, $Lhnewline,$Mhnotab);
-if    ($format eq 's') {($L,$M,$R, $Lh,$Mh,$Rh, $Lhnewline,$Mhnotab)=('','  ','', '','  ','', "\n",'');}
-elsif ($format eq 't') {($L,$M,$R, $Lh,$Mh,$Rh, $Lhnewline,$Mhnotab)=("\t","\t",'', "","\t",'', "\n",'');} # There is correctly a tab for the $L, but not the $Lh.
-elsif ($format eq 'w') {($L,$M,$R, $Lh,$Mh,$Rh, $Lhnewline,$Mhnotab)=('| ',' | ',' |', '|| ',' || ',' ||', '|| ',' || ');}
-else {die "\nInvalid output format code: '$format'. Should be 's', 't' or 'w'.\n\n";}
-
-### create output_dir if it doesn't exist
-if (-d $output_dir) {
-	print STDERR "  Directory '$output_dir' exists, so the existing fasta_summary.pl output files will be overwritten\n";
-} else {
-	mkdir $output_dir;
-	print STDERR "  Directory '$output_dir' created\n";
-}
-
-my $gc_count = 0;
-
-#--------------- Read in contigs from fasta file -------------------
-
-open INFILE, "<$infile" or die "Failed to open file: '$infile' : $!";
-open STATS, ">$output_dir/stats.txt" or die "Failed to open $output_dir/stats.txt: '' : $!";
-
-my $header = <INFILE>;
-if (! defined($header) ) {print "\n** ERROR: First line of input fasta file is undefined - so file must be empty **\n\n"; print STATS "No sequences found\n"; exit 1;}
-if ($header!~/^>/) {print "\nERROR: First line of input fasta file should start with '>' BUT first line is: '$header'\n"; print STATS "No sequences found\n"; exit 1;}
-
-my $seq = "";
-my @sequences;
-
-while (<INFILE>) {
-	if (/^>/) {
-		push @sequences, [length($seq), $header, $seq];
-		$header = $_;
-		$seq = "";
-	} else {
-		chomp;
-		$gc_count += tr/gcGC/gcGC/;
-		$seq .= $_;
-	}
-}
-push @sequences, [length($seq), $header, $seq];
-close INFILE;
-if ($#sequences==-1) {print "\nERROR: There are zero sequences in the input file: $infile\n\n"; print STATS "No sequences found\n"; exit 1;}
-
-
-my $all_contigs_length=0;
-foreach (@sequences) {$all_contigs_length += $_->[0];}
-if ($all_contigs_length==0) {print "\nERROR: Length of all contigs is zero\n\n"; exit 2;}
-
-# Find number and number of bases in reads greater than the optional cut-off length given at command-line.
-my $num_reads_above_cutoff=0;
-my $num_of_bases_in_reads_above_cutoff=0;
-if ($cutoff_length>0) 
-  {
-  foreach (@sequences)
-    {
-    if ($_->[0]>=$cutoff_length) {$num_of_bases_in_reads_above_cutoff+= $_->[0]; $num_reads_above_cutoff++;}
-    }
-  }
-
-
-#--------------- Gather Plots Data, Find N50, Print sorted contig file -------------------
-
-my $summed_contig_length = 0;
-my @summed_contig_data; # <-- For graph of summed length (in number of bases) versus number of contigs.
-my @summed_contig_data_contigLens; # <-- Added by SJBridgett to get graph of summed contig length versus min. contig length included (ie. X-axis is sort of inverse of above)
-
-my $contig1k_count = 0;
-my $contig1k_length = 0;
-
-open SORTED, ">$output_dir/sorted_contigs.fa" or die $!;
-
-# top row in stats file
-#print STATS "N50\nMax contig size\nNumber of bases in contigs\nNumber of contigs\nNumber of contigs >=1kb\nNumber of contigs in N50\nNumber of bases in contigs >=1kb\nGC Content of contigs\n";
-
-my $N50size=-1;
-my $N50_contigs = 0;
-
-my @sorted_by_contig_length = sort {$b->[0] <=> $a->[0]} @sequences;
-
-### variables and initialization for histogram (stored in @bins)
-my $max = $sorted_by_contig_length[0][0];
-my $mean= $all_contigs_length/($#sequences+1); # <-- Added by Stephen Bridgett.  Note: as $# gives the highest index number, so add 1 as arrays are zero-based.
-
-# Calculate standard deviation
-my $sumsquares = 0;
-foreach (@sequences) {$sumsquares += ($_->[0] - $mean) ** 2;} # <-- Taken from John's "mean_fasta_length.pl" script.
-my $stddev = ( $sumsquares/($#sequences+1) ) ** 0.5;
-
-my $min = 0;
-# Aim for approximately 100 bins, so 
-
-my $bin_size=1;
-my $min_max_range=$max - $min;
-# $bin_size = ($min_max_range)/(99); # (99 is 100-1) so   1000/100
-if    ($min_max_range>=100000000) {$bin_size=1000000;}
-elsif ($min_max_range>=10000000) {$bin_size=100000;}
-elsif ($min_max_range>=1000000) {$bin_size=10000;}
-elsif ($min_max_range>=100000) {$bin_size=1000;}
-elsif ($min_max_range>=10000) {$bin_size=100;}
-else  {$bin_size=10;}  # elsif  ($min_max_range>=1000) {$bin_size=10;}
-#elsif ($min_max_range>=100) {$bin_size=1;}
-#elsif ($min_max_range>=10) {}
-#elsif ($min_max_range>=1) {}
-# WAS: my $bin_size = ($type eq 'contig') ? 1000 : 10;
-
-my @bins;
-$#bins = int(($min_max_range)/$bin_size) + 1; # <-- Set the bins array size.
-foreach (@bins) {$_ = 0};
-
-foreach (@sorted_by_contig_length) {
-
-	my $curr_contig_length = $_->[0];
-	push @summed_contig_data_contigLens, $curr_contig_length; # <-- added by Stephen.
-	
-	$bins[int(($curr_contig_length + 1 - $min)/$bin_size)]++;
-	
-	$summed_contig_length += $curr_contig_length;
-	push @summed_contig_data, $summed_contig_length;
-
-	### sorted contigs file
-	print SORTED $_->[1] . $_->[2] . "\n";
-
-	if ($curr_contig_length >= 1000) {
-		$contig1k_count++;
-		$contig1k_length += $curr_contig_length;
-	}
-	
-	$N50_contigs++ unless ($N50size>-1); # Was unless $N50_found
-	
-	if ($summed_contig_length > ($all_contigs_length / 2) and $N50size == -1) {
-		$N50size = $curr_contig_length;
-	}
-}
-
-
-if ($bucket1!=0) 
-  {
-=pod
-  # This firsdt method works and agress with the second, but the lengths are in reverse order, at the @sorted_by_contig_length array was sorted with longest contig first.
-  open BUCKET1, ">$output_dir/lengths_hist1.txt" or die "Failed to open file '$output_dir/lengths_hist1.txt' : $!\n";
-  print BUCKET1 "Length\tFrequency\n";
-  my $len=-1;
-  my $count=0;
-  foreach (@sorted_by_contig_length)
-    {  
-    if ( $len != $_->[0] ) {if ($len>-1) {print BUCKET1 "$len\t$count\n";} $len=$_->[0]; $count=0;}
-    $count++;
-    }
-  if ($len>-1) {print BUCKET1 "$len\t$count\n";} # Print length of final length grouping.
-  close BUCKET1;
-=cut
-  open BUCKET1, ">$output_dir/lengths_hist1_with_zeros.txt" or die "Failed to open file '$output_dir/lengths_hist1_with_zeros.txt' : $!\n";
-  print BUCKET1 "Length\tFrequency\n";
-  my @bucket=(); # To check the result by using array.
-  foreach (@sequences)
-    {
-    my $len=$_->[0];
-    if (defined $bucket[$len]) {$bucket[$len]++;}
-    else {$bucket[$len]=1;}
-    }
-  for (my $i=0; $i<=$#bucket; $i++)  
-# for (my $i=$#bucket; $i>=0; $i--) # <-- for reverse order
-   {
-   if (defined $bucket[$i]) {print BUCKET1 "$i\t$bucket[$i]\n";} 
-   else {print BUCKET1 "$i\t0\n";} # Can uncomment this later if don't want zeros in the output.
-   }
-  close BUCKET1;
-  }
-
-
-my $type_plural=$type.'s';
-print STATS  $Lh."Statistics for $type lengths:".$Mhnotab.$Rh."\n";
-print STATS  $L."Min $type length:".$M.&commify_if($sorted_by_contig_length[$#sequences][0],$doCommify).$R."\n";
-print STATS  $L."Max $type length:".$M.&commify_if($max,$doCommify).$R."\n";
-printf STATS $L."Mean %s length:".$M."%.2f".$R."\n", $type,$mean; # <-- Added by Stephen Bridgett, April 2009.
-printf STATS $L."Standard deviation of %s length:".$M."%.2f".$R."\n", $type,$stddev;  ## <-- Added by Stephen Bridgett, May 2009.
-print STATS  $L."Median $type length:".$M.&commify_if($sorted_by_contig_length[int($#sequences/2)][0],$doCommify).$R."\n";
-print STATS  $L."N50 $type length:".$M.&commify_if($N50size,$doCommify).$R."\n";
-
-print STATS  $Lhnewline."Statistics for numbers of $type_plural:".$Mhnotab.$Rh."\n";
-print STATS  $L."Number of $type_plural:".$M.&commify_if($#sequences+1,$doCommify).$R."\n";
-print STATS  $L."Number of $type_plural >=1kb:".$M.&commify_if($contig1k_count,$doCommify).$R."\n";
-print STATS  $L."Number of $type_plural in N50:".$M.&commify_if($N50_contigs,$doCommify).$R."\n";
-
-print STATS  $Lhnewline."Statistics for bases in the $type_plural:".$Mhnotab.$Rh."\n";
-print STATS  $L."Number of bases in all $type_plural:".$M.&commify_if($all_contigs_length,$doCommify).$R."\n";
-print STATS  $L."Number of bases in $type_plural >=1kb:".$M.&commify_if($contig1k_length,$doCommify).$R."\n";
-printf STATS $L."GC Content of %s:".$M."%.2f %%".$R."\n", $type_plural,(100*$gc_count/$all_contigs_length);
-
-if ($cutoff_length>0) 
-  {
-  print STATS $Lhnewline."Statistics for $type_plural >= $cutoff_length bp in length:".$Mhnotab.$Rh."\n";
-  print STATS $L."Number of $type_plural >= $cutoff_length bp:".$M.&commify($num_reads_above_cutoff,$doCommify).$R."\n";
-  print STATS $L."\tNumber of bases in $type_plural >= $cutoff_length bp:".$M.&commify($num_of_bases_in_reads_above_cutoff,$doCommify).$R."\n";
-  }
-
-if ($repeats==1) {&countRepeats();}
-
-print STATS "\n";
-
-
-# Output random selection of reads if requested on commandline:
-my $fastaLineLen=60; # <-- The line length used for 454 sffinfo output, but could use a value read from input file (but be careful not to read a short line)
-if ($num_random_reads_to_output>0)
-  {
-  my @randlist;
-  if ($num_random_reads_to_output<($#sequences+1))
-    {    
-    print STATS "\nSome randomly selected reads:\n\n";
-    @randlist= &getListOfRandomNumbers($#sequences, $num_random_reads_to_output); # Don't use ($#sequences + 1), just ($#sequences) otherwise would be outside the array.
-    }
-  else # Just print all the sequences:
-    {
-    print STATS "\nAll ".($#sequences+1)." reads:\n\n";
-    for (my $i=0;$i<=$#sequences;$i++) {push @randlist,$i;}
-    }
-  &print_sequences(\@randlist)
-  }    
-
-
-# Print the longest read:
-if ($longest_read>0)
-  {
-  my $length_of_longest_read=-1;
-  my @longest_read=();
-  my $i=0;
-  foreach (@sequences)
-    {
-    if ($_->[0]>$length_of_longest_read) {$length_of_longest_read=$_->[0]; $longest_read[0]=$i;}
-    $i++;
-    }
-  if ($length_of_longest_read>0) {print STATS "\nLongest read:\n"}
-  &print_sequences(\@longest_read);
-  }
-
-
-=pod
-print STATS "\n$type\tSummed\nlength\tlength\n"; # <-- Added by Stephen Bridgett, but better to produce a graph instead.
-
-my $i=0;
-foreach (@summed_contig_data) {
-#	print STATS $sorted_by_contig_length[$i]->[0]."\t".$summed_contig_data_contigLens[$i]."\t".$_."\t".$summed_contig_data[$i]."\n";
-	print STATS $sorted_by_contig_length[$i]->[0]."\t".$_."\n";
-	$i++;
-}
-=cut
-
-open  SUMMED, ">$output_dir/summed_contig_lengths.dat" or die $!;
-print SUMMED join "\n",@summed_contig_data;
-close SUMMED;
-
-open  HISTOGRAMBINS, ">$output_dir/histogram_bins.dat" or die $!;
-my $bin_size_counter = 0;
-foreach (@bins) {
-	print HISTOGRAMBINS eval($bin_size_counter++ * $bin_size + $bin_size/2) . "\t$_\n";
-}
-close HISTOGRAMBINS;
-
-
-# Graph of cumulative (summed) number of reads on y-axis, versus length of read (decending order) on x-axis
-open  SUMREAD_READLEN, ">$output_dir/sum_reads_vs_read_len.dat" or die $!;
-#my $read_counter= 0;
-my $read_counter= $#sorted_by_contig_length+1;
-
-foreach (@sorted_by_contig_length) {
-#	$read_counter++;
-	$read_counter--;
-	print SUMREAD_READLEN "$_->[0]\n"; # $read_counter
-}
-close SUMREAD_READLEN;
-
-
-
-
-my $properType=ucfirst($type); # Makes the first letter an upper case letter, ie. 'Config' or 'Read'
-#if ($type eq 'contig') 
-#  {
-  # print the outcome of the gnu_plot as may have a write permissions error sometimes.
-  my $YHistogramScaleType = ($type eq 'read') ? '' : 'log y';    # Not using log scale for reads, just for contig/isotigs.
-  &plot_graph('histogram', "$output_dir/histogram_bins.dat",  "Histogram of $type lengths", "$properType length", "Number of $type_plural", '0.9', $YHistogramScaleType);
-  &plot_graph('line',      "$output_dir/summed_contig_lengths.dat", "Summed $type lengths", "Number of $type_plural", "Summed $type length in bases", '0.9', '');
-  &plot_graph('line',      "$output_dir/sum_reads_vs_read_len.dat", "X-axis gives the Number of $type_plural that are greater than the $properType-length given on the Y-axis", "$properType length", "Cummulative number of $type_plural",  '0.9', '');
-
-=pod
-  #  print `gnuplot_histogram.sh $output_dir/histogram_bins.dat`;
-
-  &plot_graph("$output_dir/summed_contig_lengths.dat", 'Summed contig lengths', 'Number of contigs', 'Summed contig length in bases', '0.9', '');
-  #  print `gnuplot_summedcontigs.sh $output_dir/summed_contig_lengths.dat`;
-
-  &plot_graph('line', "$output_dir/sum_reads_vs_read_len.dat", 'X-axis gives the Number of contigs that are greater than the Contig-length given on the Y-axis', 'Contig length', 'Cummulative number of contigs',  '0.9', '');
-  #  print `gnuplot_sum_contig_vs_contig_len.sh $output_dir/sum_reads_vs_read_len.dat`;
-  }
-elsif ($type eq 'read')
-  {
-
-  #  print `gnuplot_readshistogram_logY.sh $output_dir/histogram_bins.dat`; # There's also optionally a "...._linearY.sh"
-
-  &plot_graph('line', "$output_dir/summed_contig_lengths.dat",'Summed read lengths', 'Number of reads', 'Summed read length in bases', '0.9', '');
-  #  print `gnuplot_summedreads.sh $output_dir/summed_contig_lengths.dat`;
-
-  &plot_graph('line', "$output_dir/sum_reads_vs_read_len.dat", 'X-axis gives the Number of reads that are greater than the Read-length given on the Y-axis', 'Read length', 'Cummulative number of reads', '0.9', '');
-  #  print `gnuplot_sum_reads_vs_read_len.sh $output_dir/sum_reads_vs_read_len.dat`;  
-  }
-else  {die "\n** ERROR: Invalid type='$type' **\n\n";}
-=cut
-
-close SORTED;
-close STATS;
-
-
-# Use pipe to plot directly with gnuplot, rather than calling a separate shell script:
-# http://www.vioan.ro/wp/2008/09/30/calling-gnuplot-from-perl/
-# http://forums.devshed.com/perl-programming-6/plotting-with-gnuplot-within-perl-script-549682.html
-# Another option is the perl module: GnuplotIF: http://lug.fh-swf.de/perl/GnuplotIF.html OR: http://lug.fh-swf.de/perl/
-
-# PlPlot: Perl: http://search.cpan.org/~dhunt/PDL-Graphics-PLplot-0.47/plplot.pd
-#               http://plplot.sourceforge.net/
-# dislin: http://www.mps.mpg.de/dislin/overview.html
-# MathGL: http://mathgl.sourceforge.net/index.html
-
-
-sub plot_graph
-{
-# Plots a histogram or xy-line graph
-# Parameters: GraphType (histogram/line) DataFile, Title, X-label, Y-label, Y-range
-# Graphfile should end with '.png'
-# The $yloglinear is 'log y' for log, or '' for linear
-my ($graphtype, $datafile, $title,$xlabel,$ylabel,$yrange,$yloglinear)=@_;  # yrange for reads: 0.1, and for contigs: 0.9
-
-my $graphstyle='';
-if ($graphtype eq 'histogram') {$graphstyle="plot \"$datafile\" using 1:2 with boxes";}
-elsif ($graphtype eq 'line') {$graphstyle="plot \"$datafile\" using 1 with lines";}
-else {die "\n** ERROR: Invalid graphtype='$graphtype'\n\n";}
-my $yloglinearscale= ($yloglinear eq '') ? '' : "set $yloglinear";
-
-# To capture any errors that are normally sent from gnuplot to stderr, could use: open3 pipe interface: 
-# http://www.clintoneast.com/articles/perl-open3-example.php
-# http://hell.org.ua/Docs/oreilly/perl2/prog/ch16_03.htm
-# But the following should be fine, as the stderr will display when running the script anyway.
-# If needed a simpler way would be to sent the output to a file using eg: open (GNUPLOT, "|gnuplot > gnu_out.txt 2>&1")  or die .... The read the resulting file.
-open (GNUPLOT, "|gnuplot") or die "\n**ERROR: Failed to open gnuplot : $!\n\n **";
-print GNUPLOT <<ENDPLOT;
-set terminal png
-set output "$datafile.png"
-set nokey
-$yloglinearscale
-set xlabel "$xlabel"
-set ylabel "$ylabel"
-set yrange [$yrange:]
-set title "$title"
-$graphstyle
-ENDPLOT
-close(GNUPLOT);
-if ($? != 0) {print "\n** WARNING: GNUplot pipe returned non-zero status: '$?'\n\n";} # $? is the status returned by the last pipe close (or backtick or system operator)
-if (! -e "$datafile.png") {die "\n** ERROR: Failed to create '$datafile.png'**\n\n";}
-
-=pod
-#PNG
-set term png small xFFFFFF
-set output "$file.png"
-set size 1 ,1
-set nokey
-set data style line
-set xlabel "frequency" font "VeraMono,10"
-set title "Fast Fourier Transform" font "VeraMono,10"
-set grid xtics ytics
-set xtics 100
-plot "$file" using 1:2 w lines 1
-=cut
-
-#WAS PREVIOUSLY AS .sh script
-=pod
-# The 'gnuplot_readshistogram_logY.sh' is:
-set terminal png
-set output "$1.png"
-set log y
-set xlabel "Read length"
-set ylabel "Frequency"
-set yrange [0.9:]
-set title "Histogram of read lengths"
-plot "$1" using 1:2 with boxes
-=cut
-}
-
-
-# Was previously a separate .sh file:
-=pod
-#!/bin/sh
-gnuplot << EOF
-set terminal png
-set output "$1.png"
-set xlabel "Number of contigs"
-set ylabel "Summed contig length in bases"
-set yrange [0.9:]
-set title "Summed contig lengths"
-plot "$1" using 1 with lines
-EOF
-=cut
-
-
-
-
-# Added function to count number of simple dinucleotide repeats:
-sub countRepeats 
-  {
-  # To count the number of sequences that contain mostly repeats.
-  # This would be faster if called a C program on the file.
-
-# Common simple repeats are listed here: http://www.bioinfo.de/isb/2005/05/0041/
-# Dinucleotide
-#   AT/TA
-#   AC/TG
-#   AG/TC
-#   CG/GC
-# Trinucleotide	
-#   AAT/TTA
-#   CTA/GAT
-#   ATG/TAC
-#   ACT/TGA
-#   CTC/GAG
-#   AGG/TCC
-#   CAG/GTC
-#   AAG/TTC
-#   ATA/TAT
-#   CAA/GTT
-#   AGC/TCG
-#   ACA/TGT
-#   ACG/TGC
-#   AGA/TCT
-#   ACC/TGG
-#   Other
-# Tetranucleotide	
-#   AAAT
-#   AAAC
-#   CACG
-#   AACA
-#   AATA
-#   AAGA
-#   TGAA
-#   AAAG
-#   ACAT
-#   AATG
-#   AGCC
-#   Other
-# Pentanucleotide	
-#   AAAAC
-#   AATTG
-#   GCTAA
-#   ATAAT
-#   AAAAT
-#   AAACA
-#   ATATA
-#   TTGCC
-#   Other
-
-  # I also add mono-nucleotide repeats: - ie. just all T's, or A's, etc
-  # Just consider the dinucleotide repeats for now:
-  my ($ATseq,$CGseq,$ACseq,$TGseq,$AGseq,$TCseq)=(0,0,0,0,0,0);
-  my ($AAseq,$TTseq,$CCseq,$GGseq)=(0,0,0,0);
-  foreach (@sequences)
-    {
-    my $seq_len=$_->[0];
-    my $seq=$_->[2]; # This copy might be slow, maybe should just stick with using the reference.
-    my $mnt=0.35*$seq_len;  # Mononucleotide threshold:  HERE 0.35 also means 70%;  0.4 means 80% dinucleotide repeats, as really one base so 0.5 = 100%
-    my $dnt=0.35*$seq_len;  # Dinucleotide threshold:  0.35 means 70%;  0.4 means 80% dinucleotide repeats, as two bases so 0.5 = 100%
-    my ($AT,$CG,$AC,$TG,$AG,$TC)=(0,0,0,0,0,0);
-    my ($AA,$TT,$CC,$GG)=(0,0,0,0);
-    # See: http://www.allinterview.com/showanswers/76719.html
-
-    # AT/TA seems most common repeat so process it first to save time:
-    while ($seq=~/AT/g) {$AT++;} if ($AT>$dnt) {$ATseq++; next;} # AT is same as TA.   If has 80% AT's then won't have 80% AC etc.
-    while ($seq=~/CG/g) {$CG++;}  if ($CG>$dnt) {$CGseq++; next;} # CG is same as GC.
-    # AC,TG
-    while ($seq=~/AC/g) {$AC++;} if ($AC>$dnt) {$ACseq++; next;}
-    while ($seq=~/TG/g) {$TG++;} if ($TG>$dnt) {$TGseq++; next;}
-    # AG/TC
-    while ($seq=~/AG/g) {$AG++;} if ($AG>$dnt) {$AGseq++; next;}
-    while ($seq=~/TC/g) {$TC++;} if ($TC>$dnt) {$TCseq++; next;}
-
-    # Added my simple mononucleotde repeat count:
-    while ($seq=~/AA/g) {$AA++;} if ($AA>$mnt) {$AAseq++; next;}
-    while ($seq=~/TT/g) {$TT++;} if ($TT>$mnt) {$TTseq++; next;}
-    while ($seq=~/CC/g) {$CC++;} if ($CC>$mnt) {$CCseq++; next;}
-    while ($seq=~/GG/g) {$GG++;} if ($GG>$mnt) {$GGseq++; next;}
-    }
-
-  my $num_seq=($#sequences+1);
-  my $total_din_repeats_seq= $ACseq+$TGseq+$ATseq+$AGseq+$TCseq+$CGseq;
-  my $percent_din_repeats=100*$total_din_repeats_seq/$num_seq;
-  print STATS "\nSimple Dinucleotide repeats:\n";
-  printf STATS "\tNumber of %s with over 70%% dinucleotode repeats:\t%.2f %% (%d %s)\n", $type_plural, $percent_din_repeats, $total_din_repeats_seq, $type_plural;
-  printf STATS "\tAT:\t%.2f %% (%d %s)\n", (100*$ATseq/$num_seq),$ATseq,$type_plural;
-  printf STATS "\tCG:\t%.2f %% (%d %s)\n", (100*$CGseq/$num_seq),$CGseq,$type_plural;
-  printf STATS "\tAC:\t%.2f %% (%d %s)\n", (100*$ACseq/$num_seq),$ACseq,$type_plural;
-  printf STATS "\tTG:\t%.2f %% (%d %s)\n", (100*$TGseq/$num_seq),$TGseq,$type_plural;
-  printf STATS "\tAG:\t%.2f %% (%d %s)\n", (100*$AGseq/$num_seq),$AGseq,$type_plural;
-  printf STATS "\tTC:\t%.2f %% (%d %s)\n", (100*$TCseq/$num_seq),$TCseq,$type_plural;
-
-  my $total_mono_repeats_seq= $AAseq+$TTseq+$CCseq+$GGseq;
-  my $percent_mono_repeats=100*$total_mono_repeats_seq/$num_seq;
-  print STATS "\nSimple mononucleotide repeats:\n";
-  printf STATS "\tNumber of %s with over 50%% mononucleotode repeats:\t%.2f %% (%d %s)\n", $type_plural, $percent_mono_repeats, $total_mono_repeats_seq, $type_plural;
-  printf STATS "\tAA:\t%.2f %% (%d %s)\n", (100*$AAseq/$num_seq),$AAseq,$type_plural;
-  printf STATS "\tTT:\t%.2f %% (%d %s)\n", (100*$TTseq/$num_seq),$TTseq,$type_plural;
-  printf STATS "\tCC:\t%.2f %% (%d %s)\n", (100*$CCseq/$num_seq),$CCseq,$type_plural;
-  printf STATS "\tGG:\t%.2f %% (%d %s)\n", (100*$GGseq/$num_seq),$GGseq,$type_plural;
-
-  return $percent_din_repeats+$percent_mono_repeats;
-  }
-
-
-sub commify_if
-  {
-  # If doCommify is >0 then converts output to commas.   
-  # Formats '1234567890.01' with commas as "1,234,567,890.01
-  # Based on: http://www.perlmonks.org/?node_id=110137
-  my ($number,$doCommify)=@_;
-  if ($doCommify > 0) {$number =~ s/(\d)(?=(\d{3})+(\D|$))/$1\,/g;}
-  return $number;
-  }
-
-
-#--------------- Produce ordered list of random numbers -------------------
-# This is copied from: my_random_contigs.pl
-
-sub getListOfRandomNumbers
-{
-# Use: @list=getListOfRandomNumbers(200,20); to return sorted list of 20 numbers in range from 0 to 200 inclusive.
-my %list2=();
-my $i=0;
-my $MaxNumber=$_[0];
-my $NumToPick=$_[1];
-while ($i<$NumToPick)
-  {
-  my $intRand = int(rand($MaxNumber+1)); # For Zero-based perl-arrays. The +1 means this generates random integers between 0 and $MaxNumber. (See: http://perldoc.perl.org/functions/rand.html )
-  if ($intRand>$MaxNumber) {$intRand=$MaxNumber} # Just to be extra sure that don't exceed $MaxNumber.
-  if ( !exists($list2{$intRand}) ) {$list2{$intRand}=1; $i++;}
-  }
-#foreach my $key(keys %list2) {print "$key ";} 
-# Sort the list of numbers:
-#my @SortedList2 = sort { $a <=> $b } keys(%list2);
-#return @SortedList2;
-return (sort { $a <=> $b } keys(%list2));
-#print "Sorted list of ".$NumToPick." random numbers:\n";
-#foreach my $num(@SortedList2) {print "$num\n";}
-#print "\n\n";
-}
-
-
-sub print_sequences
-  {
-  # Print the sequences wrapping sequences using index array, at line length of '$fastaLineLen' characters:
-  # Uses the global '@sequences' array.
-  my $sequence_indexes_list=$_[0]; # This is an array reference, not the array itself.
-  foreach my $num(@{$sequence_indexes_list})
-    {
-#print "$num (max=$#sequences)\n";
-    print STATS $sequences[$num]->[1]; # Prints the header, no "\n" needed after it.
-    my $pos=0;
-    my $seqlen=$sequences[$num]->[0];
-    while ($pos<$seqlen)
-      {
-      print STATS substr($sequences[$num]->[2],$pos,$fastaLineLen)."\n";
-      $pos+=$fastaLineLen;
-      }
-    print STATS "\n";
-    }
-  }
-
-
-=pod
-# Some test runs for mono-nucleotides and dinucelotides:
->FUOMOGO01AQV42DUMMYA length=339 xy=0189_0676 region=1 run=R_2009_04_23_17_54_06_
-AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
-AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
-AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
-AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
-AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
->FUOMOGO01AQV42DUMMYB length=339 xy=0189_0676 region=1 run=R_2009_04_23_17_54_06_
-AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
-AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
-AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
-AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
-AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
->FUOMOGO01AQV42DUMMYC length=339 xy=0189_0676 region=1 run=R_2009_04_23_17_54_06_
-TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
-TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
-TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
-TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
->FUOMOGO01AQV42DUMMYD length=339 xy=0189_0676 region=1 run=R_2009_04_23_17_54_06_
-GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG
-GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG
-
->FUOMOGO01AQV42 length=339 xy=0189_0676 region=1 run=R_2009_04_23_17_54_06_
-TGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTG
-TGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTG
-TGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTG
-TGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTG
-TGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTG
-TGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGT
->FUOMOGO01AUK0D length=214 xy=0231_0843 region=1 run=R_2009_04_23_17_54_06_
-ACACACACACACACACACACACACACACACACACACACACACACACACACACACACACAC
-ACACACACACACACACACACACACACACACACACACACACACACACACACACACACACAC
-ACACACACACACACACACACACACACACACACACACACACACACACACACACACACACAC
-ACACACACACACACACACACACGACGACGACGAC
->FUOMOGO01AUB7C length=64 xy=0228_1718 region=1 run=R_2009_04_23_17_54_06_
-ATATATATATATATATATATATATATATATATATATATATATATATATATAGTACGTACG
-TACG
->FUOMOGO01AU00B length=213 xy=0236_1097 region=1 run=R_2009_04_23_17_54_06_
-ACACACACACACACACACACACACACACACACACACACACACACACACACACACACACAC
-ACACACACACACACACACACACACACACACACACACACACACACACACACACACACACAC
-ACACACACACACACACACACACACACACACACACACACACACACACACACACACACACAC
-ACACACACACACACACACACGACGACGACGACG
->FUOMOGO01ATYRT length=169 xy=0224_0695 region=1 run=R_2009_04_23_17_54_06_
-TGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTG
-TGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTG
-TGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGT
->FUOMOGO01ARMLN length=400 xy=0197_2201 region=1 run=R_2009_04_23_17_54_06_
-TATATATATATATATATATATATATATATATATATATATATATATATATATATATATATA
-TATAGTAGTAGTAGTATATATATATATATATATATATATATATATATATATATATATATA
-TATATATATATATATATATATATATATATATATATATATATATATATATATATATATATA
-TATATATATATATATATATATATATATATATATATATATATATATATATATATATATATA
-TATATATATATATATATATATATATATATATATATATATATATATATATATATATATATA
-TATATATATATATATATATATATATATATATATATATATATATATATATATATATATATA
-TATATATATATATATATATATATATATATATATATATATA
->FUOMOGO01AVGRX length=44 xy=0241_1051 region=1 run=R_2009_04_23_17_54_06_
-TATATATATATATATATATATATATATATATATATATATATATA
->FUOMOGO01ASZ6K length=315 xy=0213_0922 region=1 run=R_2009_04_23_17_54_06_
-TGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTG
-TGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTG
-TGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTG
-TGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTG
-TGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTG
-TGTGTGTGTGTGTGT
->FUOMOGO01ARSZF length=65 xy=0199_2281 region=1 run=R_2009_04_23_17_54_06_
-TATATATATATATATATATATATATATATATATATATATATATATATATATAGTACGTAC
-GTACG
->FUOMOGO01AYV8U length=49 xy=0280_1324 region=1 run=R_2009_04_23_17_54_06_
-ATATATATATATATATATATATATATATATATATATATATATATATATA
->FUOMOGO01AYV9X length=40 xy=0280_1363 region=1 run=R_2009_04_23_17_54_06_
-TATATATATATATATATATATATATATATATATATATATA
->FUOMOGO01AUX4M length=40 xy=0235_1460 region=1 run=R_2009_04_23_17_54_06_
-TATATATATATATATATATATATATATATATATATATATA
->FUOMOGO01AWOTU length=54 xy=0255_0800 region=1 run=R_2009_04_23_17_54_06_
-ATATATATATATATATATATATATATATATATATATATATATATATATATAGTA
->FUOMOGO01A11TC length=66 xy=0316_1054 region=1 run=R_2009_04_23_17_54_06_
-ATATATATATATATATATATATATATATATATATATATATATATATATATATAGTACGTA
-CGTACG
->FUOMOGO01ASRJP length=401 xy=0210_2019 region=1 run=R_2009_04_23_17_54_06_
-TATATATATATATATATATATATATATATATATATATATATATATATATATATAGTATAT
-AGTAGTAGTAGTATATATATATATATATATATATATATATATATATATATATATATATAT
-ATATATATATATATATATATATATATATATATATATATATATATATATATATATATATAT
-ATATATATATATATATATATATATATATATATATATATATATATATATATATATATATAT
-ATATATATATATATATATATATATATATATATATATATATATATATATATATATATATAT
-ATATATATATATATATATATATATATATATATATATATATATATATATATATATATATAT
-ATATATATATATATATATATATATATATATATATATATATA
->FUOMOGO01AU1ZH length=67 xy=0236_2363 region=1 run=R_2009_04_23_17_54_06_
-TATATATATATATATATATATATATATATATATATATATATATATATATATATAGTACGT
-ACGTACG
-=cut