# HG changeset patch
# User romaingred
# Date 1508139975 14400
# Node ID 8b7000eac6a0030c8d1e43daa34935fbed9ad813
# Parent  98b4a5ec8e632b84534e9cbed88ee906245c8708
Deleted selected files

diff -r 98b4a5ec8e63 -r 8b7000eac6a0 bin/html.pm
--- a/bin/html.pm	Mon Oct 16 03:34:16 2017 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,907 +0,0 @@
-package html;
-
-use strict;
-use warnings;
-use File::Basename;
-
-use Exporter;
-our @ISA = qw( Exporter );
-our @EXPORT_OK = qw( &main_page &details_pages &menu_page &ppp_page );
-
-sub main_page
-{
-	my ( $dir, $file, $list_mainTabP, $current, $ma, $ma_uni, $dir_root ) = @_;
-	my ( $futHashP, $uniqueTabP, $randTabP, $pngTabP ) = get_genome ( $dir, $dir_root );
-
-	open my $h, '>', $file || die "cannot create $file $!\n";
-	header ( $h );
-	navbar ( $h, $list_mainTabP, $current );
-	print $h "<div class=\"container\"><p><a class=\"btn\" href=\"$current-sub.html\">View details &raquo;</a></p></div>\n";
-	futurette( $h, $current, $pngTabP, $futHashP );
-	print  $h "<div class=\"container\"><h2>mappers #: $ma</h2><h2>unique mappers #: $ma_uni</h2> </div>\n";
-	carousel2( $h, $uniqueTabP, $randTabP, $dir_root );
-	footer($h);
-	close $h;
-}
-
-sub menu_page
-{
-	my ( $dir, $file, $list_mainTabP, $current, $min, $max, $simin, $simax, $pimin, $pimax, $dir_root ) = @_;
-  my $html_ref = $1 if $dir =~ /$dir_root(.*)/;
-	open my $h, '>', $file || die "cannot create $file $!\n";
-  header($h);
-  navbar ( $h, $list_mainTabP, $current );
-  span( $h, $current, $min, $max, $simin, $simax, $pimin, $pimax );
-  print $h "  <div class=\"container\"> <div class=\"row text-center\">  <img  src=\"$html_ref/pie_chart.png\"/><br />\n";
-  print $h "  <A HREF=\"$html_ref/repartition.txt\">text file</A><br/>\n </div></div>";
-  footer($h);
-  close $h;
-}
-
-sub details_pages
-{
-	my ( $dir_details, $prefix, $list_mainTabP, $current, $misTE, $dir_root ) = @_;
-  my ($Hex, $HTE, $HG, $NonUniTE, $NonUniG, $UniG ) = get_subgroups( $dir_details, $current, $misTE, $dir_root );
-
-  my $html_ref = $1.'-PPP.html' if $prefix =~ /$dir_root(.*)/;
-  open my $h, '>',  $prefix.'-TEs.html' || die "cannot create  $prefix-TEs.html $!\n";
-  header($h);
-  navbar ( $h, $list_mainTabP, $current );
-  if ( $prefix =~ /bonafide_reads$/ )
-  {
-  	print $h " <div class=\"container\">";
-  	print $h " <p><a class=\"btn\" href=\"$html_ref\">Ping Pong Partners</a></p>\n";
-  	print $h "</div>";
-  }
-  fut($h,'Transposable elements',$HTE);
-  carousel($h,$NonUniTE,$dir_root);
-  footer($h);
-  close $h;
-
-  open $h, '>',  $prefix.'-genome.html' || die "cannot create  $prefix-genome.html $!\n";
-  header($h);
-  navbar ( $h, $list_mainTabP, $current );
-  fut($h,'Genome',$HG);
-  carousel2($h,$UniG, $NonUniG,$dir_root);
-  footer($h);
-  close $h;
-
-  open  $h, '>',  $prefix.'-exons.html' || die "cannot create  $prefix-exons.html $!\n";
-  header($h);
-  navbar ( $h, $list_mainTabP, $current );
-  fut($h,'Exons',$Hex);
-  footer($h);
-  close $h;
-}
-
-sub ppp_page
-{
-	my ( $dir, $file, $list_mainTabP, $current, $ppp, $dir_root ) = @_;
-
-	my $ppp_file = $ppp.'ppp.txt';
-	open my $h, '>', $file || die "cannot create $file $!\n";
-	header($h);
- 	navbar ( $h, $list_mainTabP, $current );
- 	print $h '<div class="container"> <table class="wb-tables table table-striped table-hover">'."\n";
- 	print $h '<thead>
-  <tr>
-    <th data-sortable="true">ID</th>
-    <th data-sortable="true">overlap sum</th>
-    <th data-sortable="true">ten overlap sum</th>
-    <th data-sortable="true">mean</th>
-    <th data-sortable="true">standard deviation</th>
-  	<th data-sortable="true">z-score</th>
-  	<th data-sortable="true">p-value</th>
-	</tr>
-  </thead>
-  <tbody>';
-
- 	open my $f, '<', $ppp_file || die "cannot open $ppp_file  $!\n";
- 	while ( <$f> )
- 	{
- 		chomp;
- 		print $h '<tr>';
- 		my ( $id, $sum, $ten, $mean, $sd, $zscore, $prob) = split /\t/, $_;
- 		if( -d "$ppp/$id" ) 
- 		{
- 			my $sub_html = $ppp.$id.'.html';
-      my $sub_html_ref = $1.$id if $ppp =~ /$dir_root(.*)/;
- 			print $h "<td> <a href=\"$sub_html_ref.html\">$id</a> </td>";
-
- 			open my $sub, '>', $sub_html || die "cannot create $sub_html\n";
- 			{
- 				header($sub);
- 				print $sub "
-					<div align=\"center\">
-					<h2>$id</h2>
-					<p> <img src=\"$id/histogram.png\" width=50%/></p>
-					<p><a href=\"$id/overlap_size.txt\">ping pong signature</a></p>
-					<p><a href=\"$id/sensPPP.txt\">sens reads with PPP</a></p>
-					<p><a href=\"$id/antisensPPP.txt\">reverse reads  with PPP</a></p>
-					<p><a href=\"$id/sens.txt\">sens reads without PPP</a></p>
-					<p><a href=\"$id/antisens.txt\">reverse reads without PPP</a></p>
-					</div>";
- 				footer($sub);
- 			}
- 			close $sub;
-
- 		}
- 		else { print $h "<td> $id </td>\n"; }
- 		print $h "<td> $sum </td><td> $ten </td><td> $mean </td><td> $sd </td><td> $zscore </td><td> $prob </td>\n";
-
- 		print $h '</tr>';
- 	}
- 	close $f;
- 	print $h "</tbody></table></div>";
- 	footer($h);
- 	close $h;
-}
-
-sub get_genome
-{
-  my ( $dir, $dir_root ) = @_;
-  my ( %hash, @group,  @Unique, @NonUnique, @png );
-
-  my $fut = $dir.'/*';
-  my @fut = glob $fut;
-
-
-	foreach my $fr ( @fut )
-	{
-    my $f = $1 if $fr =~ /$dir_root(.*)/;
-		if ( $fr =~ /.*Gviz/ )
-		{
-			my $nu = $fr.'/rand/*';
-			@NonUnique =  glob $nu;
-			my $u = $fr.'/unique/*';
-			@Unique =  glob $u;
-		}
-		elsif ( $f =~ /.*distribution\.txt$/ ) { $hash{'mappers size distribution (txt)'} = $f; }
-		elsif ( $f =~ /.*distribution\.png$/ ) { push @png, $f; } 
-		elsif ( $f =~ /.*unique\.fastq$/ ) { $hash{'unique mappers (fastq.gz)'} = $f.'.gz'; `gzip $fr`; }
-		elsif ( $f =~ /.*rejected\.fastq$/ ) { $hash{'unmapped (fastq.gz)'} = $f.'.gz'; `gzip $fr`; }
-		elsif ( $f =~ /.*all\.fastq$/ ) { $hash{'mappers (fastq.gz)'} = $f.'.gz'; `gzip $fr`; }
-		elsif ( $f =~ /.*dup_unique\.txt$/ ) { $hash{'unique mappers (txt)'} = $f; }
-		elsif ( $f =~ /.*dup_mapnum\.txt$/ ) { $hash{'mappers (txt)'} = $f; }
-		elsif ( $f =~ /.*dup_nonmapp\.txt$/ ) { $hash{'unmapped (txt)'} = $f; }
-		elsif ( $f =~ /.*_unique_sorted\.bam$/ ) { $hash{'unique alignment (bam)'} = $f; }
-		elsif ( $f =~ /.*_sorted\.bam$/ ) { $hash{'alignment (bam)'} = $f; }
-		elsif ( $f =~ /.*unique_plus.bedgraph/) { $hash{'bedgraph unique plus strand'} = $f; }
-    elsif ( $f =~ /.*unique_minus.bedgraph/) { $hash{'bedgraph unique minus strand'} = $f; }
-    elsif ( $f =~ /.*plus.bedgraph/) { $hash{'bedgraph plus strand'} = $f; }
-    elsif ( $f =~ /.*minus.bedgraph/) { $hash{'bedgraph minus strand'} = $f; }
-    else { unlink $fr; }
-	}
-	return (\%hash, \@Unique, \@NonUnique, \@png);
-}
-
-sub span
-{
-  my ( $file, $name, $min, $max, $simin, $simax, $pimin, $pimax ) = @_;
-
-  print $file "
-<div class=\"container  text-center\">
-  <div class=\"row-fluid\">
-      <div class=\"span6\">
-        <h2>bonafide reads</h2>
-        reads of size between $min and $max<br>with no mi, sn, t and r RNAs
-        <p><a class=\"btn\" href=\"$name-bonafide_reads-genome.html\">Genome</a></p>
-        <p><a class=\"btn\" href=\"$name-bonafide_reads-TEs.html\">TE</a></p>
-        <p><a class=\"btn\" href=\"$name-bonafide_reads-exons.html\">Exons</a></p>
-        <div class=\"row-fluid\">
-          <div class=\"span6\">
-            <h2>siRNAs</h2>
-            bonafide reads of size between $simin and $simax
-            <p><a class=\"btn\" href=\"$name-siRNAs-genome.html\">Genome</a></p>
-            <p><a class=\"btn\" href=\"$name-siRNAs-TEs.html\">TE</a></p>
-            <p><a class=\"btn\" href=\"$name-siRNAs-exons.html\">Exons</a></p>
-          </div>
-          <div class=\"span6\">
-            <h2>piRNAs</h2>
-            bonafide reads of size between $pimin and $pimax
-            <p><a class=\"btn\" href=\"$name-piRNAs-genome.html\">Genome</a></p>
-            <p><a class=\"btn\" href=\"$name-piRNAs-TEs.html\">TE</a></p>
-            <p><a class=\"btn\" href=\"$name-piRNAs-exons.html\">Exons</a></p>
-          </div>
-        </div>
-      </div>
-    <div class=\"span6\">
-       <h2>miRNAs</h2>
-       <p><a class=\"btn\" href=\"$name-miRNAs-genome.html\">Genome</a></p>
-       <p><a class=\"btn\" href=\"$name-miRNAs-TEs.html\">TE</a></p>
-       <p><a class=\"btn\" href=\"$name-miRNAs-exons.html\">Exons</a></p>
-    </div>
-  </div>
-</div>
-";
-}
-
-sub get_subgroups
-{
-  my ( $dir, $name, $misTE, $dir_root ) = @_;
-  my (%Hex, %HTE, %HG, @group, @png, @pngTE,  @NonUniTE, @UniG, @NonUniG );
-
-  my $fut = $dir.'/*';
-  my @fut = glob $fut;
-  my $f ='';
-	foreach my $fr ( @fut )
-	{
-    $f = $1 if $fr =~  /$dir_root(.*)/;
-
-    if ( $f =~ /genome_unique_sorted\.bam$/ ) { $HG{'genome unique mappers (sorted bam)'} =  $f; }
-    elsif ( $f =~ /genome_sorted\.bam$/ ) { $HG{'genome mappers (sorted bam)'} = $f; }
-    elsif ( $f =~ /miRNAs_reads_counts\.txt$/ ) { $HG{'miRNAs per type (txt)'} = $f; }
-    elsif ( $f =~ /genome_unique_plus\.bedgraph$/) { $HG{'bedgraph unique plus strand'} = $f; }
-    elsif ( $f =~ /genome_unique_minus\.bedgraph$/) { $HG{'bedgraph unique minus strand'} = $f; }
-    elsif ( $f =~ /genome_plus\.bedgraph$/) { $HG{'bedgraph plus strand'} = $f; }
-    elsif ( $f =~ /genome_minus\.bedgraph$/) { $HG{'bedgraph minus strand'} = $f; }
-    elsif ( $f =~ /TEs_plus\.bedgraph$/) { $HTE{'bedgraph plus strand'} = $f; }
-    elsif ( $f =~ /TEs_minus\.bedgraph$/) { $HTE{'bedgraph minus strand'} = $f; }
-    elsif ( $f =~ /exons_sorted\.bam$/) { $Hex{'exons mappers (sorted bam)'} = $f;}
-    elsif ( $f =~ /exons_unique_sorted\.bam$/) { $Hex{'exons unique mappers (sorted bam)'} = $f;}        
-    elsif ( $f =~ /exons_reads_counts\.txt$/) { $Hex{'read number per exon (txt)'} = $f;}
-    elsif ( $f =~ /TEs_reads_counts\.txt$/) { $HTE{"read number per TE 0 to $misTE mismatches (txt)"} = $f; }
-    elsif ( $f =~ /TEs_reads_counts_mismatches\.txt$/) { $HTE{"read number per TE with 1 to $misTE mismatches (txt)"} = $f; }
-    elsif ( $f =~ /TEs_reads_counts_nomismatches\.txt$/) { $HTE{'read number per TE with no mismatch (txt)'} = $f; }
-    elsif ( $f =~ /TEs_unique_sorted\.bam$/) { $HTE{'TEs unique mappers (sorted bam)'} = $f; }
-    elsif ( $f =~ /TEs_sorted\.bam$/) { $HTE{'TEs mappers (sorted bam)'} = $f; }
-		elsif ( $fr =~ /.*Gviz_TEs/ )
-		{
-			my $nu = $fr.'/*';
-			@NonUniTE =  glob $nu;
-		}
-		elsif ( $fr =~ /.*Gviz_genome/ )
-		{
-			my $nu = $fr.'/rand/*';
-			@NonUniG =  glob $nu;
-			my $u = $fr.'/unique/*';
-			@UniG =  glob $u;
-		}
-    else { unlink $fr; }
-  }
-  return (\%Hex, \%HTE, \%HG, \@NonUniTE,  \@NonUniG, \@UniG);
-}
-
-sub header
-{
-  my $file = shift;
-  print $file "
-  <!DOCTYPE html>
-  <html lang=\"en\">
-  <head>
-  <meta charset=\"utf-8\">
-  <title>pipeline</title>
-  <meta name=\"viewport\" content=\"width=device-width, initial-scale=1.0\">
-  <meta name=\"description\" content=\"\">
-  <meta name=\"author\" content=\"\">
-  <!-- Le styles -->
-  <link href=\"css/bootstrap.css\" rel=\"stylesheet\">
-  <link href=\"css/bootstrap-table.css\" rel=\"stylesheet\">
-  <style type=\"text/css\">
-  body {
-    padding-top: 60px;
-    padding-bottom: 40px;
-  }
-  div#page {
-    width: 940px;
-    background-color: #fff;
-    margin: 0 auto;
-    text-align: left;
-    border-color: #fff;
-    border-style: none solid solid;
-    border-width: medium 1px 1px;
-  }
-
-  div.content {
-   	display: none;
-	  float: right;
-	  width: 550px;
-  }
-  div.content a, div.navigation a {
-    text-decoration: none;
-   	color: #777;
-  }
-  div.content a:focus, div.content a:hover, div.content a:active {
-    text-decoration: underline;
-  }
-  
-  div.controls {
-    margin-top: 5px;
-	  height: 23px;
-  }
-  
-  div.controls a {
-	  padding: 5px;
-  }
-  div.ss-controls {
-	  float: left;
-  }
-  div.nav-controls {
-	  float: right;
-  }
-  div.slideshow-container {
-	  position: relative;
-	  clear: both;
-	  height: 502px; /* This should be set to be at least the height of the largest image in the slideshow */
-  }
-  div.loader {
-  	position: absolute;
-  	top: 0;
-  	left: 0;
-    background-image: url('loader.gif');
-    background-repeat: no-repeat;
-    background-position: center;
-  	width: 550px;
-  	height: 502px; /* This should be set to be at least the height of the largest image in the slideshow */
-  }
-  div.slideshow {
-    
-  }
-  
-  div.slideshow span.image-wrapper {
-	  display: block;
-	  position: absolute;
-	  top: 0;
-	  left: 0;
-  }
-  div.slideshow a.advance-link {
-	  display: block;
- 	  width: 550px;
-    height: 502px; /* This should be set to be at least the height of the largest image in the slideshow */
-    line-height: 502px; /* This should be set to be at least the height of the largest image in the slideshow */
-    text-align: center;
-  }
-  div.slideshow a.advance-link:hover, div.slideshow a.advance-link:active, div.slideshow a.advance-link:visited {
-    text-decoration: none;
-  }
-  div.slideshow img {
-    vertical-align: middle;
-	border: 1px solid #ccc;
-  }
-
-  div.image-title {
-    font-weight: bold;
-    font-size: 1.4em;
-  }
-
-  div.image-desc {
-    line-height: 1.3em;
-    padding-top: 12px;
-  }
-  div.navigation {
-
-  }
-  ul.thumbs {
-	clear: both;
-	margin: 0;
-	padding: 0;
-  }
-  ul.thumbs li {
-	float: none;
-	padding: 0;
-	margin: 0;
-    list-style: none;
-  }
-  a.thumb {
-	padding: 0;
-	display: inline;
-	border: none;
-  }
-  ul.thumbs li.selected a.thumb {
-	color: #000;
-    font-weight: bold;
-  }
-  a.thumb:focus {
-	outline: none;
-  }
-  ul.thumbs img {
-	border: none;
-	display: block;
-  }
-  div.pagination {
-	clear: both;
-  }
-  div.navigation div.top {
-    margin-bottom: 12px;
-	height: 11px;
-  }
-  div.navigation div.bottom {
-    margin-top: 12px;
-  }
-  div.pagination a, div.pagination span.current, div.pagination span.ellipsis {
-	display: block;
-	float: left;
-    margin-right: 2px;
-	padding: 4px 7px 2px 7px;
-	border: 1px solid #ccc;
-  }
-  div.pagination a:hover {
-    background-color: #eee;
-    text-decoration: none;
-  }
-  div.pagination span.current {
-    font-weight: bold;
-    background-color: #000;
-    border-color: #000;
-	color: #fff;
-  }
-  div.pagination span.ellipsis {
-	border: none;
-	padding: 5px 0 3px 2px;
-  }
-  
-  div.download {
-	float: right;
-  }
-  
-  div.caption-container {
-	position: relative;
-	clear: left;
-	height: 75px;
-  }
-  span.image-caption {
-	display: block;
-	position: absolute;
-	width: 550px;
-	top: 0;
-	left: 0;
-  }
-  div.caption {
-	padding: 12px;
-  }
-
-  /* Featurettes
-  ------------------------- */
-
-  .featurette {
-  padding-top: 20px; /* Vertically center images part 1: add padding above and below text. */
-  overflow: hidden; /* Vertically center images part 2: clear their floats. */
-  text-align: center;
-  }
-
-  .featurette-p
-  {
-   text-align: left;
-  }
-
-  .featurette-image {
-  margin-top: 10px; /* Vertically center images part 3: negative margin up the image the same amount of the padding to center it. */
-  width: 600px;
-  height: auto;
-  }
-
-  </style>
-  <link href=\"css/bootstrap-responsive.css\" rel=\"stylesheet\">
-  </head>
-  <body>
-  ";
-}
-
-sub navbar
-{
-  my ( $file, $fastq, $actif ) = @_;
-  
-  print $file "
-  <div class=\"navbar navbar-inverse navbar-fixed-top\">
-  <div class=\"navbar-inner\">
-  <div class=\"container\">
-  <button type=\"button\" class=\"btn btn-navbar\" data-toggle=\"collapse\" data-target=\".nav-collapse\">
-  <span class=\"icon-bar\"></span>
-  <span class=\"icon-bar\"></span>
-  <span class=\"icon-bar\"></span>
-  </button>
-  <a class=\"brand\" href=\"report.txt\">Report</a>
-  <div class=\"nav-collapse collapse\">
-  <ul class=\"nav\">
-  ";
-  for (my $i = 0 ; $i <= $#{$fastq}; $i++)
-  {
-    # my $fa = basename($fastq->[$i],'.dat');
-    my $fa = $fastq->[$i];
-    if ($actif eq $fa){  print $file "<li class=\"active\"><a href=\"$fastq->[$i].html\">$fa</a></li>";}
-    else {print $file "<li><a href=\"$fastq->[$i].html\">$fa</a></li>" ;}
-  }
-  print $file "
-  </ul>
-  </div><!--/.nav-collapse -->
-  </div>
-  </div>
-  </div>";
-}
-
-sub footer
-{
-  my $file = shift;
-  print $file "
-  <!-- FOOTER -->
-  <div class=\"container\">
-  <footer>
-  
-  </footer>
-  </div>
-  <!-- Le javascript
-  ================================================== -->
-  <!-- Placed at the end of the document so the pages load faster -->
-  <script type=\"text/javascript\" src=\"js/jquery.js\"></script>
-  <script type=\"text/javascript\" src=\"js/jquery-1.3.2.js\"></script>
-  <script type=\"text/javascript\" src=\"js/jquery.galleriffic.js\"></script>
-  <script type=\"text/javascript\" src=\"js/jquery.opacityrollover.js\"></script>  
-  <script type=\"text/javascript\" src=\"js/bootstrap-table.js\"></script>
-  <script type=\"text/javascript\" src=\"js/bootstrap.min.js\"></script>
-  <script type=\"text/javascript\">
-  jQuery(document).ready(function(\$) {
-    // We only want these styles applied when javascript is enabled
-    \$('div.navigation').css({'width' : '300px', 'float' : 'left'});
-    \$('div.content').css('display', 'block');
-    
-    \$(\".each-gallery\").each(function(i){
-      // Initially set opacity on thumbs and add
-      // additional styling for hover effect on thumbs
-        var onMouseOutOpacity = 0.67;
-      \$('#thumbs + i + ul.thumbs li').opacityrollover({
-      mouseOutOpacity:   onMouseOutOpacity,
-      mouseOverOpacity:  1.0,
-      fadeSpeed:         'fast',
-      exemptionSelector: '.selected'
-      });
-      
-      // Initialize Advanced Galleriffic Gallery
-      var gallery = \$('#thumbs'+i).galleriffic({
-      delay:                     2500,
-      numThumbs:                 22,
-      preloadAhead:              10,
-      enableTopPager:            true,
-      enableBottomPager:         true,
-      maxPagesToShow:            7,
-      imageContainerSel:         '#slideshow'+ i,
-      controlsContainerSel:      '#controls' + i,
-      captionContainerSel:       '#caption' + i,
-      loadingContainerSel:       '#loading' + i,
-      renderSSControls:          true,
-      renderNavControls:         true,
-      playLinkText:              'Play',
-      pauseLinkText:             'Pause',
-      prevLinkText:              '&lsaquo; Previous',
-      nextLinkText:              'Next &rsaquo;',
-      nextPageLinkText:          'Next &rsaquo;',
-      prevPageLinkText:          '&lsaquo; Prev',
-      enableHistory:             false,
-      autoStart:                 false,
-      syncTransitions:           true,
-      defaultTransitionDuration: 900,
-      onSlideChange:             function(prevIndex, nextIndex) {
-        // 'this' refers to the gallery, which is an extension of \$('#thumbs')
-        this.find('ul.thumbs').children()
-        .eq(prevIndex).fadeTo('fast', onMouseOutOpacity).end()
-        .eq(nextIndex).fadeTo('fast', 1.0);
-      },
-      onPageTransitionOut:       function(callback) {
-        this.fadeTo('fast', 0.0, callback);
-      },
-      onPageTransitionIn:        function() {
-        this.fadeTo('fast', 1.0);
-      }
-      });
-    });
-  });
-  </script>
-  </body>
-  </html>
-  ";
-}
-
-sub carousel
-{
-  my ($file, $non_unique, $dir_root) = @_;
-  my $ac = 0;
-  print $file "
-  <div id=\"page\">
-  <div id=\"container\">
-  <div class=\"each-gallery\">
-  <div id=\"gallery\" class=\"content\">
-  <div id=\"controls0\" class=\"controls\"></div>
-  <div class=\"slideshow-container\">
-  <div id=\"loading0\" class=\"loader\"></div>
-  <div id=\"slideshow0\" class=\"slideshow\"></div>
-  </div>
-  <div id=\"caption0\" class=\"caption-container\">Reads randomly assigned</div>
-  </div>
-  <div id=\"thumbs0\" class=\"navigation\">
-  <ul class=\"thumbs noscript\">
-  ";
-  foreach my $u (@{$non_unique})
-  {
-  	my $name = basename($u,'.png');
-    $u = $1 if $u =~ /$dir_root(.*)/;
-    print $file "
-    <li>
-    <a class=\"thumb\"  href=\"$u\" title=\"$name\">$name</a>
-    </li>
-  	";
-  }
-  print $file "
-  </ul>
-  </div>
-  <div style=\"clear: both;\"></div></div>
-  </div>
-  </div>
-  ";
-}
-
-sub carousel2
-{
-  my ($file, $unique, $non_unique, $dir_root) = @_;
-  print $file "
-  <div id=\"page\">
-  <div id=\"container\">
-  <div class=\"each-gallery\">
-  <div id=\"gallery\" class=\"content\">
-  <div id=\"controls0\" class=\"controls\"></div>
-  <div class=\"slideshow-container\">
-  <div id=\"loading0\" class=\"loader\"></div>
-  <div id=\"slideshow0\" class=\"slideshow\"></div>
-  </div>
-  <div id=\"caption0\" class=\"caption-container\">Uniquely mapped reads</div>
-  </div>
-  <div id=\"thumbs0\" class=\"navigation\">
-  <ul class=\"thumbs noscript\">
-  ";
-
-  foreach my $u (@{$unique})
-  {
-  	my $name = basename($u,'.png');
-    $u = $1 if $u =~ /$dir_root(.*)/;
-    print $file "
-    <li>
-    <a class=\"thumb\"  href=\"$u\" title=\"$name\">$name</a>
-    </li>
-    ";
-  }
-  print $file "
-  </ul>
-  </div>
-  </div>
-  <div id=\"page\">
-  <div id=\"container\">
-  <div class=\"each-gallery\">
-  <div id=\"gallery\" class=\"content\">
-  <div id=\"controls1\" class=\"controls\"></div>
-  <div class=\"slideshow-container\">
-  <div id=\"loading1\" class=\"loader\"></div>
-  <div id=\"slideshow1\" class=\"slideshow\"></div>
-  </div>
-  <div id=\"caption1\" class=\"caption-container\">Reads randomly assigned</div>
-  </div>
-  <div id=\"thumbs1\" class=\"navigation\">
-  <ul class=\"thumbs noscript\">
-  ";
-
-  foreach my $nu (@{$non_unique})
-  {
-  	my $name = basename($nu,'.png');
-    $nu = $1 if $nu =~ /$dir_root(.*)/;
-    print $file "
-        <li>
-        <a class=\"thumb\"  href=\"$nu\" title=\"$name\">$name</a>
-        </li>
-        ";
-  }
-  print $file "
-  </ul>
-  </div>
-  <div style=\"clear: both;\"></div></div>
-  </div>
-  </div>
-  ";
-}
-
-sub futurette
-{
-  my ($file, $name, $png, $hash) = @_;
-  print $file "
-  <div class=\"container\">
-  <div class=\"featurette\">
-  <h1>$name</h1>
-  <p class=\"featurette-p\">
-  ";
-  foreach my $k (sort  keys %{$hash})
-  {
-    print $file "<A HREF=\"".${$hash}{$k}."\">$k</A><br/> \n" ;
-  }
-
-  print $file "
-  </p>";
-
-  foreach my $pn (@{$png}){print $file "<img  class=\"featurette-image\"  src=\"$pn\"/><br />";}
-
-  print $file "
-  </div>
-  </div>
-  ";
-}
-
-sub fut
-{
-  my ($file, $name, $hash) = @_;
-  print $file "
-  <div class=\"container\">
-  <div class=\"featurette\">
-  <h1>$name</h1>
-  <p class=\"featurette-p\">
-  ";
-
-  foreach my $k (sort { ${$hash}{$a} cmp ${$hash}{$b} } keys %{$hash})
-  {
-    print $file "<A HREF=\"".${$hash}{$k}."\">$k</A><br/> \n" ;
-  }
-
-  print $file "
-  </p>
-  </div>
-  </div>
-  ";
-}
-
-sub get_distri_exon
-{
-  my ($dir, $name) = @_;
-  my (@out,@group);
-  my $group = $dir.'/'.$name.'-subgroups-bonafide_reads-exons-*distribution-*.png';
-  @group = glob $group;
-  foreach (my $g =0; $g <= $#group; $g++)
-  {
-    if ($group[$g] =~ /.*($name-subgroups-bonafide_reads-exons-.*distribution-.*\.png)/ )
-    {
-      my $tmp = $1;
-      push @out, $1;
-    }
-  }
-  return (\@out);
-}
-
-sub get_distri_TE
-{
-  my ($dir, $name) = @_;
-  my (@out,@group);
-  my $group = $dir.'/'.$name.'-subgroups-bonafide_reads-TE-*distribution-*.png';
-  @group = glob $group;
-  foreach (my $g =0; $g <= $#group; $g++)
-  {
-    if ($group[$g] =~ /.*($name-subgroups-bonafide_reads-TE-.*distribution-.*\.png)/ )
-    {
-      my $tmp = $1;
-      push @out, $1;
-    }
-  }
-  return (\@out);
-}
-
-sub get_PPP
-{
-  my ($dir,$name) = @_;
-  my (%distri,@group);
-  my $group = $dir.'/'.$name.'-subgroups-bonafide_reads-TE-PPPartners-*';
-  @group = glob $group;
-  
-  foreach (my $g =0; $g <= $#group; $g++)
-  {
-    if ($group[$g] =~ /.*($name-subgroups-bonafide_reads-TE-PPPartners-.*)/ )
-    {
-      my $tmp = $1;
-      if ($tmp =~ /PPPartners-(.*?)-sens\.txt$/)
-      {
-        $distri{$1} = ['','','','','',''] unless exists $distri{$1};
-        $distri{$1}->[0] = $tmp;
-      }
-      elsif ($tmp =~ /PPPartners-(.*?)-antisens\.txt$/)
-      {
-        $distri{$1} = ['','','','','',''] unless exists $distri{$1};
-        $distri{$1}->[1] = $tmp;
-      }
-      elsif ($tmp =~ /PPPartners-(.*?)-sensPPP\.txt$/)
-      {
-        $distri{$1} = ['','','','','',''] unless exists $distri{$1};
-        $distri{$1}->[2] = $tmp;
-      }
-      elsif ($tmp =~ /PPPartners-(.*?)-antisensPPP\.txt$/)
-      {
-        $distri{$1} = ['','','','','',''] unless exists $distri{$1};
-        $distri{$1}->[3] = $tmp;
-      }
-      elsif ($tmp =~ /PPPartners-(.*?)-overlap_size\.txt$/)
-      {
-        $distri{$1} = ['','','','','',''] unless exists $distri{$1};
-        $distri{$1}->[4] = $tmp;
-      }
-      elsif ($tmp =~ /PPPartners-(.*?)-histogram\.png$/)
-      {
-        $distri{$1} = ['','','','','',''] unless exists $distri{$1};
-        $distri{$1}->[5] = $tmp;
-      }
-    }
-  }
-  return \%distri;
-}
-
-sub PPPrint
-{
-  my ($h, $hash) = @_;
-  my $cmp = 0;
-  
-  print $h "<div class=\"container\">\n";
-  print $h "<div class=\"row text-center\">";
-  while ( my ($k,$v) = each %{$hash} )
-  {
-    print $h "</div><div class=\"row text-center\">" if $cmp != 0 && $cmp % 2 == 0;
-    print $h "
-    
-    <div class=\"span6\">
-    <h2>$k</h2>
-    <p class=\"featurette-p\"> <img src=\"$v->[5]\"/></p>
-    <p class=\"featurette-p\"><a href=\"$v->[4]\">ping pong signature</a></p>
-    <p class=\"featurette-p\"><a href=\"$v->[2]\">sens reads with PPP</a></p>
-    <p class=\"featurette-p\"><a href=\"$v->[3]\">reverse reads  with PPP</a></p>
-    <p class=\"featurette-p\"><a href=\"$v->[0]\">sens reads without PPP</a></p>
-    <p class=\"featurette-p\"><a href=\"$v->[1]\">reverse reads without PPP</a></p>
-    </div>
-    ";
-    $cmp++;
-  }
-  
-  print $h "</div></div>";
-}
-
-sub printDistri
-{
-  my ($h, $tab) = @_;
-  my ($txt, $name);
-  my $cmp = 0;
-  print $h "<div class=\"container\">\n";
-  print $h "<div class=\"row text-center\">";
-  foreach my $k (@{$tab})
-  {
-    if ($k =~ /(.*)-(.*)\.png$/)
-    {
-      $txt = $1.'-'.$2.'.txt';
-      $name = $2;
-    }
-    print $h "</div><div class=\"row text-center\">" if $cmp != 0 && $cmp % 2 == 0;
-    print $h "
-    
-    <div class=\"span6\">
-    <h2>$name</h2>
-    <p> <img src=\"$k\"/></p>
-    <p class=\"featurette-p\"><a href=\"$txt\">text file</a></p>
-    </div>
-    ";
-    $cmp++;
-  }
-  
-  print $h "</div></div>";
-}
-
-sub mapnum
-{
-  my $dupmapnum = shift;
-  my $dupnum_genome = shift;
-  open (my $dupTE, $dupmapnum) || die "cannot open ".$dupmapnum."\n";
-  my %dupnum_TE = ();
-  my $header = <$dupTE>;
-  while (<$dupTE>)
-  {
-    chomp $_;
-    my @dupline = split /\t/, $_;
-    $dupnum_TE{$dupline[0]} = $dupline[2];
-  }
-  close $dupTE;
-  open (my $du_TE, '>'.$dupmapnum) || die "cannot open to write ".$dupmapnum."\n";
-  print $du_TE "sequence\tduplicate\tgenome map num\tmap num\n";
-  while (my ($k, $v) = each %dupnum_TE )
-  {
-    my $hashRef = ${$dupnum_genome}{$k};
-    print $du_TE "$k\t$hashRef->[0]\t$hashRef->[1]\t$v\n";
-  }
-  close $du_TE;
-}
-
-1;