Mercurial > repos > romaingred > pirna_pipeline

changeset 15:16c3c1b0362a draft

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Uploaded
author romaingred
date Mon, 16 Oct 2017 03:46:49 -0400
parents 8b7000eac6a0
children 2be918bf0efe
files bin/html.pm
diffstat 1 files changed, 907 insertions(+), 0 deletions(-) [+]
line wrap: on
line diff
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/bin/html.pm	Mon Oct 16 03:46:49 2017 -0400
@@ -0,0 +1,907 @@
+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;