Mercurial > repos > brasset_jensen > srnapipe
changeset 45:263819fdda14 draft
Uploaded
| author | pierre.pouchin |
|---|---|
| date | Thu, 06 Sep 2018 10:21:30 -0400 |
| parents | 221ea7307999 |
| children | 20547000266a |
| files | bin/html.pm bin/js/filter.js sRNAPipe.xml tool_dependencies.xml |
| diffstat | 4 files changed, 982 insertions(+), 958 deletions(-) [+] |
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--- a/bin/html.pm Thu Jul 12 08:56:18 2018 -0400 +++ b/bin/html.pm Thu Sep 06 10:21:30 2018 -0400 @@ -1,911 +1,911 @@ -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 »</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, $ppp ) = @_; - my ($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 ( $prefix =~ /piRNAs$/ && $ppp eq 'true' ) - { - 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.'-transcripts.html' || die "cannot create $prefix-transcripts.html $!\n"; - header($h); - navbar ( $h, $list_mainTabP, $current ); - fut($h,'transcripts',$Hex); - footer($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 class=\"featurette-image\" src=\"$id/histogram.png\"/></p> - <p><a href=\"$id/overlap_size.txt\">ping pong signature</a></p> - <p><a href=\"$id/sensPPP.txt\">sense reads with PPP</a></p> - <p><a href=\"$id/antisensPPP.txt\">reverse reads with PPP</a></p> - <p><a href=\"$id/sens.txt\">sense reads without PPP</a></p> - <p><a href=\"$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</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-transcripts.html\">Transcripts</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-transcripts.html\">Transcripts</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-transcripts.html\">Transcripts</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-transcripts.html\">Transcripts</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 ( $f =~ /transcripts_sorted\.bam$/) { $Hex{'transcripts mappers (sorted bam)'} = $f;} - elsif ( $f =~ /transcripts_unique_sorted\.bam$/) { $Hex{'transcripts unique mappers (sorted bam)'} = $f;} - elsif ( $f =~ /transcripts_reads_counts\.txt$/) { $Hex{'read number per transcript (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: 450px; - 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/filter.js\"></script> - <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: '‹ Previous', - nextLinkText: 'Next ›', - nextPageLinkText: 'Next ›', - prevPageLinkText: '‹ 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\"> - <input type=\"text\" id=\"myInput0\" onkeyup=\"search(this)\" placeholder=\"Search for names...\"> - <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\"> - <input type=\"text\" id=\"myInput0\" onkeyup=\"search(this)\" placeholder=\"Search for names...\"> - <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\"> - <input type=\"text\" id=\"myInput1\" onkeyup=\"search(this)\" placeholder=\"Search for names...\"> - <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-transcripts-*distribution-*.png'; - @group = glob $group; - foreach (my $g =0; $g <= $#group; $g++) - { - if ($group[$g] =~ /.*($name-subgroups-bonafide_reads-transcripts-.*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=\"$v->[2]\">sense reads with PPP</a></p> - <p class=\"featurette-p\"><a href=\"$v->[3]\">reverse reads with PPP</a></p> - <p class=\"featurette-p\"><a href=\"$v->[0]\">sense reads without PPP</a></p> - <p class=\"featurette-p\"><a href=\"$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; +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 »</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, $ppp ) = @_; + my ($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 ( $prefix =~ /piRNAs$/ && $ppp eq 'true' ) + { + 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.'-transcripts.html' || die "cannot create $prefix-transcripts.html $!\n"; + header($h); + navbar ( $h, $list_mainTabP, $current ); + fut($h,'transcripts',$Hex); + footer($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 class=\"featurette-image\" src=\"$id/histogram.png\"/></p> + <p><a href=\"$id/overlap_size.txt\">ping pong signature</a></p> + <p><a href=\"$id/sensPPP.txt\">sense reads with PPP</a></p> + <p><a href=\"$id/antisensPPP.txt\">reverse reads with PPP</a></p> + <p><a href=\"$id/sens.txt\">sense reads without PPP</a></p> + <p><a href=\"$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</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-transcripts.html\">Transcripts</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-transcripts.html\">Transcripts</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-transcripts.html\">Transcripts</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-transcripts.html\">Transcripts</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 ( $f =~ /transcripts_sorted\.bam$/) { $Hex{'transcripts mappers (sorted bam)'} = $f;} + elsif ( $f =~ /transcripts_unique_sorted\.bam$/) { $Hex{'transcripts unique mappers (sorted bam)'} = $f;} + elsif ( $f =~ /transcripts_reads_counts\.txt$/) { $Hex{'read number per transcript (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: 450px; + 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/filter.js\"></script> + <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: '‹ Previous', + nextLinkText: 'Next ›', + nextPageLinkText: 'Next ›', + prevPageLinkText: '‹ 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\"> + <input type=\"text\" id=\"myInput0\" onkeyup=\"search(this)\" placeholder=\"Search for names...\"> + <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\"> + <input type=\"text\" id=\"myInput0\" onkeyup=\"search(this)\" placeholder=\"Search for names...\"> + <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\"> + <input type=\"text\" id=\"myInput1\" onkeyup=\"search(this)\" placeholder=\"Search for names...\"> + <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-transcripts-*distribution-*.png'; + @group = glob $group; + foreach (my $g =0; $g <= $#group; $g++) + { + if ($group[$g] =~ /.*($name-subgroups-bonafide_reads-transcripts-.*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=\"$v->[2]\">sense reads with PPP</a></p> + <p class=\"featurette-p\"><a href=\"$v->[3]\">reverse reads with PPP</a></p> + <p class=\"featurette-p\"><a href=\"$v->[0]\">sense reads without PPP</a></p> + <p class=\"featurette-p\"><a href=\"$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;
--- a/bin/js/filter.js Thu Jul 12 08:56:18 2018 -0400 +++ b/bin/js/filter.js Thu Sep 06 10:21:30 2018 -0400 @@ -1,20 +1,20 @@ -function search(input) { - // Declare variables - var elt, filter, uls, li, a, i; - elt = input.parentElement; - filter = input.value.toUpperCase(); - uls = elt.getElementsByClassName('thumbs'); - - // Loop through all list items, and hide those who don't match the search query - for (j = 0; j < uls.length; j++) { - li = uls[j].getElementsByTagName('li'); - for (i = 0; i < li.length; i++) { - a = li[i].getElementsByTagName("a")[0]; - if (a.innerHTML.toUpperCase().indexOf(filter) > -1) { - li[i].style.display = ""; - } else { - li[i].style.display = "none"; - } - } - } -} +function search(input) { + // Declare variables + var elt, filter, uls, li, a, i; + elt = input.parentElement; + filter = input.value.toUpperCase(); + uls = elt.getElementsByClassName('thumbs'); + + // Loop through all list items, and hide those who don't match the search query + for (j = 0; j < uls.length; j++) { + li = uls[j].getElementsByTagName('li'); + for (i = 0; i < li.length; i++) { + a = li[i].getElementsByTagName("a")[0]; + if (a.innerHTML.toUpperCase().indexOf(filter) > -1) { + li[i].style.display = ""; + } else { + li[i].style.display = "none"; + } + } + } +}
--- a/sRNAPipe.xml Thu Jul 12 08:56:18 2018 -0400 +++ b/sRNAPipe.xml Thu Sep 06 10:21:30 2018 -0400 @@ -86,6 +86,14 @@ <requirement type="package" version="1.2">samtools</requirement> <requirement type="package" version="3.2.1">R</requirement> <requirement type="package" version="5.18.1">perl</requirement> + <requirement type="package" version="2.50">perl-getopt-long</requirement> + <requirement type="package" version="1.19">perl-parallel-forkmanager</requirement> + <requirement type="package" version="0.34" >perl-statistics-r</requirement> + <requirement type="package" version="0.29">perl-string-random</requirement> + <requirement type="package" version="3.6">r-plotrix</requirement> + <requirement type="package" version="1.14.0">bioconductor-sushi</requirement> + <requirement type="package" version="1.1_2">r-colorbrewer</requirement> + <requirement type="package" version="1.0.1">r-ggplot2</requirement> </requirements> <inputs>
--- a/tool_dependencies.xml Thu Jul 12 08:56:18 2018 -0400 +++ b/tool_dependencies.xml Thu Sep 06 10:21:30 2018 -0400 @@ -1,27 +1,43 @@ -<?xml version="1.0"?> -<tool_dependency> - <package name="bwa" version="0.7.12"> - <repository changeset_revision="dcae4134cd62" name="package_bwa_0_7_12" owner="avowinkel" toolshed="https://toolshed.g2.bx.psu.edu" /> - </package> - <package name="bedtools" version="2.24"> - <repository changeset_revision="3416a1d4a582" name="package_bedtools_2_24" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" /> - </package> - <package name="samtools" version="1.2"> - <repository changeset_revision="f6ae3ba3f3c1" name="package_samtools_1_2" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" /> - </package> - <package name="R" version="3.2.1"> - <repository changeset_revision="d9f7d84125b7" name="package_r_3_2_1" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" /> - </package> - <package name="perl" version="5.18.1"> - <repository changeset_revision="35f117d7396b" name="package_perl_5_18" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" /> - </package> - <package>https://depot.galaxyproject.org/software/plotrix/plotrix_3.6_src_all.tar.gz</package> - <package>https://depot.galaxyproject.org/software/bioconductor-sushi/bioconductor-sushi_1.14.0_src_all.tar.gz</package> - <package>https://depot.galaxyproject.org/software/RColorBrewer/RColorBrewer_1.1-2_src_all.tar.gz</package> - <package>https://depot.galaxyproject.org/software/ggplot2/ggplot2_1.0.1_src_all.tar.gz</package> - <package>https://depot.galaxyproject.org/software/perl-statistics-r/perl-statistics-r_0.34_src_all.tar.gz</package> - <package>https://cpan.metacpan.org/authors/id/Y/YA/YANICK/Parallel-ForkManager-1.19.tar.gz</package> - <package>https://cpan.metacpan.org/authors/id/F/FA/FANGLY/Statistics-R-0.34.tar.gz</package> - <package>https://cpan.metacpan.org/authors/id/J/JV/JV/Getopt-Long-2.50.tar.gz</package> - <package>https://cpan.metacpan.org/authors/id/S/SH/SHLOMIF/String-Random-0.29.tar.gz</package> -</tool_dependency> +<?xml version="1.0"?> +<tool_dependency> + <package name="bwa" version="0.7.12"> + <repository changeset_revision="dcae4134cd62" name="package_bwa_0_7_12" owner="avowinkel" toolshed="https://toolshed.g2.bx.psu.edu" /> + </package> + <package name="bedtools" version="2.24"> + <repository changeset_revision="3416a1d4a582" name="package_bedtools_2_24" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" /> + </package> + <package name="samtools" version="1.2"> + <repository changeset_revision="f6ae3ba3f3c1" name="package_samtools_1_2" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" /> + </package> + <package name="R" version="3.2.1"> + <repository changeset_revision="d9f7d84125b7" name="package_r_3_2_1" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" /> + </package> + <package name="perl" version="5.18.1"> + <repository changeset_revision="35f117d7396b" name="package_perl_5_18" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" /> + </package> + <package name="srnapipe" version="1.0"> + <install version="1.0"> + <actions> + <action type="setup_perl_environment"> + <repository changeset_revision="35f117d7396b" name="package_perl_5_18" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu"> + <package name="perl" version="5.18.1" /> + </repository> + <package>https://cpan.metacpan.org/authors/id/Y/YA/YANICK/Parallel-ForkManager-1.19.tar.gz</package> + <package>https://cpan.metacpan.org/authors/id/F/FA/FANGLY/Statistics-R-0.34.tar.gz</package> + <package>https://cpan.metacpan.org/authors/id/J/JV/JV/Getopt-Long-2.50.tar.gz</package> + <package>https://cpan.metacpan.org/authors/id/S/SH/SHLOMIF/String-Random-0.29.tar.gz</package> + </action> + <action type="setup_r_environment"> + <repository changeset_revision="d9f7d84125b7" name="package_r_3_2_1" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu"> + <package name="R" version="3.2.1" /> + </repository> + <package>https://depot.galaxyproject.org/software/plotrix/plotrix_3.6_src_all.tar.gz</package> + <package>https://depot.galaxyproject.org/software/bioconductor-sushi/bioconductor-sushi_1.14.0_src_all.tar.gz</package> + <package>https://depot.galaxyproject.org/software/RColorBrewer/RColorBrewer_1.1-2_src_all.tar.gz</package> + <package>https://depot.galaxyproject.org/software/ggplot2/ggplot2_1.0.1_src_all.tar.gz</package> + <package>https://depot.galaxyproject.org/software/perl-statistics-r/perl-statistics-r_0.34_src_all.tar.gz</package> + </action> + </actions> + </install> + </package> +</tool_dependency>