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comparison lib/sRNAPipe/html.pm @ 64:967512924317 draft

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planemo upload for repository https://github.com/GReD-Clermont/sRNAPipe/ commit 410509088292be0687b8da3ea3bb75e72866a87d
author brasset_jensen
date Mon, 28 Jan 2019 11:57:15 -0500
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63:11708af40030 64:967512924317
1 package sRNAPipe::html;
2
3 use strict;
4 use warnings;
5 use File::Basename;
6 use File::Copy::Recursive qw( dircopy );
7
8 use Exporter;
9 our @ISA = qw( Exporter );
10 our @EXPORT_OK = qw( &main_page &details_pages &menu_page &ppp_page &copy_css &copy_js );
11
12 sub main_page
13 {
14 my ( $dir, $file, $list_mainTabP, $current, $ma, $ma_uni, $dir_root ) = @_;
15 my ( $futHashP, $uniqueTabP, $randTabP, $pngTabP ) = get_genome ( $dir, $dir_root );
16
17 open my $h, '>', $file || die "cannot create $file $!\n";
18 header ( $h );
19 navbar ( $h, $list_mainTabP, $current );
20 print $h "<div class=\"container\"><p><a class=\"btn\" href=\"$current-sub.html\">View details &raquo;</a></p></div>\n";
21 futurette( $h, $current, $pngTabP, $futHashP );
22 print $h "<div class=\"container\"><h2>mappers #: $ma</h2><h2>unique mappers #: $ma_uni</h2> </div>\n";
23 carousel2( $h, $uniqueTabP, $randTabP, $dir_root );
24 footer($h);
25 close $h;
26 }
27
28 sub menu_page
29 {
30 my ( $dir, $file, $list_mainTabP, $current, $min, $max, $simin, $simax, $pimin, $pimax, $dir_root ) = @_;
31 my $html_ref = $1 if $dir =~ /$dir_root(.*)/;
32 open my $h, '>', $file || die "cannot create $file $!\n";
33 header($h);
34 navbar ( $h, $list_mainTabP, $current );
35 span( $h, $current, $min, $max, $simin, $simax, $pimin, $pimax );
36 print $h " <div class=\"container\"> <div class=\"row text-center\"> <img src=\"$html_ref/pie_chart.png\"/><br />\n";
37 print $h " <A HREF=\"$html_ref/repartition.txt\">text file</A><br/>\n </div></div>";
38 footer($h);
39 close $h;
40 }
41
42 sub details_pages
43 {
44 my ( $dir_details, $prefix, $list_mainTabP, $current, $misTE, $dir_root, $ppp ) = @_;
45 my ($Hex, $HTE, $HG, $NonUniTE, $NonUniG, $UniG ) = get_subgroups( $dir_details, $current, $misTE, $dir_root );
46
47 my $html_ref = $1.'-PPP.html' if $prefix =~ /$dir_root(.*)/;
48 open my $h, '>', $prefix.'-TEs.html' || die "cannot create $prefix-TEs.html $!\n";
49 header($h);
50 navbar ( $h, $list_mainTabP, $current );
51 if ( $prefix =~ /piRNAs$/ && $ppp eq 'true' )
52 {
53 print $h " <div class=\"container\">";
54 print $h " <p><a class=\"btn\" href=\"$html_ref\">Ping Pong Partners</a></p>\n";
55 print $h "</div>";
56 }
57 fut($h,'Transposable elements',$HTE);
58 carousel($h,$NonUniTE,$dir_root);
59 footer($h);
60 close $h;
61
62 open $h, '>', $prefix.'-genome.html' || die "cannot create $prefix-genome.html $!\n";
63 header($h);
64 navbar ( $h, $list_mainTabP, $current );
65 fut($h,'Genome',$HG);
66 carousel2($h,$UniG, $NonUniG,$dir_root);
67 footer($h);
68 close $h;
69
70 open $h, '>', $prefix.'-transcripts.html' || die "cannot create $prefix-transcripts.html $!\n";
71 header($h);
72 navbar ( $h, $list_mainTabP, $current );
73 fut($h,'transcripts',$Hex);
74 footer($h);
75 close $h;
76 }
77
78 sub ppp_page
79 {
80 my ( $dir, $file, $list_mainTabP, $current, $ppp, $dir_root ) = @_;
81
82 my $ppp_file = $ppp.'ppp.txt';
83 open my $h, '>', $file || die "cannot create $file $!\n";
84 header($h);
85 navbar ( $h, $list_mainTabP, $current );
86 print $h '<div class="container"> <table class="wb-tables table table-striped table-hover">'."\n";
87 print $h '<thead>
88 <tr>
89 <th data-sortable="true">ID</th>
90 <th data-sortable="true">overlap sum</th>
91 <th data-sortable="true">ten overlap sum</th>
92 <th data-sortable="true">mean</th>
93 <th data-sortable="true">standard deviation</th>
94 <th data-sortable="true">z-score</th>
95 <th data-sortable="true">p-value</th>
96 </tr>
97 </thead>
98 <tbody>';
99
100 open my $f, '<', $ppp_file || die "cannot open $ppp_file $!\n";
101 while ( <$f> )
102 {
103 chomp;
104 print $h '<tr>';
105 my ( $id, $sum, $ten, $mean, $sd, $zscore, $prob) = split /\t/, $_;
106 if( -d "$ppp/$id" )
107 {
108 my $sub_html = $ppp.$id.'.html';
109 my $sub_html_ref = $1.$id if $ppp =~ /$dir_root(.*)/;
110 print $h "<td> <a href=\"$sub_html_ref.html\">$id</a> </td>";
111
112 open my $sub, '>', $sub_html || die "cannot create $sub_html\n";
113 {
114 header($sub);
115 print $sub "
116 <div align=\"center\">
117 <h2>$id</h2>
118 <p> <img class=\"featurette-image\" src=\"$id/histogram.png\"/></p>
119 <p><a href=\"$id/overlap_size.txt\">ping pong signature</a></p>
120 <p><a href=\"$id/sensPPP.txt\">sense reads with PPP</a></p>
121 <p><a href=\"$id/antisensPPP.txt\">reverse reads with PPP</a></p>
122 <p><a href=\"$id/sens.txt\">sense reads without PPP</a></p>
123 <p><a href=\"$id/antisens.txt\">reverse reads without PPP</a></p>
124 </div>";
125 footer($sub);
126 }
127 close $sub;
128 }
129 else { print $h "<td> $id </td>\n"; }
130 print $h "<td> $sum </td><td> $ten </td><td> $mean </td><td> $sd </td><td> $zscore </td><td> $prob </td>\n";
131
132 print $h '</tr>';
133 }
134 close $f;
135 print $h "</tbody></table></div>";
136 footer($h);
137 close $h;
138 }
139
140 sub get_genome
141 {
142 my ( $dir, $dir_root ) = @_;
143 my ( %hash, @group, @Unique, @NonUnique, @png );
144
145 my $fut = "'$dir'".'/*';
146 my @fut = glob $fut;
147
148
149 foreach my $fr ( @fut )
150 {
151 my $f = $1 if $fr =~ /$dir_root(.*)/;
152 if ( $fr =~ /.*Gviz/ )
153 {
154 my $nu = "'$fr'".'/rand/*';
155 @NonUnique = glob $nu;
156 my $u = "'$fr'".'/unique/*';
157 @Unique = glob $u;
158 }
159 elsif ( $f =~ /.*distribution\.txt$/ ) { $hash{'mappers size distribution (txt)'} = $f; }
160 elsif ( $f =~ /.*distribution\.png$/ ) { push @png, $f; }
161 elsif ( $f =~ /.*unique\.fastq$/ ) { $hash{'unique mappers (fastq.gz)'} = $f.'.gz'; `gzip '$fr'`; }
162 elsif ( $f =~ /.*rejected\.fastq$/ ) { $hash{'unmapped (fastq.gz)'} = $f.'.gz'; `gzip '$fr'`; }
163 elsif ( $f =~ /.*all\.fastq$/ ) { $hash{'mappers (fastq.gz)'} = $f.'.gz'; `gzip '$fr'`; }
164 elsif ( $f =~ /.*dup_unique\.txt$/ ) { $hash{'unique mappers (txt)'} = $f; }
165 elsif ( $f =~ /.*dup_mapnum\.txt$/ ) { $hash{'mappers (txt)'} = $f; }
166 elsif ( $f =~ /.*dup_nonmapp\.txt$/ ) { $hash{'unmapped (txt)'} = $f; }
167 elsif ( $f =~ /.*_unique_sorted\.bam$/ ) { $hash{'unique alignment (bam)'} = $f; }
168 elsif ( $f =~ /.*_sorted\.bam$/ ) { $hash{'alignment (bam)'} = $f; }
169 elsif ( $f =~ /.*unique_plus.bedgraph/) { $hash{'bedgraph unique plus strand'} = $f; }
170 elsif ( $f =~ /.*unique_minus.bedgraph/) { $hash{'bedgraph unique minus strand'} = $f; }
171 elsif ( $f =~ /.*plus.bedgraph/) { $hash{'bedgraph plus strand'} = $f; }
172 elsif ( $f =~ /.*minus.bedgraph/) { $hash{'bedgraph minus strand'} = $f; }
173 else { unlink $fr; }
174 }
175 return (\%hash, \@Unique, \@NonUnique, \@png);
176 }
177
178 sub span
179 {
180 my ( $file, $name, $min, $max, $simin, $simax, $pimin, $pimax ) = @_;
181
182 print $file "
183 <div class=\"container text-center\">
184 <div class=\"row-fluid\">
185 <div class=\"span6\">
186 <h2>Bonafide</h2>
187 reads of size between $min and $max<br>with no mi, sn, t and r RNAs
188 <p><a class=\"btn\" href=\"$name-bonafide_reads-genome.html\">Genome</a></p>
189 <p><a class=\"btn\" href=\"$name-bonafide_reads-TEs.html\">TE</a></p>
190 <p><a class=\"btn\" href=\"$name-bonafide_reads-transcripts.html\">Transcripts</a></p>
191 <div class=\"row-fluid\">
192 <div class=\"span6\">
193 <h2>siRNAs</h2>
194 bonafide reads of size between $simin and $simax
195 <p><a class=\"btn\" href=\"$name-siRNAs-genome.html\">Genome</a></p>
196 <p><a class=\"btn\" href=\"$name-siRNAs-TEs.html\">TE</a></p>
197 <p><a class=\"btn\" href=\"$name-siRNAs-transcripts.html\">Transcripts</a></p>
198 </div>
199 <div class=\"span6\">
200 <h2>piRNAs</h2>
201 bonafide reads of size between $pimin and $pimax
202 <p><a class=\"btn\" href=\"$name-piRNAs-genome.html\">Genome</a></p>
203 <p><a class=\"btn\" href=\"$name-piRNAs-TEs.html\">TE</a></p>
204 <p><a class=\"btn\" href=\"$name-piRNAs-transcripts.html\">Transcripts</a></p>
205 </div>
206 </div>
207 </div>
208 <div class=\"span6\">
209 <h2>miRNAs</h2>
210 <p><a class=\"btn\" href=\"$name-miRNAs-genome.html\">Genome</a></p>
211 <p><a class=\"btn\" href=\"$name-miRNAs-TEs.html\">TE</a></p>
212 <p><a class=\"btn\" href=\"$name-miRNAs-transcripts.html\">Transcripts</a></p>
213 </div>
214 </div>
215 </div>
216 ";
217 }
218
219 sub get_subgroups
220 {
221 my ( $dir, $name, $misTE, $dir_root ) = @_;
222 my (%Hex, %HTE, %HG, @group, @png, @pngTE, @NonUniTE, @UniG, @NonUniG );
223
224 my $fut = "'$dir'".'/*';
225 my @fut = glob $fut;
226 my $f ='';
227 foreach my $fr ( @fut )
228 {
229 $f = $1 if $fr =~ /$dir_root(.*)/;
230
231 if ( $f =~ /genome_unique_sorted\.bam$/ ) { $HG{'genome unique mappers (sorted bam)'} = $f; }
232 elsif ( $f =~ /genome_sorted\.bam$/ ) { $HG{'genome mappers (sorted bam)'} = $f; }
233 elsif ( $f =~ /miRNAs_reads_counts\.txt$/ ) { $HG{'miRNAs per type (txt)'} = $f; }
234 elsif ( $f =~ /genome_unique_plus\.bedgraph$/) { $HG{'bedgraph unique plus strand'} = $f; }
235 elsif ( $f =~ /genome_unique_minus\.bedgraph$/) { $HG{'bedgraph unique minus strand'} = $f; }
236 elsif ( $f =~ /genome_plus\.bedgraph$/) { $HG{'bedgraph plus strand'} = $f; }
237 elsif ( $f =~ /genome_minus\.bedgraph$/) { $HG{'bedgraph minus strand'} = $f; }
238 elsif ( $f =~ /TEs_plus\.bedgraph$/) { $HTE{'bedgraph plus strand'} = $f; }
239 elsif ( $f =~ /TEs_minus\.bedgraph$/) { $HTE{'bedgraph minus strand'} = $f; }
240 elsif ( $f =~ /transcripts_sorted\.bam$/) { $Hex{'transcripts mappers (sorted bam)'} = $f;}
241 elsif ( $f =~ /transcripts_unique_sorted\.bam$/) { $Hex{'transcripts unique mappers (sorted bam)'} = $f;}
242 elsif ( $f =~ /transcripts_reads_counts\.txt$/) { $Hex{'read number per transcript (txt)'} = $f;}
243 elsif ( $f =~ /TEs_reads_counts\.txt$/) { $HTE{"read number per TE 0 to $misTE mismatches (txt)"} = $f; }
244 elsif ( $f =~ /TEs_reads_counts_mismatches\.txt$/) { $HTE{"read number per TE with 1 to $misTE mismatches (txt)"} = $f; }
245 elsif ( $f =~ /TEs_reads_counts_nomismatches\.txt$/) { $HTE{'read number per TE with no mismatch (txt)'} = $f; }
246 elsif ( $f =~ /TEs_unique_sorted\.bam$/) { $HTE{'TEs unique mappers (sorted bam)'} = $f; }
247 elsif ( $f =~ /TEs_sorted\.bam$/) { $HTE{'TEs mappers (sorted bam)'} = $f; }
248 elsif ( $fr =~ /.*Gviz_TEs/ )
249 {
250 my $nu = "'$fr'".'/*';
251 @NonUniTE = glob $nu;
252 }
253 elsif ( $fr =~ /.*Gviz_genome/ )
254 {
255 my $nu = "'$fr'".'/rand/*';
256 @NonUniG = glob $nu;
257 my $u = "'$fr'".'/unique/*';
258 @UniG = glob $u;
259 }
260 else { unlink $fr; }
261 }
262 return (\%Hex, \%HTE, \%HG, \@NonUniTE, \@NonUniG, \@UniG);
263 }
264
265 sub header
266 {
267 my $file = shift;
268 print $file "
269 <!DOCTYPE html>
270 <html lang=\"en\">
271 <head>
272 <meta charset=\"utf-8\">
273 <title>pipeline</title>
274 <meta name=\"viewport\" content=\"width=device-width, initial-scale=1.0\">
275 <meta name=\"description\" content=\"\">
276 <meta name=\"author\" content=\"\">
277 <!-- Le styles -->
278 <link href=\"css/bootstrap.css\" rel=\"stylesheet\">
279 <link href=\"css/bootstrap-table.css\" rel=\"stylesheet\">
280 <style type=\"text/css\">
281 body {
282 padding-top: 60px;
283 padding-bottom: 40px;
284 }
285 div#page {
286 width: 940px;
287 background-color: #fff;
288 margin: 0 auto;
289 text-align: left;
290 border-color: #fff;
291 border-style: none solid solid;
292 border-width: medium 1px 1px;
293 }
294
295 div.content {
296 display: none;
297 float: right;
298 width: 550px;
299 }
300 div.content a, div.navigation a {
301 text-decoration: none;
302 color: #777;
303 }
304 div.content a:focus, div.content a:hover, div.content a:active {
305 text-decoration: underline;
306 }
307
308 div.controls {
309 margin-top: 5px;
310 height: 23px;
311 }
312
313 div.controls a {
314 padding: 5px;
315 }
316 div.ss-controls {
317 float: left;
318 }
319 div.nav-controls {
320 float: right;
321 }
322 div.slideshow-container {
323 position: relative;
324 clear: both;
325 height: 502px; /* This should be set to be at least the height of the largest image in the slideshow */
326 }
327 div.loader {
328 position: absolute;
329 top: 0;
330 left: 0;
331 background-image: url('loader.gif');
332 background-repeat: no-repeat;
333 background-position: center;
334 width: 550px;
335 height: 502px; /* This should be set to be at least the height of the largest image in the slideshow */
336 }
337 div.slideshow {
338
339 }
340
341 div.slideshow span.image-wrapper {
342 display: block;
343 position: absolute;
344 top: 0;
345 left: 0;
346 }
347 div.slideshow a.advance-link {
348 display: block;
349 width: 550px;
350 height: 502px; /* This should be set to be at least the height of the largest image in the slideshow */
351 line-height: 502px; /* This should be set to be at least the height of the largest image in the slideshow */
352 text-align: center;
353 }
354 div.slideshow a.advance-link:hover, div.slideshow a.advance-link:active, div.slideshow a.advance-link:visited {
355 text-decoration: none;
356 }
357 div.slideshow img {
358 vertical-align: middle;
359 border: 1px solid #ccc;
360 }
361
362 div.image-title {
363 font-weight: bold;
364 font-size: 1.4em;
365 }
366
367 div.image-desc {
368 line-height: 1.3em;
369 padding-top: 12px;
370 }
371 div.navigation {
372
373 }
374 ul.thumbs {
375 clear: both;
376 margin: 0;
377 padding: 0;
378 }
379 ul.thumbs li {
380 float: none;
381 padding: 0;
382 margin: 0;
383 list-style: none;
384 }
385 a.thumb {
386 padding: 0;
387 display: inline;
388 border: none;
389 }
390 ul.thumbs li.selected a.thumb {
391 color: #000;
392 font-weight: bold;
393 }
394 a.thumb:focus {
395 outline: none;
396 }
397 ul.thumbs img {
398 border: none;
399 display: block;
400 }
401 div.pagination {
402 clear: both;
403 }
404 div.navigation div.top {
405 margin-bottom: 12px;
406 height: 11px;
407 }
408 div.navigation div.bottom {
409 margin-top: 12px;
410 }
411 div.pagination a, div.pagination span.current, div.pagination span.ellipsis {
412 display: block;
413 float: left;
414 margin-right: 2px;
415 padding: 4px 7px 2px 7px;
416 border: 1px solid #ccc;
417 }
418 div.pagination a:hover {
419 background-color: #eee;
420 text-decoration: none;
421 }
422 div.pagination span.current {
423 font-weight: bold;
424 background-color: #000;
425 border-color: #000;
426 color: #fff;
427 }
428 div.pagination span.ellipsis {
429 border: none;
430 padding: 5px 0 3px 2px;
431 }
432
433 div.download {
434 float: right;
435 }
436
437 div.caption-container {
438 position: relative;
439 clear: left;
440 height: 75px;
441 }
442 span.image-caption {
443 display: block;
444 position: absolute;
445 width: 550px;
446 top: 0;
447 left: 0;
448 }
449 div.caption {
450 padding: 12px;
451 }
452
453 /* Featurettes
454 ------------------------- */
455
456 .featurette {
457 padding-top: 20px; /* Vertically center images part 1: add padding above and below text. */
458 overflow: hidden; /* Vertically center images part 2: clear their floats. */
459 text-align: center;
460 }
461
462 .featurette-p
463 {
464 text-align: left;
465 }
466
467 .featurette-image {
468 margin-top: 10px; /* Vertically center images part 3: negative margin up the image the same amount of the padding to center it. */
469 width: 450px;
470 height: auto;
471 }
472
473 </style>
474 <link href=\"css/bootstrap-responsive.css\" rel=\"stylesheet\">
475 </head>
476 <body>
477 ";
478 }
479
480 sub navbar
481 {
482 my ( $file, $fastq, $actif ) = @_;
483
484 print $file "
485 <div class=\"navbar navbar-inverse navbar-fixed-top\">
486 <div class=\"navbar-inner\">
487 <div class=\"container\">
488 <button type=\"button\" class=\"btn btn-navbar\" data-toggle=\"collapse\" data-target=\".nav-collapse\">
489 <span class=\"icon-bar\"></span>
490 <span class=\"icon-bar\"></span>
491 <span class=\"icon-bar\"></span>
492 </button>
493 <a class=\"brand\" href=\"report.txt\">Report</a>
494 <div class=\"nav-collapse collapse\">
495 <ul class=\"nav\">
496 ";
497 for (my $i = 0 ; $i <= $#{$fastq}; $i++)
498 {
499 # my $fa = basename($fastq->[$i],'.dat');
500 my $fa = $fastq->[$i];
501 if ($actif eq $fa){ print $file "<li class=\"active\"><a href=\"$fastq->[$i].html\">$fa</a></li>";}
502 else {print $file "<li><a href=\"$fastq->[$i].html\">$fa</a></li>" ;}
503 }
504 print $file "
505 </ul>
506 </div><!--/.nav-collapse -->
507 </div>
508 </div>
509 </div>";
510 }
511
512 sub footer
513 {
514 my $file = shift;
515 print $file "
516 <!-- FOOTER -->
517 <div class=\"container\">
518 <footer>
519
520 </footer>
521 </div>
522 <!-- Le javascript
523 ================================================== -->
524 <!-- Placed at the end of the document so the pages load faster -->
525 <script type=\"text/javascript\" src=\"js/filter.js\"></script>
526 <script type=\"text/javascript\" src=\"js/jquery.js\"></script>
527 <script type=\"text/javascript\" src=\"js/jquery-1.3.2.js\"></script>
528 <script type=\"text/javascript\" src=\"js/jquery.galleriffic.js\"></script>
529 <script type=\"text/javascript\" src=\"js/jquery.opacityrollover.js\"></script>
530 <script type=\"text/javascript\" src=\"js/bootstrap-table.js\"></script>
531 <script type=\"text/javascript\" src=\"js/bootstrap.min.js\"></script>
532 <script type=\"text/javascript\">
533 jQuery(document).ready(function(\$) {
534 // We only want these styles applied when javascript is enabled
535 \$('div.navigation').css({'width' : '300px', 'float' : 'left'});
536 \$('div.content').css('display', 'block');
537
538 \$(\".each-gallery\").each(function(i){
539 // Initially set opacity on thumbs and add
540 // additional styling for hover effect on thumbs
541 var onMouseOutOpacity = 0.67;
542 \$('#thumbs + i + ul.thumbs li').opacityrollover({
543 mouseOutOpacity: onMouseOutOpacity,
544 mouseOverOpacity: 1.0,
545 fadeSpeed: 'fast',
546 exemptionSelector: '.selected'
547 });
548
549 // Initialize Advanced Galleriffic Gallery
550 var gallery = \$('#thumbs'+i).galleriffic({
551 delay: 2500,
552 numThumbs: 22,
553 preloadAhead: 10,
554 enableTopPager: true,
555 enableBottomPager: true,
556 maxPagesToShow: 7,
557 imageContainerSel: '#slideshow'+ i,
558 controlsContainerSel: '#controls' + i,
559 captionContainerSel: '#caption' + i,
560 loadingContainerSel: '#loading' + i,
561 renderSSControls: true,
562 renderNavControls: true,
563 playLinkText: 'Play',
564 pauseLinkText: 'Pause',
565 prevLinkText: '&lsaquo; Previous',
566 nextLinkText: 'Next &rsaquo;',
567 nextPageLinkText: 'Next &rsaquo;',
568 prevPageLinkText: '&lsaquo; Prev',
569 enableHistory: false,
570 autoStart: false,
571 syncTransitions: true,
572 defaultTransitionDuration: 900,
573 onSlideChange: function(prevIndex, nextIndex) {
574 // 'this' refers to the gallery, which is an extension of \$('#thumbs')
575 this.find('ul.thumbs').children()
576 .eq(prevIndex).fadeTo('fast', onMouseOutOpacity).end()
577 .eq(nextIndex).fadeTo('fast', 1.0);
578 },
579 onPageTransitionOut: function(callback) {
580 this.fadeTo('fast', 0.0, callback);
581 },
582 onPageTransitionIn: function() {
583 this.fadeTo('fast', 1.0);
584 }
585 });
586 });
587 });
588 </script>
589 </body>
590 </html>
591 ";
592 }
593
594 sub carousel
595 {
596 my ($file, $non_unique, $dir_root) = @_;
597 my $ac = 0;
598 print $file "
599 <div id=\"page\">
600 <div id=\"container\">
601 <div class=\"each-gallery\">
602 <div id=\"gallery\" class=\"content\">
603 <div id=\"controls0\" class=\"controls\"></div>
604 <div class=\"slideshow-container\">
605 <div id=\"loading0\" class=\"loader\"></div>
606 <div id=\"slideshow0\" class=\"slideshow\"></div>
607 </div>
608 <div id=\"caption0\" class=\"caption-container\">Reads randomly assigned</div>
609 </div>
610 <div id=\"thumbs0\" class=\"navigation\">
611 <input type=\"text\" id=\"myInput0\" onkeyup=\"search(this)\" placeholder=\"Search for names...\">
612 <ul class=\"thumbs noscript\">
613 ";
614 foreach my $u (@{$non_unique})
615 {
616 my $name = basename($u,'.png');
617 $u = $1 if $u =~ /$dir_root(.*)/;
618 print $file "
619 <li>
620 <a class=\"thumb\" href=\"$u\" title=\"$name\">$name</a>
621 </li>
622 ";
623 }
624 print $file "
625 </ul>
626 </div>
627 <div style=\"clear: both;\"></div></div>
628 </div>
629 </div>
630 ";
631 }
632
633 sub carousel2
634 {
635 my ($file, $unique, $non_unique, $dir_root) = @_;
636 print $file "
637 <div id=\"page\">
638 <div id=\"container\">
639 <div class=\"each-gallery\">
640 <div id=\"gallery\" class=\"content\">
641 <div id=\"controls0\" class=\"controls\"></div>
642 <div class=\"slideshow-container\">
643 <div id=\"loading0\" class=\"loader\"></div>
644 <div id=\"slideshow0\" class=\"slideshow\"></div>
645 </div>
646 <div id=\"caption0\" class=\"caption-container\">Uniquely mapped reads</div>
647 </div>
648 <div id=\"thumbs0\" class=\"navigation\">
649 <input type=\"text\" id=\"myInput0\" onkeyup=\"search(this)\" placeholder=\"Search for names...\">
650 <ul class=\"thumbs noscript\">
651 ";
652
653 foreach my $u (@{$unique})
654 {
655 my $name = basename($u,'.png');
656 $u = $1 if $u =~ /$dir_root(.*)/;
657 print $file "
658 <li>
659 <a class=\"thumb\" href=\"$u\" title=\"$name\">$name</a>
660 </li>
661 ";
662 }
663 print $file "
664 </ul>
665 </div>
666 </div>
667 <div id=\"page\">
668 <div id=\"container\">
669 <div class=\"each-gallery\">
670 <div id=\"gallery\" class=\"content\">
671 <div id=\"controls1\" class=\"controls\"></div>
672 <div class=\"slideshow-container\">
673 <div id=\"loading1\" class=\"loader\"></div>
674 <div id=\"slideshow1\" class=\"slideshow\"></div>
675 </div>
676 <div id=\"caption1\" class=\"caption-container\">Reads randomly assigned</div>
677 </div>
678 <div id=\"thumbs1\" class=\"navigation\">
679 <input type=\"text\" id=\"myInput1\" onkeyup=\"search(this)\" placeholder=\"Search for names...\">
680 <ul class=\"thumbs noscript\">
681 ";
682
683 foreach my $nu (@{$non_unique})
684 {
685 my $name = basename($nu,'.png');
686 $nu = $1 if $nu =~ /$dir_root(.*)/;
687 print $file "
688 <li>
689 <a class=\"thumb\" href=\"$nu\" title=\"$name\">$name</a>
690 </li>
691 ";
692 }
693 print $file "
694 </ul>
695 </div>
696 <div style=\"clear: both;\"></div></div>
697 </div>
698 </div>
699 ";
700 }
701
702 sub futurette
703 {
704 my ($file, $name, $png, $hash) = @_;
705 print $file "
706 <div class=\"container\">
707 <div class=\"featurette\">
708 <h1>$name</h1>
709 <p class=\"featurette-p\">
710 ";
711 foreach my $k (sort keys %{$hash})
712 {
713 print $file "<A HREF=\"".${$hash}{$k}."\">$k</A><br/> \n" ;
714 }
715
716 print $file "
717 </p>";
718
719 foreach my $pn (@{$png}){print $file "<img class=\"featurette-image\" src=\"$pn\"/><br />";}
720
721 print $file "
722 </div>
723 </div>
724 ";
725 }
726
727 sub fut
728 {
729 my ($file, $name, $hash) = @_;
730 print $file "
731 <div class=\"container\">
732 <div class=\"featurette\">
733 <h1>$name</h1>
734 <p class=\"featurette-p\">
735 ";
736
737 foreach my $k (sort { ${$hash}{$a} cmp ${$hash}{$b} } keys %{$hash})
738 {
739 print $file "<A HREF=\"".${$hash}{$k}."\">$k</A><br/> \n" ;
740 }
741
742 print $file "
743 </p>
744 </div>
745 </div>
746 ";
747 }
748
749 sub get_distri_exon
750 {
751 my ($dir, $name) = @_;
752 my (@out,@group);
753 my $group = "'$dir'".'/'."'$name'".'-subgroups-bonafide_reads-transcripts-*distribution-*.png';
754 @group = glob $group;
755 foreach (my $g =0; $g <= $#group; $g++)
756 {
757 if ($group[$g] =~ /.*($name-subgroups-bonafide_reads-transcripts-.*distribution-.*\.png)/ )
758 {
759 my $tmp = $1;
760 push @out, $1;
761 }
762 }
763 return (\@out);
764 }
765
766 sub get_distri_TE
767 {
768 my ($dir, $name) = @_;
769 my (@out,@group);
770 my $group = "'$dir'".'/'."'$name'".'-subgroups-bonafide_reads-TE-*distribution-*.png';
771 @group = glob $group;
772 foreach (my $g =0; $g <= $#group; $g++)
773 {
774 if ($group[$g] =~ /.*($name-subgroups-bonafide_reads-TE-.*distribution-.*\.png)/ )
775 {
776 my $tmp = $1;
777 push @out, $1;
778 }
779 }
780 return (\@out);
781 }
782
783 sub get_PPP
784 {
785 my ($dir,$name) = @_;
786 my (%distri,@group);
787 my $group = "'$dir'".'/'."'$name'".'-subgroups-bonafide_reads-TE-PPPartners-*';
788 @group = glob $group;
789
790 foreach (my $g =0; $g <= $#group; $g++)
791 {
792 if ($group[$g] =~ /.*($name-subgroups-bonafide_reads-TE-PPPartners-.*)/ )
793 {
794 my $tmp = $1;
795 if ($tmp =~ /PPPartners-(.*?)-sens\.txt$/)
796 {
797 $distri{$1} = ['','','','','',''] unless exists $distri{$1};
798 $distri{$1}->[0] = $tmp;
799 }
800 elsif ($tmp =~ /PPPartners-(.*?)-antisens\.txt$/)
801 {
802 $distri{$1} = ['','','','','',''] unless exists $distri{$1};
803 $distri{$1}->[1] = $tmp;
804 }
805 elsif ($tmp =~ /PPPartners-(.*?)-sensPPP\.txt$/)
806 {
807 $distri{$1} = ['','','','','',''] unless exists $distri{$1};
808 $distri{$1}->[2] = $tmp;
809 }
810 elsif ($tmp =~ /PPPartners-(.*?)-antisensPPP\.txt$/)
811 {
812 $distri{$1} = ['','','','','',''] unless exists $distri{$1};
813 $distri{$1}->[3] = $tmp;
814 }
815 elsif ($tmp =~ /PPPartners-(.*?)-overlap_size\.txt$/)
816 {
817 $distri{$1} = ['','','','','',''] unless exists $distri{$1};
818 $distri{$1}->[4] = $tmp;
819 }
820 elsif ($tmp =~ /PPPartners-(.*?)-histogram\.png$/)
821 {
822 $distri{$1} = ['','','','','',''] unless exists $distri{$1};
823 $distri{$1}->[5] = $tmp;
824 }
825 }
826 }
827 return \%distri;
828 }
829
830 sub PPPrint
831 {
832 my ($h, $hash) = @_;
833 my $cmp = 0;
834
835 print $h "<div class=\"container\">\n";
836 print $h "<div class=\"row text-center\">";
837 while ( my ($k,$v) = each %{$hash} )
838 {
839 print $h "</div><div class=\"row text-center\">" if $cmp != 0 && $cmp % 2 == 0;
840 print $h "
841
842 <div class=\"span6\">
843 <h2>$k</h2>
844 <p class=\"featurette-p\"> <img src=\"$v->[5]\"/></p>
845 <p class=\"featurette-p\"><a href=\"$v->[4]\">ping pong signature</a></p>
846 <p class=\"featurette-p\"><a href=\"$v->[2]\">sense reads with PPP</a></p>
847 <p class=\"featurette-p\"><a href=\"$v->[3]\">reverse reads with PPP</a></p>
848 <p class=\"featurette-p\"><a href=\"$v->[0]\">sense reads without PPP</a></p>
849 <p class=\"featurette-p\"><a href=\"$v->[1]\">reverse reads without PPP</a></p>
850 </div>
851 ";
852 $cmp++;
853 }
854
855 print $h "</div></div>";
856 }
857
858 sub printDistri
859 {
860 my ($h, $tab) = @_;
861 my ($txt, $name);
862 my $cmp = 0;
863 print $h "<div class=\"container\">\n";
864 print $h "<div class=\"row text-center\">";
865 foreach my $k (@{$tab})
866 {
867 if ($k =~ /(.*)-(.*)\.png$/)
868 {
869 $txt = $1.'-'.$2.'.txt';
870 $name = $2;
871 }
872 print $h "</div><div class=\"row text-center\">" if $cmp != 0 && $cmp % 2 == 0;
873 print $h "
874
875 <div class=\"span6\">
876 <h2>$name</h2>
877 <p> <img src=\"$k\"/></p>
878 <p class=\"featurette-p\"><a href=\"$txt\">text file</a></p>
879 </div>
880 ";
881 $cmp++;
882 }
883
884 print $h "</div></div>";
885 }
886
887 sub mapnum
888 {
889 my $dupmapnum = shift;
890 my $dupnum_genome = shift;
891 open (my $dupTE, $dupmapnum) || die "cannot open ".$dupmapnum."\n";
892 my %dupnum_TE = ();
893 my $header = <$dupTE>;
894 while (<$dupTE>)
895 {
896 chomp $_;
897 my @dupline = split /\t/, $_;
898 $dupnum_TE{$dupline[0]} = $dupline[2];
899 }
900 close $dupTE;
901 open (my $du_TE, '>'.$dupmapnum) || die "cannot open to write ".$dupmapnum."\n";
902 print $du_TE "sequence\tduplicate\tgenome map num\tmap num\n";
903 while (my ($k, $v) = each %dupnum_TE )
904 {
905 my $hashRef = ${$dupnum_genome}{$k};
906 print $du_TE "$k\t$hashRef->[0]\t$hashRef->[1]\t$v\n";
907 }
908 close $du_TE;
909 }
910
911 sub copy_css
912 {
913 my $dir = shift;
914 my $path = dirname(__FILE__);
915 dircopy( $path.'/css', $dir.'/css' );
916 }
917
918
919 sub copy_js
920 {
921 my $dir = shift;
922 my $path = dirname(__FILE__);
923 dircopy( $path.'/js', $dir.'/js' );
924 }
925
926 1;