Mercurial > repos > romaingred > pirna_pipeline

comparison bin/html.pm @ 0:198009598544 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Uploaded
author romaingred
date Wed, 11 Oct 2017 09:57:58 -0400
parents
children 0ee4dadfdca3
comparison
equal deleted inserted replaced
-1:000000000000 0:198009598544
1 package html;
2
3 use strict;
4 use warnings;
5 use File::Basename;
6
7 use Exporter;
8 our @ISA = qw( Exporter );
9 our @EXPORT_OK = qw( &main_page &details_pages &menu_page &ppp_page );
10
11 sub main_page
12 {
13 my ( $dir, $file, $list_mainTabP, $current, $ma, $ma_uni, $dir_root ) = @_;
14 my ( $futHashP, $uniqueTabP, $randTabP, $pngTabP ) = get_genome ( $dir, $dir_root );
15
16 open my $h, '>', $file || die "cannot create $file $!\n";
17 header ( $h );
18 navbar ( $h, $list_mainTabP, $current );
19 print $h "<div class=\"container\"><p><a class=\"btn\" href=\"$current-sub.html\">View details &raquo;</a></p></div>\n";
20 futurette( $h, $current, $pngTabP, $futHashP );
21 print $h "<div class=\"container\"><h2>mappers #: $ma</h2><h2>unique mappers #: $ma_uni</h2> </div>\n";
22 carousel2( $h, $uniqueTabP, $randTabP, $dir_root );
23 footer($h);
24 close $h;
25 }
26
27 sub menu_page
28 {
29 my ( $dir, $file, $list_mainTabP, $current, $min, $max, $simin, $simax, $pimin, $pimax, $dir_root ) = @_;
30 my $html_ref = $1 if $dir =~ /$dir_root(.*)/;
31 open my $h, '>', $file || die "cannot create $file $!\n";
32 header($h);
33 navbar ( $h, $list_mainTabP, $current );
34 span( $h, $current, $min, $max, $simin, $simax, $pimin, $pimax );
35 print $h " <div class=\"container\"> <div class=\"row text-center\"> <img src=\"$html_ref/pie_chart.png\"/><br />\n";
36 print $h " <A HREF=\"$html_ref/repartition.txt\">text file</A><br/>\n </div></div>";
37 footer($h);
38 close $h;
39 }
40
41 sub details_pages
42 {
43 my ( $dir_details, $prefix, $list_mainTabP, $current, $misTE, $dir_root ) = @_;
44 my ($Hex, $HTE, $HG, $NonUniTE, $NonUniG, $UniG ) = get_subgroups( $dir_details, $current, $misTE, $dir_root );
45
46 my $html_ref = $1.'-PPP.html' if $prefix =~ /$dir_root(.*)/;
47 open my $h, '>', $prefix.'-TEs.html' || die "cannot create $prefix-TEs.html $!\n";
48 header($h);
49 navbar ( $h, $list_mainTabP, $current );
50 if ( $prefix =~ /bonafide_reads$/ )
51 {
52 print $h " <div class=\"container\">";
53 print $h " <p><a class=\"btn\" href=\"$html_ref\">Ping Pong Partners</a></p>\n";
54 print $h "</div>";
55 }
56 fut($h,'Transposable elements',$HTE);
57 carousel($h,$NonUniTE,$dir_root);
58 footer($h);
59 close $h;
60
61 open $h, '>', $prefix.'-genome.html' || die "cannot create $prefix-genome.html $!\n";
62 header($h);
63 navbar ( $h, $list_mainTabP, $current );
64 fut($h,'Genome',$HG);
65 carousel2($h,$UniG, $NonUniG,$dir_root);
66 footer($h);
67 close $h;
68
69 open $h, '>', $prefix.'-exons.html' || die "cannot create $prefix-exons.html $!\n";
70 header($h);
71 navbar ( $h, $list_mainTabP, $current );
72 fut($h,'Exons',$Hex);
73 footer($h);
74 close $h;
75 }
76
77 sub ppp_page
78 {
79 my ( $dir, $file, $list_mainTabP, $current, $ppp, $dir_root ) = @_;
80
81 my $ppp_file = $ppp.'ppp.txt';
82 open my $h, '>', $file || die "cannot create $file $!\n";
83 header($h);
84 navbar ( $h, $list_mainTabP, $current );
85 print $h '<div class="container"> <table class="wb-tables table table-striped table-hover">'."\n";
86 print $h '<thead>
87 <tr>
88 <th data-sortable="true">ID</th>
89 <th data-sortable="true">overlap sum</th>
90 <th data-sortable="true">ten overlap sum</th>
91 <th data-sortable="true">mean</th>
92 <th data-sortable="true">standard deviation</th>
93 <th data-sortable="true">z-score</th>
94 <th data-sortable="true">p-value</th>
95 </tr>
96 </thead>
97 <tbody>';
98
99 open my $f, '<', $ppp_file || die "cannot open $ppp_file $!\n";
100 while ( <$f> )
101 {
102 chomp;
103 print $h '<tr>';
104 my ( $id, $sum, $ten, $mean, $sd, $zscore, $prob) = split /\t/, $_;
105 if( -d "$ppp/$id" )
106 {
107 my $sub_html = $ppp.$id.'.html';
108 my $sub_html_ref = $1.$id if $ppp =~ /$dir_root(.*)/;
109 print $h "<td> <a href=\"$sub_html_ref.html\">$id</a> </td>";
110
111 open my $sub, '>', $sub_html || die "cannot create $sub_html\n";
112 {
113 header($sub);
114 print $sub "
115 <div align=\"center\">
116 <h2>$id</h2>
117 <p> <img src=\"$id/histogram.png\" width=50%/></p>
118 <p><a href=\"$id/overlap_size.txt\">ping pong signature</a></p>
119 <p><a href=\"$id/sensPPP.txt\">sens reads with PPP</a></p>
120 <p><a href=\"$id/antisensPPP.txt\">reverse reads with PPP</a></p>
121 <p><a href=\"$id/sens.txt\">sens reads without PPP</a></p>
122 <p><a href=\"$id/antisens.txt\">reverse reads without PPP</a></p>
123 </div>";
124 footer($sub);
125 }
126 close $sub;
127
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 reads</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-exons.html\">Exons</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-exons.html\">Exons</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-exons.html\">Exons</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-exons.html\">Exons</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 ( $f =~ /exons_sorted\.bam$/) { $Hex{'exons mappers (sorted bam)'} = $f;}
235 elsif ( $f =~ /exons_unique_sorted\.bam$/) { $Hex{'exons unique mappers (sorted bam)'} = $f;}
236 elsif ( $f =~ /exons_reads_counts\.txt$/) { $Hex{'read number per exon (txt)'} = $f;}
237 elsif ( $f =~ /TEs_reads_counts\.txt$/) { $HTE{'read number per TE 0 to $misTE mismatches (txt)'} = $f; }
238 elsif ( $f =~ /TEs_reads_counts_mismatches\.txt$/) { $HTE{"read number per TE with 1 to $misTE mismatches (txt)"} = $f; }
239 elsif ( $f =~ /TEs_reads_counts_nomismatches\.txt$/) { $HTE{'read number per TE with no mismatch (txt)'} = $f; }
240 elsif ( $f =~ /TEs_unique_sorted\.bam$/) { $HTE{'TEs unique mappers (sorted bam)'} = $f; }
241 elsif ( $f =~ /TEs_sorted\.bam$/) { $HTE{'TEs mappers (sorted bam)'} = $f; }
242 elsif ( $fr =~ /.*Gviz_TEs/ )
243 {
244 my $nu = $fr.'/*';
245 @NonUniTE = glob $nu;
246 }
247 elsif ( $fr =~ /.*Gviz_genome/ )
248 {
249 my $nu = $fr.'/rand/*';
250 @NonUniG = glob $nu;
251 my $u = $fr.'/unique/*';
252 @UniG = glob $u;
253 }
254 else { unlink $fr; }
255 }
256 return (\%Hex, \%HTE, \%HG, \@NonUniTE, \@NonUniG, \@UniG);
257 }
258
259 sub header
260 {
261 my $file = shift;
262 print $file "
263 <!DOCTYPE html>
264 <html lang=\"en\">
265 <head>
266 <meta charset=\"utf-8\">
267 <title>pipeline</title>
268 <meta name=\"viewport\" content=\"width=device-width, initial-scale=1.0\">
269 <meta name=\"description\" content=\"\">
270 <meta name=\"author\" content=\"\">
271 <!-- Le styles -->
272 <link href=\"css/bootstrap.css\" rel=\"stylesheet\">
273 <link href=\"css/bootstrap-table.css\" rel=\"stylesheet\">
274 <style type=\"text/css\">
275 body {
276 padding-top: 60px;
277 padding-bottom: 40px;
278 }
279 div#page {
280 width: 940px;
281 background-color: #fff;
282 margin: 0 auto;
283 text-align: left;
284 border-color: #fff;
285 border-style: none solid solid;
286 border-width: medium 1px 1px;
287 }
288
289 div.content {
290 display: none;
291 float: right;
292 width: 550px;
293 }
294 div.content a, div.navigation a {
295 text-decoration: none;
296 color: #777;
297 }
298 div.content a:focus, div.content a:hover, div.content a:active {
299 text-decoration: underline;
300 }
301
302 div.controls {
303 margin-top: 5px;
304 height: 23px;
305 }
306
307 div.controls a {
308 padding: 5px;
309 }
310 div.ss-controls {
311 float: left;
312 }
313 div.nav-controls {
314 float: right;
315 }
316 div.slideshow-container {
317 position: relative;
318 clear: both;
319 height: 502px; /* This should be set to be at least the height of the largest image in the slideshow */
320 }
321 div.loader {
322 position: absolute;
323 top: 0;
324 left: 0;
325 background-image: url('loader.gif');
326 background-repeat: no-repeat;
327 background-position: center;
328 width: 550px;
329 height: 502px; /* This should be set to be at least the height of the largest image in the slideshow */
330 }
331 div.slideshow {
332
333 }
334
335 div.slideshow span.image-wrapper {
336 display: block;
337 position: absolute;
338 top: 0;
339 left: 0;
340 }
341 div.slideshow a.advance-link {
342 display: block;
343 width: 550px;
344 height: 502px; /* This should be set to be at least the height of the largest image in the slideshow */
345 line-height: 502px; /* This should be set to be at least the height of the largest image in the slideshow */
346 text-align: center;
347 }
348 div.slideshow a.advance-link:hover, div.slideshow a.advance-link:active, div.slideshow a.advance-link:visited {
349 text-decoration: none;
350 }
351 div.slideshow img {
352 vertical-align: middle;
353 border: 1px solid #ccc;
354 }
355
356 div.image-title {
357 font-weight: bold;
358 font-size: 1.4em;
359 }
360
361 div.image-desc {
362 line-height: 1.3em;
363 padding-top: 12px;
364 }
365 div.navigation {
366
367 }
368 ul.thumbs {
369 clear: both;
370 margin: 0;
371 padding: 0;
372 }
373 ul.thumbs li {
374 float: none;
375 padding: 0;
376 margin: 0;
377 list-style: none;
378 }
379 a.thumb {
380 padding: 0;
381 display: inline;
382 border: none;
383 }
384 ul.thumbs li.selected a.thumb {
385 color: #000;
386 font-weight: bold;
387 }
388 a.thumb:focus {
389 outline: none;
390 }
391 ul.thumbs img {
392 border: none;
393 display: block;
394 }
395 div.pagination {
396 clear: both;
397 }
398 div.navigation div.top {
399 margin-bottom: 12px;
400 height: 11px;
401 }
402 div.navigation div.bottom {
403 margin-top: 12px;
404 }
405 div.pagination a, div.pagination span.current, div.pagination span.ellipsis {
406 display: block;
407 float: left;
408 margin-right: 2px;
409 padding: 4px 7px 2px 7px;
410 border: 1px solid #ccc;
411 }
412 div.pagination a:hover {
413 background-color: #eee;
414 text-decoration: none;
415 }
416 div.pagination span.current {
417 font-weight: bold;
418 background-color: #000;
419 border-color: #000;
420 color: #fff;
421 }
422 div.pagination span.ellipsis {
423 border: none;
424 padding: 5px 0 3px 2px;
425 }
426
427 div.download {
428 float: right;
429 }
430
431 div.caption-container {
432 position: relative;
433 clear: left;
434 height: 75px;
435 }
436 span.image-caption {
437 display: block;
438 position: absolute;
439 width: 550px;
440 top: 0;
441 left: 0;
442 }
443 div.caption {
444 padding: 12px;
445 }
446
447 /* Featurettes
448 ------------------------- */
449
450 .featurette {
451 padding-top: 20px; /* Vertically center images part 1: add padding above and below text. */
452 overflow: hidden; /* Vertically center images part 2: clear their floats. */
453 text-align: center;
454 }
455
456 .featurette-p
457 {
458 text-align: left;
459 }
460
461 .featurette-image {
462 margin-top: 10px; /* Vertically center images part 3: negative margin up the image the same amount of the padding to center it. */
463 width: 600px;
464 height: auto;
465 }
466
467 </style>
468 <link href=\"css/bootstrap-responsive.css\" rel=\"stylesheet\">
469 </head>
470 <body>
471 ";
472 }
473
474 sub navbar
475 {
476 my ( $file, $fastq, $actif ) = @_;
477
478 print $file "
479 <div class=\"navbar navbar-inverse navbar-fixed-top\">
480 <div class=\"navbar-inner\">
481 <div class=\"container\">
482 <button type=\"button\" class=\"btn btn-navbar\" data-toggle=\"collapse\" data-target=\".nav-collapse\">
483 <span class=\"icon-bar\"></span>
484 <span class=\"icon-bar\"></span>
485 <span class=\"icon-bar\"></span>
486 </button>
487 <a class=\"brand\" href=\"report.txt\">Report</a>
488 <div class=\"nav-collapse collapse\">
489 <ul class=\"nav\">
490 ";
491 for (my $i = 0 ; $i <= $#{$fastq}; $i++)
492 {
493 # my $fa = basename($fastq->[$i],'.dat');
494 my $fa = $fastq->[$i];
495 if ($actif eq $fa){ print $file "<li class=\"active\"><a href=\"$fastq->[$i].html\">$fa</a></li>";}
496 else {print $file "<li><a href=\"$fastq->[$i].html\">$fa</a></li>" ;}
497 }
498 print $file "
499 </ul>
500 </div><!--/.nav-collapse -->
501 </div>
502 </div>
503 </div>";
504 }
505
506 sub footer
507 {
508 my $file = shift;
509 print $file "
510 <!-- FOOTER -->
511 <div class=\"container\">
512 <footer>
513
514 </footer>
515 </div>
516 <!-- Le javascript
517 ================================================== -->
518 <!-- Placed at the end of the document so the pages load faster -->
519 <script type=\"text/javascript\" src=\"js/jquery.js\"></script>
520 <script type=\"text/javascript\" src=\"js/jquery-1.3.2.js\"></script>
521 <script type=\"text/javascript\" src=\"js/jquery.galleriffic.js\"></script>
522 <script type=\"text/javascript\" src=\"js/jquery.opacityrollover.js\"></script>
523 <script type=\"text/javascript\" src=\"js/bootstrap-table.js\"></script>
524 <script type=\"text/javascript\" src=\"js/bootstrap.min.js\"></script>
525 <script type=\"text/javascript\">
526 jQuery(document).ready(function(\$) {
527 // We only want these styles applied when javascript is enabled
528 \$('div.navigation').css({'width' : '300px', 'float' : 'left'});
529 \$('div.content').css('display', 'block');
530
531 \$(\".each-gallery\").each(function(i){
532 // Initially set opacity on thumbs and add
533 // additional styling for hover effect on thumbs
534 var onMouseOutOpacity = 0.67;
535 \$('#thumbs + i + ul.thumbs li').opacityrollover({
536 mouseOutOpacity: onMouseOutOpacity,
537 mouseOverOpacity: 1.0,
538 fadeSpeed: 'fast',
539 exemptionSelector: '.selected'
540 });
541
542 // Initialize Advanced Galleriffic Gallery
543 var gallery = \$('#thumbs'+i).galleriffic({
544 delay: 2500,
545 numThumbs: 22,
546 preloadAhead: 10,
547 enableTopPager: true,
548 enableBottomPager: true,
549 maxPagesToShow: 7,
550 imageContainerSel: '#slideshow'+ i,
551 controlsContainerSel: '#controls' + i,
552 captionContainerSel: '#caption' + i,
553 loadingContainerSel: '#loading' + i,
554 renderSSControls: true,
555 renderNavControls: true,
556 playLinkText: 'Play',
557 pauseLinkText: 'Pause',
558 prevLinkText: '&lsaquo; Previous',
559 nextLinkText: 'Next &rsaquo;',
560 nextPageLinkText: 'Next &rsaquo;',
561 prevPageLinkText: '&lsaquo; Prev',
562 enableHistory: false,
563 autoStart: false,
564 syncTransitions: true,
565 defaultTransitionDuration: 900,
566 onSlideChange: function(prevIndex, nextIndex) {
567 // 'this' refers to the gallery, which is an extension of \$('#thumbs')
568 this.find('ul.thumbs').children()
569 .eq(prevIndex).fadeTo('fast', onMouseOutOpacity).end()
570 .eq(nextIndex).fadeTo('fast', 1.0);
571 },
572 onPageTransitionOut: function(callback) {
573 this.fadeTo('fast', 0.0, callback);
574 },
575 onPageTransitionIn: function() {
576 this.fadeTo('fast', 1.0);
577 }
578 });
579 });
580 });
581 </script>
582 </body>
583 </html>
584 ";
585 }
586
587 sub carousel
588 {
589 my ($file, $non_unique, $dir_root) = @_;
590 my $ac = 0;
591 print $file "
592 <div id=\"page\">
593 <div id=\"container\">
594 <div class=\"each-gallery\">
595 <div id=\"gallery\" class=\"content\">
596 <div id=\"controls0\" class=\"controls\"></div>
597 <div class=\"slideshow-container\">
598 <div id=\"loading0\" class=\"loader\"></div>
599 <div id=\"slideshow0\" class=\"slideshow\"></div>
600 </div>
601 <div id=\"caption0\" class=\"caption-container\">Reads randomly assigned</div>
602 </div>
603 <div id=\"thumbs0\" class=\"navigation\">
604 <ul class=\"thumbs noscript\">
605 ";
606 foreach my $u (@{$non_unique})
607 {
608 my $name = basename($u,'.png');
609 $u = $1 if $u =~ /$dir_root(.*)/;
610 print $file "
611 <li>
612 <a class=\"thumb\" href=\"$u\" title=\"$name\">$name</a>
613 </li>
614 ";
615 }
616 print $file "
617 </ul>
618 </div>
619 <div style=\"clear: both;\"></div></div>
620 </div>
621 </div>
622 ";
623 }
624
625 sub carousel2
626 {
627 my ($file, $unique, $non_unique, $dir_root) = @_;
628 print $file "
629 <div id=\"page\">
630 <div id=\"container\">
631 <div class=\"each-gallery\">
632 <div id=\"gallery\" class=\"content\">
633 <div id=\"controls0\" class=\"controls\"></div>
634 <div class=\"slideshow-container\">
635 <div id=\"loading0\" class=\"loader\"></div>
636 <div id=\"slideshow0\" class=\"slideshow\"></div>
637 </div>
638 <div id=\"caption0\" class=\"caption-container\">Uniquely mapped reads</div>
639 </div>
640 <div id=\"thumbs0\" class=\"navigation\">
641 <ul class=\"thumbs noscript\">
642 ";
643
644 foreach my $u (@{$unique})
645 {
646 my $name = basename($u,'.png');
647 $u = $1 if $u =~ /$dir_root(.*)/;
648 print $file "
649 <li>
650 <a class=\"thumb\" href=\"$u\" title=\"$name\">$name</a>
651 </li>
652 ";
653 }
654 print $file "
655 </ul>
656 </div>
657 </div>
658 <div id=\"page\">
659 <div id=\"container\">
660 <div class=\"each-gallery\">
661 <div id=\"gallery\" class=\"content\">
662 <div id=\"controls1\" class=\"controls\"></div>
663 <div class=\"slideshow-container\">
664 <div id=\"loading1\" class=\"loader\"></div>
665 <div id=\"slideshow1\" class=\"slideshow\"></div>
666 </div>
667 <div id=\"caption1\" class=\"caption-container\">Reads randomly assigned</div>
668 </div>
669 <div id=\"thumbs1\" class=\"navigation\">
670 <ul class=\"thumbs noscript\">
671 ";
672
673 foreach my $nu (@{$non_unique})
674 {
675 my $name = basename($nu,'.png');
676 $nu = $1 if $nu =~ /$dir_root(.*)/;
677 print $file "
678 <li>
679 <a class=\"thumb\" href=\"$nu\" title=\"$name\">$name</a>
680 </li>
681 ";
682 }
683 print $file "
684 </ul>
685 </div>
686 <div style=\"clear: both;\"></div></div>
687 </div>
688 </div>
689 ";
690 }
691
692 sub futurette
693 {
694 my ($file, $name, $png, $hash) = @_;
695 print $file "
696 <div class=\"container\">
697 <div class=\"featurette\">
698 <h1>$name</h1>
699 <p class=\"featurette-p\">
700 ";
701 foreach my $k (sort keys %{$hash})
702 {
703 print $file "<A HREF=\"".${$hash}{$k}."\">$k</A><br/> \n" ;
704 }
705
706 print $file "
707 </p>";
708
709 foreach my $pn (@{$png}){print $file "<img class=\"featurette-image\" src=\"$pn\"/><br />";}
710
711 print $file "
712 </div>
713 </div>
714 ";
715 }
716
717 sub fut
718 {
719 my ($file, $name, $hash) = @_;
720 print $file "
721 <div class=\"container\">
722 <div class=\"featurette\">
723 <h1>$name</h1>
724 <p class=\"featurette-p\">
725 ";
726
727 foreach my $k (sort { ${$hash}{$a} cmp ${$hash}{$b} } keys %{$hash})
728 {
729 print $file "<A HREF=\"".${$hash}{$k}."\">$k</A><br/> \n" ;
730 }
731
732 print $file "
733 </p>
734 </div>
735 </div>
736 ";
737 }
738
739 sub get_distri_exon
740 {
741 my ($dir, $name) = @_;
742 my (@out,@group);
743 my $group = $dir.'/'.$name.'-subgroups-bonafide_reads-exons-*distribution-*.png';
744 @group = glob $group;
745 foreach (my $g =0; $g <= $#group; $g++)
746 {
747 if ($group[$g] =~ /.*($name-subgroups-bonafide_reads-exons-.*distribution-.*\.png)/ )
748 {
749 my $tmp = $1;
750 push @out, $1;
751 }
752 }
753 return (\@out);
754 }
755
756 sub get_distri_TE
757 {
758 my ($dir, $name) = @_;
759 my (@out,@group);
760 my $group = $dir.'/'.$name.'-subgroups-bonafide_reads-TE-*distribution-*.png';
761 @group = glob $group;
762 foreach (my $g =0; $g <= $#group; $g++)
763 {
764 if ($group[$g] =~ /.*($name-subgroups-bonafide_reads-TE-.*distribution-.*\.png)/ )
765 {
766 my $tmp = $1;
767 push @out, $1;
768 }
769 }
770 return (\@out);
771 }
772
773 sub get_PPP
774 {
775 my ($dir,$name) = @_;
776 my (%distri,@group);
777 my $group = $dir.'/'.$name.'-subgroups-bonafide_reads-TE-PPPartners-*';
778 @group = glob $group;
779
780 foreach (my $g =0; $g <= $#group; $g++)
781 {
782 if ($group[$g] =~ /.*($name-subgroups-bonafide_reads-TE-PPPartners-.*)/ )
783 {
784 my $tmp = $1;
785 if ($tmp =~ /PPPartners-(.*?)-sens\.txt$/)
786 {
787 $distri{$1} = ['','','','','',''] unless exists $distri{$1};
788 $distri{$1}->[0] = $tmp;
789 }
790 elsif ($tmp =~ /PPPartners-(.*?)-antisens\.txt$/)
791 {
792 $distri{$1} = ['','','','','',''] unless exists $distri{$1};
793 $distri{$1}->[1] = $tmp;
794 }
795 elsif ($tmp =~ /PPPartners-(.*?)-sensPPP\.txt$/)
796 {
797 $distri{$1} = ['','','','','',''] unless exists $distri{$1};
798 $distri{$1}->[2] = $tmp;
799 }
800 elsif ($tmp =~ /PPPartners-(.*?)-antisensPPP\.txt$/)
801 {
802 $distri{$1} = ['','','','','',''] unless exists $distri{$1};
803 $distri{$1}->[3] = $tmp;
804 }
805 elsif ($tmp =~ /PPPartners-(.*?)-overlap_size\.txt$/)
806 {
807 $distri{$1} = ['','','','','',''] unless exists $distri{$1};
808 $distri{$1}->[4] = $tmp;
809 }
810 elsif ($tmp =~ /PPPartners-(.*?)-histogram\.png$/)
811 {
812 $distri{$1} = ['','','','','',''] unless exists $distri{$1};
813 $distri{$1}->[5] = $tmp;
814 }
815 }
816 }
817 return \%distri;
818 }
819
820 sub PPPrint
821 {
822 my ($h, $hash) = @_;
823 my $cmp = 0;
824
825 print $h "<div class=\"container\">\n";
826 print $h "<div class=\"row text-center\">";
827 while ( my ($k,$v) = each %{$hash} )
828 {
829 print $h "</div><div class=\"row text-center\">" if $cmp != 0 && $cmp % 2 == 0;
830 print $h "
831
832 <div class=\"span6\">
833 <h2>$k</h2>
834 <p class=\"featurette-p\"> <img src=\"$v->[5]\"/></p>
835 <p class=\"featurette-p\"><a href=\"$v->[4]\">ping pong signature</a></p>
836 <p class=\"featurette-p\"><a href=\"$v->[2]\">sens reads with PPP</a></p>
837 <p class=\"featurette-p\"><a href=\"$v->[3]\">reverse reads with PPP</a></p>
838 <p class=\"featurette-p\"><a href=\"$v->[0]\">sens reads without PPP</a></p>
839 <p class=\"featurette-p\"><a href=\"$v->[1]\">reverse reads without PPP</a></p>
840 </div>
841 ";
842 $cmp++;
843 }
844
845 print $h "</div></div>";
846 }
847
848 sub printDistri
849 {
850 my ($h, $tab) = @_;
851 my ($txt, $name);
852 my $cmp = 0;
853 print $h "<div class=\"container\">\n";
854 print $h "<div class=\"row text-center\">";
855 foreach my $k (@{$tab})
856 {
857 if ($k =~ /(.*)-(.*)\.png$/)
858 {
859 $txt = $1.'-'.$2.'.txt';
860 $name = $2;
861 }
862 print $h "</div><div class=\"row text-center\">" if $cmp != 0 && $cmp % 2 == 0;
863 print $h "
864
865 <div class=\"span6\">
866 <h2>$name</h2>
867 <p> <img src=\"$k\"/></p>
868 <p class=\"featurette-p\"><a href=\"$txt\">text file</a></p>
869 </div>
870 ";
871 $cmp++;
872 }
873
874 print $h "</div></div>";
875 }
876
877 sub mapnum
878 {
879 my $dupmapnum = shift;
880 my $dupnum_genome = shift;
881 open (my $dupTE, $dupmapnum) || die "cannot open ".$dupmapnum."\n";
882 my %dupnum_TE = ();
883 my $header = <$dupTE>;
884 while (<$dupTE>)
885 {
886 chomp $_;
887 my @dupline = split /\t/, $_;
888 $dupnum_TE{$dupline[0]} = $dupline[2];
889 }
890 close $dupTE;
891 open (my $du_TE, '>'.$dupmapnum) || die "cannot open to write ".$dupmapnum."\n";
892 print $du_TE "sequence\tduplicate\tgenome map num\tmap num\n";
893 while (my ($k, $v) = each %dupnum_TE )
894 {
895 my $hashRef = ${$dupnum_genome}{$k};
896 print $du_TE "$k\t$hashRef->[0]\t$hashRef->[1]\t$v\n";
897 }
898 close $du_TE;
899 }
900
901 1;