-
Notifications
You must be signed in to change notification settings - Fork 2
/
png_to_html.pl
461 lines (393 loc) · 13.7 KB
/
png_to_html.pl
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
294
295
296
297
298
299
300
301
302
303
304
305
306
307
308
309
310
311
312
313
314
315
316
317
318
319
320
321
322
323
324
325
326
327
328
329
330
331
332
333
334
335
336
337
338
339
340
341
342
343
344
345
346
347
348
349
350
351
352
353
354
355
356
357
358
359
360
361
362
363
364
365
366
367
368
369
370
371
372
373
374
375
376
377
378
379
380
381
382
383
384
385
386
387
388
389
390
391
392
393
394
395
396
397
398
399
400
401
402
403
404
405
406
407
408
409
410
411
412
413
414
415
416
417
418
419
420
421
422
423
424
425
426
427
428
429
430
431
432
433
434
435
436
437
438
439
440
441
442
443
444
445
446
447
448
449
450
451
452
453
454
455
456
457
458
459
460
461
#!/usr/bin/perl -w
use strict;
use warnings;
use POSIX qw(strftime);
use File::Basename qw(basename dirname);
use File::Spec::Functions qw(catdir catfile);
# Tables: http://www.textfixer.com/html/html-table-generator.php
# Input the list filefie and dir of images (named by id)
# Create multiple html files
# 1. Home.html
# 2. by_IDs.html
# 3. by_details.html
# 4. Html_lists.html
# 5. html_lists/A_to_B.html
#
# 6. css/style.css
my $usage = 'perl $0 infile.txt out.dir
infile.txt : a tab-separated file with at least 6-columns
out.dir : store the html files of the images
';
my $infile = shift or die "Input a tab file:\n $usage";
my $outdir = shift or die "A directory to store the html files";
$outdir =~ s/(^\s+|\s+$)//g;
## check existence of image/
die "Not found [image/] in folder in $outdir ..." unless -d "$outdir/images";
## parse the current Date
my $cur_date = strftime("%Y-%m-%d %H:%M:%S\n", localtime(time));
#my $cur_date = '2015-03-19';
#my $css = catdir($outdir, "css");
my $nav_bars = catdir($outdir, "nav_bars");
my $html_split = catdir($outdir, "html_split");
## Checking output directory
#mkdir $css unless -d $css;
mkdir $nav_bars unless -d $nav_bars;
mkdir $html_split unless -d $html_split;
# parsing infile
my %seq_ids = ();
open F, "< $infile" or die "$!";
while(<F>){
chomp;
my $id = (split /\t/, $_)[0];
$seq_ids{$id} = $_;
}
close F;
#####################################
# The elements of html files
my $html_header = '<!DOCTYPE html>
<html>
<head>
<title>Reads Coverage Maps</title>
<meta name="R drop plots" content="Reads coverage.">
<meta name="R coverage maps" content="Reads coverage.">
<style type="text/css">
.tftable {font-size:15px;color:#333333;width:90%;border-width: 1px;border-color: #9dcc7a;border-collapse: collapse;}
.tftable th {font-size:14px;background-color:#abd28e;border-width: 1px;padding: 10px;border-style: solid;border-color: #9dcc7a;text-align:left;}
.tftable tr {background-color:#ffffff;}
.tftable td {font-size:14px;border-width: 1px;padding: 10px;border-style: solid;border-color: #9dcc7a;}
.tftable tr:hover {background-color:#ffff99;}
</style>
<style>
nav {
line-height: 20px;
background-color: #E6E6E6;
width: 90%;
float: left;
padding: 1px;
}
nav ul {
list-style-type: none;
margin: 0;
padding: 0;
overflow: hidden;
}
nav ul li {
float: left;
}
nav > ul > li > a:link, nav > ul > li > a:visited {
display: block;
width: 100px;
font-weight: bold;
color: #FFFFFF;
background-color: #6E6E6E;
text-align: center;
padding: 2px;
text-decoration: none;
}
nav > ul > li > a:hover, a:active {
background-color: #98bf21; # green
}
header {
background-color: #E6E6E6;
color: #424242;
text-align: left;
padding: 1px;
width: 90%;
}
body {
width: 80%;
margin-left: 200px;
margin-right: 200px;
font-family: "Helvetica", sans-serif;
}
section {
width: 90%;
float: left;
padding: 1px;
}
footer {
height: 40px;
width: 80%;
#background-color:black;
color:#6E6E6E;
#clear:both;
text-align:center;
}
</style>
</head>
<body>
';
my $nav_bar = '
<nav>
<ul>
<li><a href="index.html">Home</a></li>
<li><a href="nav_bars/1.by_details.html">Seq List</a></li>
<li><a href="nav_bars/2.by_IDs.html">ID List</a></li>
<li><a href="nav_bars/3.html_split.html">Tables</a></li>
</ul>
</nav>
';
my $nav_bar_sub = '
<nav>
<ul>
<li><a href="../index.html">Home</a></li>
<li><a href="../nav_bars/1.by_details.html">Seq List</a></li>
<li><a href="../nav_bars/2.by_IDs.html">ID List</a></li>
<li><a href="../nav_bars/3.html_split.html">Tables</a></li>
</ul>
</nav>
';
my $html_section = 'Content';
my $html_footer = '
<footer>
<p><small>Generated at: ' . $cur_date . ' by @Ming, IBP</small></p>
</footer>
</body>
</html>
';
########################################
my $image_cont = '';
my @f1_table_new_tabs;
my %by_id_sub = ();
my %tab_12 = ();
my $f1_count = 1;
foreach my $id (sort keys %seq_ids){
## 1.by_ids.html
my $image_dir = catdir($outdir, "images");
my $image = catfile($image_dir, "$id\.png");
warn "Image of $id - $image not found... \n" unless -e $image;
my $by_id_group = sprintf "%d", (($f1_count-1)/50 + 1);
push @{$by_id_sub{$by_id_group}}, $id;
## 2.by_details.html
my @tabs = split /\t/, $seq_ids{$id}, 7;
my @tabs_links = id_to_link($tabs[0]);
$tabs[0] = $tabs_links[0];
my $new_tab = join "\t", ($f1_count, @tabs);
push @f1_table_new_tabs, $new_tab;
## 3.html_split.html
my $tab_group = sprintf "%d", (($f1_count-1)/12 + 1);
push @{$tab_12{$tab_group}}, $id;
$f1_count ++;
}
####################################
# Generate 0. index.html #
####################################
my $home_header = '
<header>
<h1>Draw reads coverage maps of each sequence</h1>
</header>
';
my $home_section = '
<section>
<h2>Examples:</h2>
</section>
<figure>
<img src="http://7xi7ro.com1.z0.glb.clouddn.com/Example.png" alt="PNG" width="500" height="375">
<img src="http://7xi7ro.com1.z0.glb.clouddn.com/Example-freey.png" alt="PNG" width="500" height="375">
<figcaption>Fig-1. Reads coverage of map of Rvnr01. <i>(left: fixed Y-axis, right: free Y-axis scal)</i></figcaption>
</figure>
<section>
<pre>
<p title="About Coverage map">
This file will present the coverage maps of a sequence.
x-axis: the coordination of the genome,
y-axis: the read counts in each library
Library:
1. 18-40 nt: the library was constructed using RNAs from 18 nt to 40 nt.
2. 40-80 nt: 40 nt to 80 nt RNAs included in this library.
3. 80-140 nt: 80 nt to 140 nt RNAs included in this library.
4. >140 nt: longer than 140 nt RNAs were included in this library.
</p>
</pre>
<pre><code>
Notes:
1. All of the files and images were created by <b>R</b> and <b>PERL</b>.
2. The structure of the folder are:
dir/
|-index.html # home page
|
|- html_split/
| |-seed0001-seed0012.html ... #pages
|
|-images/
| |-seed0001.png... # images
|
|-nav_bars/
| |-1.by_details.html # display details of seq
| |-2.by_IDs.html # search images by id
| |-3.html_split.html # organize the split_html files
</code></pre>
</section>
';
my $home_html = join "\n", ($html_header, $home_header, $nav_bar, $home_section, $html_footer);
my $home_html_file = catfile($outdir, "index.html");
open OUT, "> $home_html_file" or die "$!";
print OUT $home_html, "\n";
close OUT;
####################################
# Generate 1. by_details.html
####################################
my $det_header = '<header> <h1>List of genome info of sequences</h1> </header>
';
my $table_header = tabs_to_table('header', 'NUM', 'ID', 'Chr', 'Length /nt', 'Start', 'End', 'Strand', 'Note');
my @table_lines;
foreach my $t (@f1_table_new_tabs){
my @tmp_tabs = split /\t/, $t, 8;
my $tmp_line = tabs_to_table('line', @tmp_tabs);
push @table_lines, $tmp_line;
}
my $table_line = join "\n", (@table_lines);
my $f1_table_section = $table_header . "\n" . $table_line;
my $table_block = join "\n", ('<table class="tftable" border="1">',
$f1_table_section, '</table>');
## image to ../image
$table_block =~ s/\=\"images/\=\"\.\.\/images/g;
my $det_section = join "\n", ('<section>', $table_block, '</section>');
my $det_html = join "\t", ($html_header, $det_header, $nav_bar_sub,
$det_section, $html_footer);
my $det_html_file = catfile("$outdir/nav_bars", "1.by_details.html");
open OUT, "> $det_html_file" or die "$!";
print OUT $det_html, "\n";
close OUT;
####################################
# Generate 2. by_IDs.html #
####################################
my $id_header = '
<header>
<h1>List of IDs</h1>
</header>
';
my @id_sections = '';
my $id_count = 1;
foreach my $id (sort {$a<=>$b} keys %by_id_sub){
my @ids = sort @{$by_id_sub{$id}};
my $id_start = $ids[0];
my $id_end = $ids[-1];
my $id_group_header = join "", ('<h3>', $id_count, '. ', $id_start,
' to ', $id_end, '</h3>');
my @id_links = id_to_link(@ids);
my $id_group_section = join "\n", @id_links;
push @id_sections, ($id_group_header, $id_group_section, "\n");
$id_count ++;
}
my $id_section = join "\n", ('<section>', @id_sections, '</section>');
## image to ../image
$id_section =~ s/\=\"images/\=\"\.\.\/images/g;
#$id_section = $id_header . "\n" . $id_section;
my $id_html = join "\n", ($html_header, $id_header, $nav_bar_sub, $id_section,
$html_footer);
my $id_html_file = catfile("$outdir/nav_bars", "2.by_IDs.html");
open OUT, "> $id_html_file" or die "$!";
print OUT $id_html, "\n";
close OUT;
####################################
# Generate 3. html_split.html / Table
####################################
my $tab_header = '
<header>
<h1>Table of Sequences</h1>
</header>
';
my $tab_table_header = '<tr><th>Num</th><th>File Name</th><th>Content</th></tr>';
my @tab_table_lines;
my $tab_count = 1;
foreach my $tab (sort {$a<=>$b} keys %tab_12){
my @tab_ids = sort @{$tab_12{$tab}};
my $tab_ids_start = $tab_ids[0];
my $tab_ids_end = $tab_ids[-1];
my $tab_html_file = catfile("../html_split", "$tab_ids_start\-$tab_ids_end\.html");
my $tab_html_file_name = basename($tab_html_file);
my $tab_id = join ", ", @tab_ids;
my $tab_html_link = '<a href="'. $tab_html_file . '">' . $tab_html_file_name . '</a>';
my $tab_table_line = tabs_to_table('line', $tab_count, $tab_html_link, $tab_id);
push @tab_table_lines, $tab_table_line;
$tab_count ++;
#######################################
## Generate 4. Create separate html files
#######################################
my $tab_sub_table_section = ids_to_table_block(@tab_ids);
my @tab_sub_fig_sections = ids_to_image_block(@tab_ids);
my $tab_sub_fig_section = join "\n", @tab_sub_fig_sections;
my $tab_sub_header = '
<header>
<h1> Table of ' . $tab_html_file_name . '
</header>';
my $tab_sub_fig_header = '<h3> Figures. Coverage maps of ' . $tab_html_file_name . '</h3>';
my $tab_sub_section = join "\n", ('<section>', $tab_sub_table_section, $tab_sub_fig_header,
$tab_sub_fig_section, '</section>');
# image to ../image
$tab_sub_section =~ s/\=\"images/\=\"\.\.\/images/g;
my $tab_sub_html = join "\n", ($html_header, $tab_sub_header, $nav_bar_sub,
$tab_sub_section, $html_footer);
my $tab_sub_html_file = catfile("$outdir\/html_split", $tab_html_file_name);
open OUT, "> $tab_sub_html_file" or die "$!";
print OUT $tab_sub_html, "\n";
close OUT;
}
my $tab_table_section = join "\n", ('<section>', '<table class="tftable" border="1">',
$tab_table_header,
@tab_table_lines,
'</table>', </section>);
my $tab_html = join "\n", ($html_header, $tab_header, $nav_bar_sub,
$tab_table_section, $html_footer);
my $tab_html_file = catfile("$outdir/nav_bars", "3.html_split.html");
open OUT, "> $tab_html_file" or die "$!";
print OUT $tab_html, "\n";
close OUT;
sub ids_to_image_block{
my @ids = @_;
# *.png and *-freey.png
my @img_blocks;
foreach my $i (@ids){
warn ("PNG of $i not found") unless -e "$outdir/images/$i\.png";
warn ("freey.PNG of $i not fount") unless -e "$outdir/images/$i\-freey\.png";
my $cap = join "", ('<figcaption>', $i, '</figcaption>');
my $img1 = join "", ('<img src="images/', $i, '.png" alt="', $i,
'" style="width:500px;height:375px;border:0">');
my $img2 = join "", ('<img src="images/', $i, '-freey.png" alt="', $i,
'-freey" style="width:500px;height:375px;border:0">');
my $i_block = join "\n", ('<figure>', $cap, $img1, $img2, '</figure>');
push @img_blocks, ($i_block, "\n");
}
return @img_blocks;
}
sub ids_to_table_block{
my @ids = @_;
my $header = '<tr><th>Num</th><th>ID</td><th>Chr</td><th>Length /nt</td><th>Start</td><th>End</td><th>Strand</td><th>Note</td></tr>';
my @lines;
my $count = 1;
foreach my $i (@ids){
warn "$i not found..." unless(exists $seq_ids{$i});
my @tabs = split /\t/, $seq_ids{$i}, 7;
my $i_line = tabs_to_table('line', $count, @tabs);
push @lines, $i_line;
$count ++;
}
my $table_block = join "\n", ('<table class="tftable" border="1">', $header, @lines, '</table>');
return $table_block;
}
sub id_to_link{
my @in_ids = @_;
#<a href="pics/t1.png">ID1</a>
my @in_ids_links;
foreach my $i (@in_ids){
my $id_to_image = catfile("$outdir\/images", "$i\.png");
warn("Image of $i not found...\n") unless -e $id_to_image;
my $id_link = '<a href="'. "images\/$i\.png" . '">' . $i . '</a>';
push @in_ids_links, $id_link;
}
return @in_ids_links;
}
sub tabs_to_table{
my $table_type = shift(@_); # header or line
die"Input table type should be [header] or [line].\n" unless($table_type eq 'header' || $table_type eq 'line');
my @tabs = @_;
my @tabs_fmt = ();
foreach my $tab (@tabs){
my $tab_fmt = '<td>'. $tab . '</td>';
push @tabs_fmt, $tab_fmt;
}
my $line = join "", ('<tr>', @tabs_fmt, '</tr>');
$line =~ s/<td>/<th>/g if($table_type eq 'header');
return $line;
}