-
Notifications
You must be signed in to change notification settings - Fork 0
/
geexview
executable file
·595 lines (491 loc) · 19.9 KB
/
geexview
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
462
463
464
465
466
467
468
469
470
471
472
473
474
475
476
477
478
479
480
481
482
483
484
485
486
487
488
489
490
491
492
493
494
495
496
497
498
499
500
501
502
503
504
505
506
507
508
509
510
511
512
513
514
515
516
517
518
519
520
521
522
523
524
525
526
527
528
529
530
531
532
533
534
535
536
537
538
539
540
541
542
543
544
545
546
547
548
549
550
551
552
553
554
555
556
557
558
559
560
561
562
563
564
565
566
567
568
569
570
571
572
573
574
575
576
577
578
579
580
581
582
583
584
585
586
587
588
589
590
591
592
593
594
595
#!/usr/local/bin/perl -wT
#########
# Author: rmp
# Maintainer: rmp
# Created: 2002-06-25
# Last Modified: 2002-10-14
# S.pombe Gene Expression viewer
#
package SPGE::geexview;
use strict;
use warnings;
use lib qw(/var/www/lib/core);
use lib '/var/www/cgi-bin/SPGE/modules';
use lib qw(/var/www/lib/S_pombe);
use SangerWeb;
use lib qw(/var/www/lib/ensembl-53/ensembl-draw/modules);
#use SangerPaths qw(core bioperl ensembl); # spge);
use GD;
use CGI qw/:cgi/;
use CGI::Carp qw(fatalsToBrowser);
use Getopt::Long;
use Sanger::Graphics::JSTools;
use SPGE::WebUserConfig::geexview;
use SPGE::WebUserConfig::geexview_group;
use SPGE::WebUserConfig::geexview_key;
use SPGE::DrawableContainer;
use SPGE::Experiment;
use SPGE::GeneSynonym;
use SPGE::ExperimentGroup;
use Spreadsheet::WriteExcel;
use Website::Utilities::IdGenerator;
use vars qw($TMPURI $TMPDIR $EMPOWERED);
use Data::Dumper;
#BEGIN {
#@INC = grep { $_ !~ m!/nfs/WWW/SANGER_docs/perl/SPGE/modules! } @INC;
#push @INC, '/nfs/WWWdev/SANGER_docs/perl/SPGE/modules';
#}
#print STDERR "[@INC]\n";
$TMPURI = "/tmp/spge";
$TMPDIR = $ENV{'DOCUMENT_ROOT'} . $TMPURI;
$EMPOWERED = qq(<p align="right"><a href="http://www.ensembl.org/"><img src="/gfx/empowered-small.png" alt="Powered by Ensembl" border="" /></a></p>\n);
sub main {
my $cgi = CGI->new();
if(!defined $ENV{'SCRIPT_NAME'}) {
my ($gn, $experiment, $act, $format, $match);
&GetOptions(
"exp_name=s" => \$experiment,
"q=s" => \$gn,
"action=s" => \$act,
"format=s" => \$format,
"match=s" => \$match,
);
$cgi->param('exp_name', $experiment);
$cgi->param('q', $gn);
$cgi->param('action', $act);
$cgi->param('format', $format);
$cgi->param('match', $match);
}
my $action = $cgi->param('action') || "";
my @pgene_names = $cgi->param('q');
my $experiment_name = $cgi->param('exp_name');
my $match_type = $cgi->param('match') || "exact";
my $scale_type = $cgi->param('scale') || "log2";
my $format = $cgi->param('format') || "html";
my $nodecor = $cgi->param('nodecor');
my $groupid = $cgi->param('group');
my $scale_auto = $cgi->param('scale_auto') || "off";
my $scale_min = $cgi->param('scale_min') || -2;
my $scale_max = $cgi->param('scale_max') || 2;
my $scriptname = $ENV{'SCRIPT_NAME'};
$scriptname =~ s/\/\//\//g;
my @gene_names = ();
for my $pg (@pgene_names) {
my ($clean_pg) = $pg =~ /([a-zA-Z0-9:\-\|\.,_ ]+)/g;
next if(!defined $clean_pg);
push @gene_names, grep { ($match_type ne "exact")?length($_) >= 3:1 } split(/[\|,]/, $clean_pg);
}
my $sw_refs = {
'title' => qq(S.pombe Gene Expression Viewer),
'banner' => qq(<i>S.pombe</i> Gene Expression Viewer),
'author' => 'rmp',
'jsfile' => qq(/js/zmenu.js),
'description' => qq(S.pombe Gene Expression Viewer),
# 'inifile' => qq($ENV{'DOCUMENT_ROOT'}/PostGenomics/S_pombe/header.ini),
};
if($action eq "export" && $format eq "printable") {
$nodecor = 1;
$action = "";
}
if(defined $nodecor || $action eq "help") {
$sw_refs->{'decor'} = "half";
}
if($ENV{'QUERY_STRING'} ne "") {
$sw_refs->{'navigator2'} .= qq(,Printable Page||$ENV{'REQUEST_URI'}&nodecor=1);
}
my $sw = SangerWeb->new($sw_refs);
if($action eq "export") {
my $mime = "text/plain";
if($format eq "html") {
$mime = "text/html";
} elsif($format eq "xls") {
$mime = "application/vnd.ms-excel";
}
if($format eq "html") {
# print $sw->header();
print "Content-tye:text/html\n\n";
print qq(<br/>
<br/>
<html xmlns="http://www.w3.org/1999/xhtml">
<head>
<meta http-equiv="content-type" content="text/html; charset=utf-8" />
<title>Bahler Lab</title>
<meta name="keywords" content="" />
<meta name="description" content="" />
<link href="/css/other.css" rel="stylesheet" type="text/css" />
</head>
<script type="text/javascript">
var _gaq = _gaq || [];
_gaq.push(['_setAccount', 'UA-23429289-1']);
_gaq.push(['_trackPageview']);
(function() {
var ga = document.createElement('script'); ga.type = 'text/javascript'; ga.async = true;
ga.src = ('https:' == document.location.protocol ? 'https://ssl' : 'http://www') + '.google-analytics.com/ga.js';
var s = document.getElementsByTagName('script')[0]; s.parentNode.insertBefore(ga, s);
})();
</script>
<body>
<div id="header">
<div style="text-align:left; margin-left:70px; margin-bottom:0px; margin-top:0px;"><span style="text-shadow:#FFF; font-family:'Arial Black', Gadget, sans-serif; font-size:32pt; color:#EBF1DE; ">bähler</span><span style="text-shadow:auto; font-family:'Arial Black', Gadget, sans-serif; font-size:32pt; color:#77933C; ">lab </span></div>
<div style="text-align:left; margin-left:30px; margin-top:0px;"><span style="font-family:'Arial Black', Gadget, sans-serif; font-size:20pt; color:#4F6228; "> Genome Regulation</span></div>
<div class="O">
<div style="text-align:center; margin-bottom:0; margin-top:-63px; margin-left:120px;margin-right:-20px;"><span style="font-family:Arial, Helvetica, sans-serif; font-size:40pt; color:#D7E4BD; "><strong><em>expression viewer </em></strong></span></div>
<div style="text-align:right; margin-bottom:0px; margin-top:-127px; margin-left:150px;"><span style="font-family:'Arial Black', Helvetica, sans-serif; font-size:36pt; color:white; ">
<img src="/images/uclogo.gif";/></span></div>
<div></div>
</div>
</div>);
} else {
print qq(Content-type: $mime\n\n);
}
&export($cgi, &x_gene_names(\@gene_names, $match_type), $format, $sw);
print $EMPOWERED if($format eq "html");
} elsif($action eq "help") {
# print $sw->header();
print qq(content-type: text/html\n\n);
print qq (<html xmlns="http://www.w3.org/1999/xhtml">
<head>
<meta http-equiv="content-type" content="text/html; charset=utf-8" />
<title>Bahler Lab</title>
<meta name="keywords" content="" />
<meta name="description" content="" />
<link href="/css/other.css" rel="stylesheet" type="text/css" />
</head>
<body>
<div id="header">
<div style="text-align:left; margin-left:70px; margin-bottom:0px; margin-top:0px;"><span style="text-shadow:#FFF; font-family:'Arial Black', Gadget, sans-serif; font-size:32pt; color:#EBF1DE; ">bähler</span><span style="text-shadow:auto; font-family:'Arial Black', Gadget, sans-serif; font-size:32pt; color:#77933C; ">lab </span></div>
<div style="text-align:left; margin-left:30px; margin-top:0px;"><span style="font-family:'Arial Black', Gadget, sans-serif; font-size:20pt; color:#4F6228; "> Genome Regulation</span></div>
<div class="O">
<div style="text-align:center; margin-bottom:0; margin-top:-26px; margin-left:120px;margin-right:-20px;"><span style="font-family:Arial, Helvetica, sans-serif; font-size:55pt; color:#D7E4BD; "><strong><em>expression viewer </em></strong></span></div>
<div style="text-align:right; margin-bottom:0px; margin-top:-127px; margin-left:150px;"><span style="font-family:'Arial Black', Helvetica, sans-serif; font-size:36pt; color:white; ">
<img src="/images/uclogo.gif";/></span></div>
<div></div>
</div>
</div>
<br />
);
&help($cgi);
print $EMPOWERED, $sw->footer();
} else {
print qq(Content-type: text/html\n\n);
print qq (<html xmlns="http://www.w3.org/1999/xhtml">
<head>
<meta http-equiv="content-type" content="text/html; charset=utf-8" />
<title>Bahler Lab</title>
<meta name="keywords" content="" />
<meta name="description" content="" />
<link href="/css/other.css" rel="stylesheet" type="text/css" />
</head>
<body>
<div id="header">
<div style="text-align:left; margin-left:70px; margin-bottom:0px; margin-top:0px;"><span style="text-shadow:#FFF; font-family:'Arial Black', Gadget, sans-serif; font-size:32pt; color:#EBF1DE; ">bähler</span><span style="text-shadow:auto; font-family:'Arial Black', Gadget, sans-serif; font-size:32pt; color:#77933C; ">lab </span></div>
<div style="text-align:left; margin-left:30px; margin-top:0px;"><span style="font-family:'Arial Black', Gadget, sans-serif; font-size:20pt; color:#4F6228; "> Genome Regulation</span></div>
<div class="O">
<div style="text-align:center; margin-bottom:0; margin-top:-26px; margin-left:120px;margin-right:-20px;"><span style="font-family:Arial, Helvetica, sans-serif; font-size:55pt; color:#D7E4BD; "><strong><em>expression viewer </em></strong></span></div>
<div style="text-align:right; margin-bottom:0px; margin-top:-127px; margin-left:150px;"><span style="font-family:'Arial Black', Helvetica, sans-serif; font-size:36pt; color:white; ">
<img src="/images/uclogo.gif";/></span></div>
<div></div>
</div>
</div>
<div id="sidebar">
<div id="menu">
<ul>
<li ><a href="/index.html" title="">Home</a></li>
<li><a href="/people" title="">People</a></li>
<li><a href="/research.htm" title="">Research</a></li>
<li><a href="/publications" title="">Publications</a></li>
<li class="active first"><a href="/resources" title="">Resources</a></li>
<li ><a href="/contact.htm" title="">Contact</a></li>
</ul>
</div>
</div><br /> <br /> <br /> <br />
);
# print $sw->header();
# print "\n", &js_menu_div(), "\n";
print qq(<img src="/gfx/close.gif" width="0" height="0" alt="" />\n);
my @groups = SPGE::ExperimentGroup->groups();
my $gene_name = join(',', @gene_names);
print qq(
<form action="$scriptname" method="POST">
<table border="0" align="center" class="violet1">
<tr>
<td class="smarial">Experiment</td>
<td>
<select name="group">\n);
$groupid ||= $groups[0]->id();
for my $group (@groups) {
my $id = $group->id();
my $desc = $group->description();
my $selected = "";
$selected = "selected" if($id == $groupid);
print qq(\t<option value="$id" $selected>$desc</option>\n);
}
print qq(
</select>
</td>
<td colspan="2" class="smarial" align="right">[<a href="/projects/citation.shtml" target="geexviewhelp">How to cite these data</a>] [<a href="$scriptname?action=help" target="geexviewhelp">Help</a>]</td>
</tr>
<tr>
<td class="smarial">Gene name</td>
<td><input type="entry" name="q" value="$gene_name"></td>
</tr>
<tr>\n);
#########
# match type
#
print qq(<td class="smarial">match type\n<select name="match">\n);
for my $f (qw(exact partial)) {
my $selected = "";
$selected = "selected" if($match_type eq $f);
print qq( <option value="$f" $selected>$f</option>\n);
}
print qq(</select></td>\n);
#########
# scale type
#
print qq(<td class="smarial">scale type\n<select name="scale">\n);
for my $f (qw(linear log10 log2 loge)) {
my $selected = "";
$selected = "selected" if($scale_type eq $f);
print qq( <option value="$f" $selected>$f</option>\n);
}
print qq(</select></td>\n);
print qq(<input type="hidden" name="nodecor" value="1">\n) if(defined $nodecor);
print qq(<td class="smarial">
<input type="submit" name="action" value="display"> or</td><td class="smarial">
<input type="submit" name="action" value="export">
as
<select name="format">
<option value="html">HTML tables</option>
<option value="csv">Comma-separated text</option>
<option value="tsv">Tab-separated text</option>
<option value="xls">Excel workbook</option>
<option value="printable">Printable Page</option>
</select></td>
</tr>
<tr>
<td colspan="3">
Scale auto <input type="checkbox" name="scale_auto" value="on" @{[($scale_auto eq "on")?"checked":""]} />
or set manually to
min=<input type="text" size="4" name="scale_min" value="$scale_min" />
and max=<input type="text" size="4" name="scale_max" value="$scale_max" />
</td>
</tr>
</table>
</form>
);
my $q = $cgi->param('q');
if(defined $q && length($q) < 3 && $match_type ne "exact") {
print qq(Your search term is too short for partial matching. Please try again.);
} elsif(scalar @gene_names > 0) {
my $x_gene_ref = &x_gene_names(\@gene_names, $match_type);
if(scalar @{$x_gene_ref} <= 0) {
print qq(No matches found for '<b>$q</b>'.<br />\n);
} else {
# wild type diploid meiosis
# pat1 diploid meiosis
# add link to /PostGenomics/S_pombe/projects/sexualdifferentiation/experiments.shtml
my $group = SPGE::ExperimentGroup->new({
'id' => $groupid,
'gene_names' => $x_gene_ref,
});
print &draw($cgi, $group, $x_gene_ref);
$cgi->param('key', 1);
print &draw($cgi, ($group->experiments())[0], $x_gene_ref);
}
}
# print $EMPOWERED, $sw->footer();
print $EMPOWERED;
}
}
sub draw {
my ($cgi, $container, $x_gene_ref) = @_;
if($container->can("groupstyle") && $container->groupstyle() == 1) {
for my $experiment ($container->experiments()) {
print &draw($cgi, $experiment, $x_gene_ref);
}
return "";
}
my $image_type = (GD::Image->can("png")) ? 'png' : 'gif';
my $scale_type = $cgi->param('scale') || "linear";
my $scale_auto = $cgi->param('scale_auto') || "off";
my $scale_min = $cgi->param('scale_min') || -2;
my $scale_max = $cgi->param('scale_max') || 2;
my $log_base = 10;
my $groupid = $container->id() if($container->isa("SPGE::ExperimentGroup"));
my $group = $groupid?"_group":"";
my $config = undef;
if(defined $cgi->param('key')) {
$config = SPGE::WebUserConfig::geexview_key->new();
} else {
if(substr($scale_type, 0, 3) eq "log") {
($scale_type, $log_base) = $scale_type =~ /^(log)(.*)$/g;
}
if(defined $groupid) {
$config = SPGE::WebUserConfig::geexview_group->new();
} else {
$config = SPGE::WebUserConfig::geexview->new();
}
my $gid = $container->isa("SPGE::ExperimentGroup")?$groupid:$container->experiment_group_id();
$config->{'general'}->{'geexview'}->{"SPGE_expression$group"}->{'scale'} = $scale_type;
$config->{'general'}->{'geexview'}->{"SPGE_expression$group"}->{'log_base'} = $log_base;
$config->{'general'}->{'geexview'}->{"SPGE_expression$group"}->{'scale_auto'} = $scale_auto;
$config->{'general'}->{'geexview'}->{"SPGE_expression$group"}->{'scale_min'} = $scale_min;
$config->{'general'}->{'geexview'}->{"SPGE_expression$group"}->{'scale_max'} = $scale_max;
$config->{'general'}->{'geexview'}->{"SPGE_meiosis"}->{'label'} = {
1 => "meiotic stage",
2 => "",
3 => "cell cycle phase",
4 => "experimental repeats"
}->{$gid} || ""; # BAD BAD BAD!! Query the db for this sort of data!
}
$config->{'cgi'} = $cgi;
$config->container_width($container->length());
my $fout;
my ($fpath) = $TMPDIR =~ m|([a-zA-Z0-9_\-/\.]+)|;
my $id = Website::Utilities::IdGenerator->get_unique_id();
my $dc = SPGE::DrawableContainer->new($container, $config);
$fpath .= "/$id.$image_type";
open($fout, ">$fpath") or die qq($fpath: $!);
binmode($fout);
print $fout $dc->render($image_type);
close($fout);
my $content = qq(<map name="$id">\n) . $dc->render("imagemap") . qq(</map>\n);
$content .= qq(<center><img src="$TMPURI/$id.$image_type" border="0" alt="Expression Profile" usemap="#$id" /></center><br />);
return $content;
}
sub export {
my ($cgi, $genes_ref, $format, $sw) = @_;
my $workbook = undef;
$workbook = Spreadsheet::WriteExcel->new(\*STDOUT) if($format eq "xls");
my $groupid = $cgi->param('group');
my $group = SPGE::ExperimentGroup->new({
'id' => $groupid,
'gene_names' => $genes_ref,
});
for my $experiment ($group->experiments()) {
my $exname = $experiment->name();
my $text_delim = "\t";
if($format eq "csv") {
$text_delim = ",";
$format = "tsv";
}
if($format eq "html") {
#########
# HTML fancy
#
my $violet = 2;
print qq(
<table border="0" cellspacing="0" cellpadding="2">
<tr class="violet3"valign="top">
<th align="right" class="barial">Experiment</th>
<td class="smarial">$exname</td>
</tr>
<tr class="violet1" valign="top">
<th align="right" class="barial">Points</th>);
print '<td class="smarial">', join('</td><td class="smarial">', map { $_=$_->time() ; $_ = "veg" if($_ < 0); $_; } $experiment->time_points()), "</td>\n </tr>\n";
for my $gene ($experiment->genes()) {
print qq(<tr class="violet$violet"valign="top"><td class="smarial">), $gene->name(), "</td>";
print '<td class="smarial">', join('</td><td class="smarial">', map { $_=$_->data() ; $_ ||= 0;} $gene->expressions()), "</td>\n </tr>\n";
$violet = 1+!($violet-1);
}
print qq(</table><br />\n);
} elsif($format eq "xls") {
my $worksheet = $workbook->addworksheet($exname);
$worksheet->write(0,0, "Points");
my $i = 1;
for my $p (map { $_=$_->time() } $experiment->time_points()) {
$worksheet->write_number(0,$i, $p);
$i++;
}
my $row = 1;
for my $gene ($experiment->genes()) {
$worksheet->write($row, 0, $gene->name());
my $col = 1;
for my $e (map { $_=$_->data() ; $_ ||= 0;} $gene->expressions()) {
$worksheet->write_number($row,$col, $e);
$col++;
}
$row++;
}
} else {
#########
# Plain text (tsv/csv)
#
print qq(Experiment$text_delim$exname\n);
print qq(Points$text_delim), join($text_delim, map { $_=$_->time() ; $_ = "veg" if($_ < 0); $_; } $experiment->time_points()), "\n";
for my $gene ($experiment->genes()) {
print $gene->name(), "${text_delim}";
print join("${text_delim}", map { $_=$_->data() ; $_ ||= 0;} $gene->expressions()), "\n";
}
print "\n\n";
}
}
}
sub x_gene_names {
my ($gene_names_ref, $match_type) = @_;
my @x_gene_names = ();
#########
# more specific results first
#
for my $xg (@{$gene_names_ref}) {
push @x_gene_names, sort SPGE::GeneSynonym->new({
'name' => $xg,
'fuzzy' => ($match_type eq "partial")?1:undef,
})->gene_names();
}
#########
# now synonyms
#
for my $xg (@{$gene_names_ref}) {
push @x_gene_names, sort SPGE::GeneSynonym->new({
'synonym' => $xg,
'fuzzy' => ($match_type eq "partial")?1:undef,
})->gene_names();
}
# my @tmp = @x_gene_names[0..19];
return \@x_gene_names;
# return \@tmp;
}
sub help {
print qq(
<h3 align="center">Help</h3>
<a name="searching"><h4>Searching for genes</h4></a>
<p>
<ul>
<li>Enter your gene name in the box marked '<b>gene name</b>' and press '<b>display</b>'.</li>
<li>To display more than one gene enter a comma or pipe '|' separated list e.g. '<b>act1,pap1</b>'.</li>
<li>To search for partial gene names change the '<b>match type</b>' to '<b>partial</b>'. Partial matching also applies to multiple names, e.g. '<b>rps,rpn</b>'</li>
</ul>
</p>
<a name="expressionscale"><h4>Expression Scale</h4></a>
<p>
<ul>
<li>The expression ratio track can be scaled in four ways:
<ul>
<li>linear</li>
<li>log<sub><small>10</small></sub>(ratio)</li>
<li>log<sub><small>2</small></sub>(ratio)</li>
<li>log<sub><small>e</small></sub>(ratio)</li>
</ul>
</li>
</ul>
</p>
<a name="exportingdata"><h4>Exporting Data</h4></a>
<p>
The expression data from a display can be exported (dumped) in three ways:
<ul>
<li>HTML marked up</li>
<li>Tab-separated text</li>
<li>Comma-separated text</li>
</ul>
After executing a search for your gene(s) of interest, select your preferred export format and press '<b>export</b>'.
</p>
<a name="printablepage"><h4>Printer-Friendly version</h4></a>
<p>
For a printer-friendly formatted page, use the '<b>Printable Page</b>' link from the sidebar.
</p>
);
}
1;
SPGE::geexview::main();