-
Notifications
You must be signed in to change notification settings - Fork 3
/
display_genotype.bkp.php
479 lines (354 loc) · 15.5 KB
/
display_genotype.bkp.php
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
<?php
require 'config.php';
include($config['root_dir'] . 'includes/bootstrap.inc');
require_once 'Spreadsheet/Excel/Writer.php';
connect();
new ShowData($_GET['function']);
class ShowData
{
private $delimiter = "\t";
//
// Using the class's constructor to decide which action to perform
public function __construct($function = null)
{
switch($function)
{
case 'typeTabDelimiter':
$this->type_Tab_Delimiter(); /* Displaying in tab demilited fashion */
break;
default:
$this->typeData();
break;
}
}
//
// The wrapper action for the type1 download. Handles outputting the header
// and footer and calls the first real action of the type1 download.
private function typeData()
{
global $config;
include($config['root_dir'].'theme/normal_header.php');
$trial_code=$_GET['trial_code'];
echo " <h2>".$trial_code. "</h2>";
$this->type_DataInformation($trial_code);
$footer_div = 1;
include($config['root_dir'].'theme/footer.php');
}
private function type_DataInformation($trial_code)
{
/* Query for getting the experiment type uid to check the type of experiment */
$sql = "SELECT CAPdata_programs_uid, experiment_type_uid, experiment_uid, experiment_short_name FROM experiments where trial_code = '".$trial_code."' ";
$res = mysql_query($sql) or die(mysql_error());
$row = mysql_fetch_assoc($res);
$experiment_uid = $row['experiment_uid'];
$CAPdata_programs_uid = $row['CAPdata_programs_uid'];
$experiment_short_name = $row['experiment_short_name'];
$sql_data_code = "SELECT data_program_code, data_program_name FROM CAPdata_programs where CAPdata_programs_uid = '".$CAPdata_programs_uid."' ";
$res_data_code = mysql_query($sql_data_code) or die(mysql_error());
$row_data_code = mysql_fetch_assoc($res_data_code);
$data_program_code = $row_data_code['data_program_code'];
$data_program_name = $row_data_code['data_program_name'];
/* Checking if the experiment is a phenotype or genetype experiment and displaying details only for phenotype experiment*/
/* Currently not implemented */
if ($row['experiment_type_uid']==1)
{
$this->type_PhenoInformation($trial_code,$experiment_uid);
}
/* Displaying data for genetype experiments */
else
{
/* Displaying the Data For Genptype Experiment */
$sql_Gen_Info = "SELECT manifest_file_name, cluster_file_name, OPA_name, sample_sheet_filename, raw_datafile_archive FROM genotype_experiment_info where experiment_uid = '".$experiment_uid."' ";
$res_Gen_Info = mysql_query($sql_Gen_Info) or die(mysql_error());
$row_Gen_Info = mysql_fetch_assoc($res_Gen_Info);
$sql_CAP = "SELECT data_program_code FROM CAPdata_programs where CAPdata_programs_uid = '".$CAPdata_programs_uid."' ";
$res_CAP = mysql_query($sql_CAP) or die(mysql_error());
$row_CAP = mysql_fetch_assoc($res_CAP);
$data_program_code = $row_CAP['data_program_code'];
$sql_Gen_Info = "SELECT manifest_file_name, cluster_file_name, OPA_name, sample_sheet_filename, raw_datafile_archive, genotype_experiment_info_uid FROM genotype_experiment_info where experiment_uid = '".$experiment_uid."' ";
$res_Gen_Info = mysql_query($sql_Gen_Info) or die(mysql_error());
$row_Gen_Info = mysql_fetch_assoc($res_Gen_Info);
$manifest_file_name = $row_Gen_Info['manifest_file_name'];
$cluster_file_name = $row_Gen_Info['cluster_file_name'];
$OPA_name = $row_Gen_Info['OPA_name'];
$sample_sheet_filename = $row_Gen_Info['sample_sheet_filename'];
$raw_datafile_archive = $row_Gen_Info['raw_datafile_archive'];
$genotype_experiment_info_uid = $row_Gen_Info['genotype_experiment_info_uid'];
?>
<script type="text/javascript">
function load_tab_delimiter(experiment_uid, max_missing, min_maf)
{
//alert (experiment_uid);
var url='<?php echo $_SERVER[PHP_SELF];?>?function=typeTabDelimiter'+ '&expuid=' + experiment_uid+ '&mm='+max_missing+'&mmaf='+min_maf;
// Opens the url in the same window
window.open(url, "_self");
}
function mrefresh(trial_code) {
var mm = $('mm').getValue();
var mmaf = $('mmaf').getValue();
var url='<?php echo $_SERVER[PHP_SELF];?>?function=typeData'+ '&mm='+mm+'&mmaf='+mmaf+ '&trial_code='+trial_code;
// Opens the url in the same window
window.open(url, "_self");
}
</script>
<?php
$max_missing = 100;//IN PERCENT
if (isset($_GET['mm']) && !empty($_GET['mm']) && is_numeric($_GET['mm']))
$max_missing = $_GET['mm'];
if ($max_missing>100)
$max_missing = 100;
elseif ($max_missing<0)
$max_missing = 0;
$min_maf = 0;//IN PERCENT
if (isset($_GET['mmaf']) && !empty($_GET['mmaf']) && is_numeric($_GET['mmaf']))
$min_maf = $_GET['mmaf'];
if ($min_maf>100)
$min_maf = 100;
elseif ($min_maf<0)
$min_maf = 0;
$sql_mstat = "SELECT af.marker_uid as marker, SUM(af.aa_cnt) as sumaa, SUM(af.missing)as summis, SUM(af.bb_cnt) as sumbb,
SUM(af.total) as total, SUM(af.ab_cnt) AS sumab
FROM allele_frequencies AS af
WHERE af.experiment_uid = '".$experiment_uid."'
group by af.marker_uid";
$res = mysql_query($sql_mstat) or die(mysql_error());
$num_mark = mysql_num_rows($res);
$num_maf = $num_miss = 0;
while ($row = mysql_fetch_array($res)){
$marker_uid[] = $row["marker"];
$maf = round(100*min((2*$row["sumaa"]+$row["sumab"])/$row["total"],($row["sumab"]+2*$row["sumbb"])/$row["total"]),1);
$miss = round(100*$row["summis"]/$row["total"],1);
if ($maf>$min_maf)
$num_maf++;
if ($miss>=$max_missing)
$num_miss++;
}
/* Computing the summary and other details for the experiment */
$sql_Gen_Stat = "
SELECT
m.marker_uid,
CONCAT(m.marker_name,' (',ms.value,')') AS name,
CONCAT(map.map_name,' ',cast(mim.start_position as char),' cM') as position,
a.missing,
a.aa_freq,
a.ab_freq,
a.bb_freq,
a.total,
a.monomorphic,
ROUND(a.maf, 2) AS maf
FROM
markers m INNER JOIN (allele_frequencies a, marker_synonyms ms, markers_in_maps mim, map)
ON m.marker_uid = a.marker_uid
AND m.marker_uid = ms.marker_uid
AND m.marker_uid = mim.marker_uid
AND mim.map_uid = map.map_uid
AND a.experiment_uid = '".$experiment_uid."'
WHERE
a.missing / a.total <= '".$max_missing."'
AND a.maf >= '".$min_maf."'
AND ms.marker_synonym_type_uid = '1'
GROUP BY name
";
$res_Gen_Stat = mysql_query($sql_Gen_Stat) or die(mysql_error());
?>
<style type="text/css">
th {background: #5B53A6 !important; color: white !important; border-left: 2px solid #5B53A6}
table {background: none; border-collapse: collapse}
td {border: 1px solid #eee !important;}
h3 {border-left: 4px solid #5B53A6; padding-left: .5em;}
</style>
<div style="width: 840px;"><b>Summary:</b><br><br>
<table >
<tr>
<th style="width: 180px;" > Marker Name </th>
<th style="width: 100px;" > Map Name and Position </th>
<th style="width: 60px;" > Missing </th>
<th style="width: 100px;" > AA Freq </th>
<th style="width: 100px;" > AB Freq </th>
<th style="width: 100px;"> BB Freq </th>
<th style="width: 100px;" > Total </th>
<th style="width: 20px;" > Monomorphic </th>
<th style="width: 100px;" > MAF </th>
</tr>
</table>
</div>
<div style="padding: 0; width: 840px; height: 400px; overflow: scroll; border: 1px solid #5b53a6; clear: both">
<?php
echo "<table>";
while ($row_Gen_Stat = mysql_fetch_assoc($res_Gen_Stat))
{
?>
<tr>
<td style="width: 100px;" >
<?php echo $row_Gen_Stat['name']; ?>
</td>
<td style="width: 100px;" >
<?php echo $row_Gen_Stat['position']; ?>
</td>
<td style="width: 80px;" >
<?php echo $row_Gen_Stat['missing']; ?>
</td>
<td style="width: 100px;" >
<?php echo $row_Gen_Stat['aa_freq']; ?>
</td>
<td style="width: 100px;" >
<?php echo $row_Gen_Stat['ab_freq']; ?>
</td>
<td style="width: 100px;" >
<?php echo $row_Gen_Stat['bb_freq']; ?>
</td>
<td style="width: 100px;">
<?php echo $row_Gen_Stat['total']; ?>
</td>
<td style="width: 120px;">
<?php echo $row_Gen_Stat['monomorphic']; ?>
</td>
<td style="width: 70px;">
<?php echo $row_Gen_Stat['maf']; ?>
</td>
</tr>
<?php
}/* End of while loop*/
?>
</table>
</div>
<br/>
<br/><center><input type="button" value="Download Allele Data" onclick="javascript:load_tab_delimiter('<?php echo $experiment_uid ?>','<?php echo $max_missing ?>','<?php echo $min_maf ?>');"/></center>
<br><br>
<?php
echo "<table>";
echo "<tr> <td>Manifest File Name</td><td><a href='/tht/raw/genotype/".$row_Gen_Info['manifest_file_name']."'>". $row_Gen_Info['manifest_file_name']." </a></td></tr>";
echo "<tr> <td>Cluster File Name</td><td><a href='/tht/raw/genotype/".$row_Gen_Info['cluster_file_name']."'>".$row_Gen_Info['cluster_file_name']."</a></td></tr>";
echo "<tr> <td>Sample Sheet File Name</td><td><a href='/tht/raw/genotype/".$row_Gen_Info['sample_sheet_filename']."'>".$row_Gen_Info['sample_sheet_filename']."</a></td></tr>";
echo "<tr> <td>Raw Data File Archive </td><td><a href='/tht/raw/genotype/".$row_Gen_Info['raw_datafile_archive']."'>".$row_Gen_Info['raw_datafile_archive']."</a></td></tr>";
echo "<tr> <td>OPA Name</td><td>".$row_Gen_Info['OPA_name']."</td></tr>";
echo "<tr> <td>Experiment Short Name</td><td>".$experiment_short_name."</td></tr>";
echo "<tr> <td>Data Program Code</td><td>".$data_program_code."</td></tr>";
echo "<tr> <td>Data Program Name</td><td>".$data_program_name."</td></tr>";
echo "</table>";
echo "<br>";
?>
<div style="padding-left: 20px;border: 1px">
<p style="font-style: italic">There are <?php echo ($num_mark) ?> distinct markers.</p>
<p style="font-style: italic"><?php echo ($num_maf) ?> markers have a minor allele frequency larger than <?php echo ($min_maf) ?>%.</p>
<p style="font-style: italic"><?php echo ($num_miss) ?> markers are missing at least <?php echo ($max_missing) ?> % of measurements.</p>
Maximum Missing Data (%): <input type="text" name="mm" id="mm" size="3" value="<?php echo ($max_missing) ?>" /> |
Minimum MAF (%): <input type="text" name="mmaf" id="mmaf" size="3" value="<?php echo ($min_maf) ?>" /> |
<input type="button" value="Refresh" onclick="javascript:mrefresh('<?php echo $trial_code ?>');return false;" />
</div><br><br>
<?php
} /* end of else */
} /* End of function type_DataInformation*/
private function type_Tab_Delimiter()
{
$experiment_uid = $_GET['expuid'];
$max_missing = 100;//IN PERCENT
if (isset($_GET['mm']) && !empty($_GET['mm']) && is_numeric($_GET['mm']))
$max_missing = $_GET['mm'];
if ($max_missing>100)
$max_missing = 100;
elseif ($max_missing<0)
$max_missing = 0;
$min_maf = 0;//IN PERCENT
if (isset($_GET['mmaf']) && !empty($_GET['mmaf']) && is_numeric($_GET['mmaf']))
$min_maf = $_GET['mmaf'];
if ($min_maf>100)
$min_maf = 100;
elseif ($min_maf<0)
$min_maf = 0;
//$firephp = FirePHP::getInstance(true);
$outputheader = '';
$output = '';
$doneheader = false;
$delimiter ="\t";
//get lines and filter to get a list of markers which meet the criteria selected by the user
$sql_mstat = "SELECT af.marker_uid as marker, m.marker_name as name, SUM(af.aa_cnt) as sumaa, SUM(af.missing)as summis, SUM(af.bb_cnt) as sumbb,
SUM(af.total) as total, SUM(af.ab_cnt) AS sumab
FROM allele_frequencies AS af, markers as m
WHERE m.marker_uid = af.marker_uid
AND af.experiment_uid ='".$experiment_uid."'
group by af.marker_uid";
$res = mysql_query($sql_mstat) or die(mysql_error());
$num_mark = mysql_num_rows($res);
$num_maf = $num_miss = 0;
while ($row = mysql_fetch_array($res)){
$maf = round(100*min((2*$row["sumaa"]+$row["sumab"])/$row["total"],($row["sumab"]+2*$row["sumbb"])/$row["total"]),1);
$miss = round(100*$row["summis"]/$row["total"],1);
if (($maf>=$min_maf)AND ($miss<=$max_missing)) {
$marker_names[] = $row["name"];
$outputheader .= $delimiter.$row["name"];
$marker_uid[] = $row["marker"];
}
}
$marker_uid = implode(",",$marker_uid);
$lookup = array(
'AA' => 'AA',
'BB' => 'BB',
'--' => '-',
'AB' => 'AB'
);
// get a list of marker names which meet the criteria selected by the user
$sql_mstat = "SELECT marker_name as name
FROM markers
WHERE marker_uid IN ($marker_uid)";
$res = mysql_query($sql_mstat) or die(mysql_error());
while ($row = mysql_fetch_array($res)){
$marker_names[] = $row["name"];
}
$nelem = count($marker_uid);
// make an empty line with the markers as array keys, set default value
// to the default missing value for either qtlminer or tassel
// places where the lines may have different values
$empty = array_combine($marker_names,array_fill(0,$nelem,'NA'));
$sql = "SELECT lr.line_record_name, m.marker_name AS name,
CONCAT(a.allele_1,a.allele_2) AS value
FROM
markers as m,
line_records as lr,
alleles as a,
tht_base as tb,
genotyping_data as gd
WHERE
a.genotyping_data_uid = gd.genotyping_data_uid
AND m.marker_uid = gd.marker_uid
AND gd.marker_uid IN ($marker_uid)
AND tb.line_record_uid = lr.line_record_uid
AND gd.tht_base_uid = tb.tht_base_uid
AND tb.experiment_uid ='".$experiment_uid."'
ORDER BY lr.line_record_name, m.marker_uid";
$last_line = "some really silly name that noone would call a plant";
$res = mysql_query($sql) or die(mysql_error());
$outarray = $empty;
$cnt = $num_lines = 0;
while ($row = mysql_fetch_array($res)){
//first time through loop
if ($cnt==0) {
$last_line = $row['line_record_name'];
}
if ($last_line != $row['line_record_name']){
// Close out the last line
$output .= "$last_line\t";
$outarray = implode($delimiter,$outarray);
$output .= $outarray."\n";
//reset output arrays for the next line
$outarray = $empty;
$mname = $row['name'];
$outarray[$mname] = $lookup[$row['value']];
$last_line = $row['line_record_name'];
$num_lines++;
} else {
$mname = $row['name'];
$outarray[$mname] = $lookup[$row['value']];
}
$cnt++;
}
//save data from the last line
$output .= "$last_line$delimiter";
$outarray = implode($delimiter,$outarray);
$output .= $outarray."\n";
$num_lines++;
echo $outputheader."\n".$output;
}
} /* End of class*/
?>