-
Notifications
You must be signed in to change notification settings - Fork 3
/
modify_pedigree.php
executable file
·327 lines (259 loc) · 16.2 KB
/
modify_pedigree.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
<?php
$body_class = "no-sidebar";
require 'php_header.php'; // Require the PHP header housing required PHP functions
require 'html_header.php'; // Require the HTML header housing the HTML structure of the page
?>
</div>
<!-- Main -->
<div class="wrapper">
<div class="container" id="main">
<!-- Content -->
<article id="content">
<header>
<h2>Let's change things up.</h2>
<p>You can modify the pedigree information of any database you have access to on the web without needing to create a pedigree (ped) file. Simply modify and submit the form below and the database will be updated.</p>
</header>
<?php
// Check whether the user is in the group specified
if (isset($_GET["group"])) {
$user_in_group = is_user_in_group($_SESSION["logged_in"]["email"], $_GET["group"]);
} elseif (isset($_POST["group"])) {
$user_in_group = is_user_in_group($_SESSION["logged_in"]["email"], $_POST["group"]);
}
// Make sure the user is logged in
if (!is_user_logged_in()) {
error("You must be logged in to make modifications to databases.");
} elseif (!isset($user_in_group) || $user_in_group !== true) {
error("You do not have access to the group specified.");
} else {
#############################################
# IF THE PEDIGREE MODIFICATION FORM HAS BEEN SUBMITTED
#############################################
if (isset($_POST["database"], $_POST["num_samples"], $_POST["group"])) {
$form_error = 0;
// Make sure there are more than 0 samples
if ($_POST["num_samples"] > 0) {
// Go through every sample that should have been submitted
for ($i = 1; $i <= $_POST["num_samples"]; $i++) {
// Make sure the sample name has been set (required for phenotype and gender)
if (isset($_POST["sample_".$i])) {
// If the sample name contains periods (.), that will come through in the value of $_POST["sample_".$i], however, for the _phenotype, _gender, etc PHP converts these dots to underscores, so do a preg replace to for compatibility
$safe_php_sample_name = preg_replace("/\./", "_", $_POST["sample_".$i]);
// Make sure the phenotype and gender have been submitted for the sample
if (!isset($_POST[$safe_php_sample_name."_phenotype"]) || !isset($_POST[$safe_php_sample_name."_gender"]) || !isset($_POST[$safe_php_sample_name."_family"])) {
error("A phenotype, gender or family name have not been supplied for sample ID ".$i."(".$_POST["sample_".$i].").");
$form_error = 1; // Set the form error flag to true to stop further processing
break; // Stop the loop execution
}
} else {
error("Sample name not specified for sample ID ".$i);
$form_error = 1; // Set the form error flag to true to stop further processing
break; // Stop the loop execution
}
}
} else {
error("The number of samples must be 1 or more.");
}
// If an error has occurred with the from, don't go any further with processing it
if ($form_error == 1) {
error("An error has occurred with processing the pedigree modification page. Please go back and try again.");
} else {
// Create a path to a temporary ped file based on an md5 hash of the database name
$output_filename = "/tmp/".md5($_POST["database"]).".ped";
// Open the temporary file for writing
if ($output = fopen($output_filename, "w")) {
// Go through every sample that was submitted
for ($i = 1; $i <= $_POST["num_samples"]; $i++) {
// If the sample name contains periods (.), that will come through in the value of $_POST["sample_".$i], however, for the _phenotype, _gender, etc PHP converts these dots to underscores, so do a preg replace to for compatibility
$safe_php_sample_name = preg_replace("/\./", "_", $_POST["sample_".$i]);
// Set the gender to the PED file equivalent
if ($_POST[$safe_php_sample_name."_gender"] == "male") {
$gender = "1";
} elseif ($_POST[$safe_php_sample_name."_gender"] == "female") {
$gender = "2";
} else {
$gender = "3";
}
// Set the phenotype to the PED file equivalent
if ($_POST[$safe_php_sample_name."_phenotype"] == "affected") {
$phenotype = "2";
} elseif ($_POST[$safe_php_sample_name."_phenotype"] == "unaffected") {
$phenotype = "1";
} elseif ($_POST[$safe_php_sample_name."_phenotype"] == "unknown") {
$phenotype = "-9";
}
// If the family submitted was empty, set it to 0 (i.e. None value)
if ($_POST[$safe_php_sample_name."_family"] == "") {
$family = "0";
} else {
$family = htmlspecialchars($_POST[$safe_php_sample_name."_family"], ENT_QUOTES, 'UTF-8');
}
// Write each sample to the temporary PED file
fwrite($output, $family."\t".$_POST["sample_".$i]."\t0\t0\t".$gender."\t".$phenotype."\n");
}
// Close the temporary file
fclose($output);
// Annotate the Gemini database with the new information
exec($GLOBALS["configuration_file"]["gemini"]["binary"].' amend --sample '.$output_filename.' '.$GLOBALS["configuration_file"]["gemini"]["db_dir"].'/'.$_POST["group"].'/'.escape_database_filename($_POST["database"]), $query_result, $exit_code); # Execute the Gemini query
if ($exit_code == 0) {
log_website_event("Manually modified pedigree information using the web form for database '".$_POST['database']."'");
echo "<h3>Successfully updated the pedigree annotation for the database ".$_POST['database']."!</h3>";
echo "<br><br><a href=\"analysis_selection?group=".$_POST["group"]."&query_db=".$_POST["database"]."&hasped=Yes\" class=\"button\">Start filtering variants in this database</a>";
echo "<br><br><a href=\"modify_pedigree?group=".$_POST["group"]."&query_db=".$_POST["database"]."\" class=\"button\" style=\"padding: 0.4em 1em 0.4em 1em;\">Back to modifying this database</a>";
echo "<br><br><a href=\"databases?restart=true\" class=\"button\" style=\"padding: 0.4em 1em 0.4em 1em;\">Back to databases</a>";
} else {
error("Could not update annotation. GEMINI error.");
}
// Delete the temporary PED file
unlink($output_filename);
// Delete the TSV cache for the database forcing a refresh of the PED status
delete_database_cache($GLOBALS["configuration_file"]["gemini"]["db_dir"]."/".$_POST["group"]."/".$_POST["database"], "tsv_only"); // Only delete the TSV with the second parameter, don't want to delete the DB summaries
} else {
error("Cannot create temporary ped file.");
}
}
#############################################
# IF A DATABASE HAS BEEN SUPPLIED FOR EDITING
#############################################
} elseif (isset($_GET["query_db"], $_GET["group"])) {
// Extract familial information from the database for each family
if ($family_info = extract_familial_information($_GET["group"]."/".$_GET["query_db"])) {
echo "<div class=\"row\">";
echo "<section style=\"padding-top:20px;\">";
echo "<h3>Database selected</h3>";
echo "<p>".htmlspecialchars($_GET["query_db"], ENT_QUOTES, 'UTF-8')."</p>";
echo "</section>";
echo "</div>";
echo "<section style=\"padding-top:20px;\">";
echo "<h3>View and modify pedigree information</h3>";
echo "<form method=\"post\" style=\"padding-top:10px;\" action=\"modify_pedigree\">";
echo "<input type=\"hidden\" name=\"group\" value=\"".htmlspecialchars($_GET["group"], ENT_QUOTES, 'UTF-8')."\">"; // Hidden field for the database to modify
echo "<input type=\"hidden\" name=\"database\" value=\"".htmlspecialchars($_GET["query_db"], ENT_QUOTES, 'UTF-8')."\">"; // Hidden field for the database to modify
echo "<div class=\"row 25%\">";
echo "<div class=\"3u 3u(mobile)\">";
echo "Sample";
echo "</div>";
echo "<div class=\"3u 3u(mobile)\">";
echo "Family";
echo "</div>";
echo "<div class=\"3u 3u(mobile)\">";
echo "Phenotype";
echo "</div>";
echo "<div class=\"2u$ 2u(mobile)\">";
echo "Gender";
echo "</div>";
echo "</div>";
$sample_counter = 1; // Counter for the number of samples - to be used in a hidden submit field
// Define a variable to store the family's pedigree for output to a PED file
$ped_output = "";
// Go through every family
foreach (array_keys($family_info) as $family) {
// Go through every sample
foreach (array_keys($family_info[$family]) as $sample) {
$safe_php_sample_name = htmlspecialchars($sample, ENT_QUOTES, 'UTF-8');
echo "<div class=\"row 25%\">";
// The static sample name
echo "<div class=\"3u 3u(mobile)\">";
echo "<p style=\"padding-top:0.5em; min-width: 200px;\">".$safe_php_sample_name."</p>";
echo "<input type=\"hidden\" name=\"sample_".$sample_counter."\" value=\"".$safe_php_sample_name."\">";
$sample_counter++; // Iterate the sample counter for the next sample
echo "</div>";
// The family name input box
echo "<div class=\"3u 3u(mobile)\">";
echo "<input name=\"".$safe_php_sample_name."_family\" type=\"text\" style=\"padding: 0.5em; width:90%;\" value=\"".htmlspecialchars($family, ENT_QUOTES, 'UTF-8')."\">";
echo "</div>";
// The phenotype radios
echo "<div class=\"3u 3u(mobile)\">";
echo "<input type=\"radio\" id=\"".$safe_php_sample_name."_phenotype_affected\" name=\"".$safe_php_sample_name."_phenotype\" value=\"affected\"";
// Check the radio if the sample is affected
if (is_affected($family_info[$family][$sample]["phenotype"])) {
echo " checked=\"\"";
}
echo ">";
echo "<label for=\"".$safe_php_sample_name."_phenotype_affected\" style=\"width:80px;\">Affected</label>"; // Radio label
echo "<input type=\"radio\" id=\"".$safe_php_sample_name."_phenotype_unaffected\" name=\"".$safe_php_sample_name."_phenotype\" value=\"unaffected\"";
// Check the radio if the sample is unaffected
if (is_unaffected($family_info[$family][$sample]["phenotype"])) {
echo " checked=\"\"";
}
echo ">";
echo "<label for=\"".$safe_php_sample_name."_phenotype_unaffected\" style=\"width:80px;\">Unaffected</label>"; // Radio label
echo "<input type=\"radio\" id=\"".$safe_php_sample_name."_phenotype_unknown\" name=\"".$safe_php_sample_name."_phenotype\" value=\"unknown\"";
// Check the radio if the sample is unknown
if (is_unknown_phenotype($family_info[$family][$sample]["phenotype"])) {
echo " checked=\"\"";
}
echo ">";
echo "<label for=\"".$safe_php_sample_name."_phenotype_unknown\" style=\"width:80px;\">Unknown</label>"; // Radio label
echo "</div>";
// The gender radios
echo "<div class=\"2u$ 2u(mobile)\">";
echo "<input type=\"radio\" id=\"".$safe_php_sample_name."_gender_male\" name=\"".$safe_php_sample_name."_gender\" value=\"male\"";
// Check the radio if the sample is male
if ($family_info[$family][$sample]["sex"] == "1") {
echo " checked=\"\"";
}
echo ">";
echo "<label for=\"".$safe_php_sample_name."_gender_male\" style=\"width:40px;\">M</label>"; // Radio label
echo "<input type=\"radio\" id=\"".$safe_php_sample_name."_gender_female\" name=\"".$safe_php_sample_name."_gender\" value=\"female\"";
// Check the radio if the sample is female
if ($family_info[$family][$sample]["sex"] == "2") {
echo " checked=\"\"";
}
echo ">";
echo "<label for=\"".$safe_php_sample_name."_gender_female\" style=\"width:40px;\">F</label>"; // Radio label
echo "<input type=\"radio\" id=\"".$safe_php_sample_name."_gender_unknown\" name=\"".$safe_php_sample_name."_gender\" value=\"unknown\"";
// Check the radio if the sample is not male or female (i.e. unknown)
if ($family_info[$family][$sample]["sex"] != "1" && $family_info[$family][$sample]["sex"] != "2") {
echo " checked=\"\"";
}
echo ">";
echo "<label for=\"".$safe_php_sample_name."_gender_unknown\" style=\"width:40px;\">U</label>"; // Radio label
echo "</div>";
echo "</div>";
#############################################
# PROCESS AND SAVE FAMILIAL INFORMATION IN PED FORMAT
#############################################
// Check whether the gender of the sample has not been set and change it to the unknown value if so
if ($family_info[$family][$sample]["sex"] == "None") {
$sex_ped_output = "-9";
} else {
$sex_ped_output = $family_info[$family][$sample]["sex"];
}
// Check whether the phenotype of the sample has not been set and change it to the unknown value if so
if ($family_info[$family][$sample]["phenotype"] == "None") {
$phenotype_ped_output = "-9";
} else {
$phenotype_ped_output = $family_info[$family][$sample]["phenotype"];
}
// Save a row to the pedigree output file variable in case the user wants to download it as a file
$ped_output .= $family."\t".$sample."\t0\t0\t".$sex_ped_output."\t".$phenotype_ped_output."\n";
}
}
echo "<input type=\"hidden\" name=\"num_samples\" value=\"".($sample_counter - 1)."\">";
echo "<div class=\"row 50%\">";
echo "<div class=\"12u\">";
echo "<ul class=\"actions\">";
echo "<li><input type=\"submit\" value=\"Modify pedigree\" /></li>";
echo "</ul>";
echo "</div>";
echo "</div>";
echo "</form>";
// Form for downloading the pedigree as a file
echo "<form method=\"post\" action=\"download_pedigree\">";
echo "<input type=\"submit\" value=\"Download current pedigree as PED file\" style=\"padding: 0.4em 1em 0.4em 1em;\">";
echo "<input type=\"hidden\" name=\"filename\" value=\"".$_GET["query_db"]."\">"; // Hidden field for the database filename to use for the PED filename
echo "<input type=\"hidden\" name=\"content\" value=\"".$ped_output."\">"; // Hidden field for the database to modify
echo "</form><br>";
echo "<a href=\"databases?restart=true\" class=\"button\" style=\"padding: 0.4em 1em 0.4em 1em;\">Back to databases</a>";
echo "</section>";
}
}
}
?>
</article>
</div>
</div>
<?php
require 'html_footer.php';
?>