-
Notifications
You must be signed in to change notification settings - Fork 0
/
genes.html
329 lines (241 loc) · 7.62 KB
/
genes.html
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
<!doctype html>
<html lang="en">
<head>
<title>Quick gene lookup</title>
<meta charset="utf-8">
<meta name="viewport" content="width=device-width, initial-scale=1">
<script src="https://ajax.googleapis.com/ajax/libs/jquery/3.4.1/jquery.min.js"></script>
<script src="https://cdnjs.cloudflare.com/ajax/libs/popper.js/1.14.7/umd/popper.min.js" integrity="sha384-UO2eT0CpHqdSJQ6hJty5KVphtPhzWj9WO1clHTMGa3JDZwrnQq4sF86dIHNDz0W1" crossorigin="anonymous"></script>
<link rel="stylesheet" href="https://stackpath.bootstrapcdn.com/bootstrap/4.3.1/css/bootstrap.min.css" integrity="sha384-ggOyR0iXCbMQv3Xipma34MD+dH/1fQ784/j6cY/iJTQUOhcWr7x9JvoRxT2MZw1T" crossorigin="anonymous">
<script src="https://stackpath.bootstrapcdn.com/bootstrap/4.3.1/js/bootstrap.min.js" integrity="sha384-JjSmVgyd0p3pXB1rRibZUAYoIIy6OrQ6VrjIEaFf/nJGzIxFDsf4x0xIM+B07jRM" crossorigin="anonymous"></script>
<link href="https://unpkg.com/tabulator-tables@4.2.7/dist/css/bootstrap/tabulator_bootstrap4.min.css" rel="stylesheet">
<script type="text/javascript" src="https://unpkg.com/tabulator-tables@4.2.7/dist/js/tabulator.min.js"></script>
</head>
<body>
<div class="container mt-3">
<div class="row mb-3">
<div class="col-12 col-md-3 themed-grid-col">
<div class="form-group">
<label for="textarea">Paste a list of genes:</label>
<textarea class="form-control" id="textarea" rows="5"></textarea>
<button id="button-search" type="button" class="btn btn-primary mt-2">Search</button>
</div>
</div>
<div class="col-12 col-md-9 themed-grid-col">
<label class="mr-sm-2" for="select-api">Choose an API:</label>
<select class="custom-select mr-sm-2" id="select-api">
<option value="ensembl">Ensembl</option>
<option value="mygene" selected>MyGene.info</option>
</select>
<div id="example-table" class="mt-3"></div>
<div class="progress mt-2">
<div id="progress-api" class="progress-bar" role="progressbar" aria-valuenow="0" aria-valuemin="0" aria-valuemax="100"></div>
</div>
<div id="state" class="alert mt-2 mb-2"></div>
<button id="download-tsv" type="button" class="btn btn-primary">Download TSV</button>
</div>
</div>
</div>
<script>
var oldVal = "";
var selected_api = "mygene";
var x = null;
var table = null;
var state = {};
var fileFormatter = function(columns, data, options, setFileContents){
var titles = [];
var fields = [];
var delimiter = "\t";
columns.forEach(function(column){
if(column.field){
titles.push(column.title)
fields.push(column.field)
}
});
var fileContents = [titles.join(delimiter)];
data.data.forEach(function(row){
var rowData = [];
fields.forEach(function(field){
rowData.push(row[field]);
})
fileContents.push(rowData.join(delimiter));
});
setFileContents(fileContents.join("\n"), "text/plain");
}
$("#download-tsv").click(function(){
table.download(fileFormatter, selected_api + "-data.tsv");
});
$("#button-search").on("click", function() {
var currentVal = $("#textarea").val();
if (currentVal == oldVal) {
return;
}
oldVal = currentVal;
do_query(oldVal);
});
$("#select-api").on("change", function() {
selected_api = this.value;
do_query(oldVal);
});
var table = new Tabulator("#example-table", {
height: 300,
layout: "fitColumns",
layoutColumnsOnNewData: true,
columns: [
{title:"query", field:"query"},
{title:"symbol", field:"symbol"},
{title:"id", field:"_id"},
{title:"name", field:"name", width: 200},
{title:"score", field:"_score"},
{title:"taxid", field:"taxid"}
]
});
function do_query(q) {
if (selected_api === "mygene") {
query_mygene(q);
} else if (selected_api === "ensembl") {
query_ensembl(q);
}
}
function update_state() {
let progress = Math.round(
100 * state.n_received / state.n_queries
);
if (state.n_queries === state.n_received) {
var s = "Done. ";
$("#state").text(
s + state.n_queries + " queries, " + state.n_results + " results, " +
(state.n_queries - state.n_results) + ' not found'
);
$("#state")
.removeClass("alert-success")
.removeClass("alert-warning")
.removeClass("alert-info");
if (state.n_results == state.n_queries) {
$("#state").addClass("alert-success");
} else {
$("#state").addClass("alert-warning");
}
} else {
var s = "Loading. ";
$("#state").text(
s + state.n_queries + " queries, " + state.n_results + " results"
);
$("#state").addClass("alert-info");
}
$('#progress-api')
.attr('aria-valuenow', progress)
.css('width', progress + "%");
}
function parse_queries(s) {
var queries = s
.replace(/['"]/g, "")
.split(/[\r?\n ,]/)
.filter((d) => d !== "" && d !== "-");
return queries;
}
function query_mygene(q) {
var queries = parse_queries(q);
table = new Tabulator("#example-table", {
height: 300,
layout: "fitColumns",
layoutColumnsOnNewData: true,
clipboardCopySelector:"table",
columns: [
{title:"order", field:"i", width: 90},
{title:"query", field:"query", width: 110},
{title:"symbol", field:"symbol", width: 110},
{title:"id", field:"_id", width: 110},
{title:"name", field:"name", width: 200},
{title:"score", field:"_score", width: 110},
{title:"taxid", field:"taxid", width: 110}
]
});
state.n_queries = queries.length;
state.n_received = 0;
state.n_results = 0;
update_state();
var url = "https://mygene.info/v3/query";
var cb = function(i, query, data) {
state.n_received += 1;
x = data;
console.log(data);
if (data.max_score) {
var d = data.hits[0];
d.query = query;
d.i = i;
table.addData([d]);
state.n_results += 1;
} else {
var empty = {"i": i, "query": query, "symbol": "", "_id": "", "name": "", "_score": "", "taxid": ""};
table.addData([empty]);
}
table.setSort([{column: "i", dir: "asc"}]);
update_state();
};
for (let i = 0; i < queries.length; i++) {
var query = queries[i];
console.log(query);
$.getJSON(
url,
{"q": query, "species": "human"},
(data) => {
return cb(i + 1, queries[i], data);
}
);
}
}
function query_ensembl(q) {
var queries = parse_queries(q);
table = new Tabulator("#example-table", {
height: 300,
layout: "fitColumns",
layoutColumnsOnNewData: true,
columnMinWidth: 110,
columns: [
{title: "order", field: "i", width: 20},
{title:"query", field:"query"},
{title:"id", field:"id"},
{title:"type", field:"type"}
]
});
state.n_queries = queries.length;
state.n_received = 0;
state.n_results = 0;
update_state();
var url = "https://rest.ensembl.org/xrefs/symbol/homo_sapiens/";
var cb = function(i, query, data) {
x = data;
state.n_received += 1;
if (data.length) {
var d = data[0];
d.query = query;
d.i = i;
console.log(d);
table.addData([d]);
state.n_results += 1;
} else {
var empty = {"i": i, "query": query, "id": "", "type": ""};
table.addData([empty]);
}
table.setSort([{column: "i", dir: "asc"}]);
update_state();
};
for (let i = 0; i < queries.length; i++) {
var query = queries[i];
console.log(query);
$.getJSON(
url + query,
{"content-type": "application/json"},
(d) => {
return cb(i + 1, queries[i], d);
}
);
}
}
$("#textarea").val('STAT1 IRF8 ISG15 NEMO');
oldVal = $("#textarea").val();
do_query(oldVal);
</script>
</body>
</html>