sealion/test_genbank_parser.html at main · artic-network/sealion · GitHub

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
<!DOCTYPE html>
<html lang="en">
<head>
    <meta charset="UTF-8">
    <meta name="viewport" content="width=device-width, initial-scale=1.0">
    <title>GenBank Parser Test</title>
    <style>
        body {
            font-family: 'Segoe UI', Tahoma, Geneva, Verdana, sans-serif;
            max-width: 1200px;
            margin: 0 auto;
            padding: 20px;
            background: #f5f5f5;
        }
        .container {
            background: white;
            padding: 30px;
            border-radius: 8px;
            box-shadow: 0 2px 8px rgba(0,0,0,0.1);
        }
        h1 {
            color: #333;
            border-bottom: 3px solid #4A90E2;
            padding-bottom: 10px;
        }
        h2 {
            color: #555;
            margin-top: 30px;
        }
        .input-section {
            margin: 20px 0;
        }
        .file-input {
            margin: 10px 0;
            padding: 10px;
            border: 2px dashed #ccc;
            border-radius: 4px;
            background: #fafafa;
        }
        input[type="file"] {
            display: block;
            margin: 10px 0;
        }
        button {
            background: #4A90E2;
            color: white;
            border: none;
            padding: 10px 20px;
            border-radius: 4px;
            cursor: pointer;
            font-size: 14px;
            margin: 5px 5px 5px 0;
        }
        button:hover {
            background: #357ABD;
        }
        button:disabled {
            background: #ccc;
            cursor: not-allowed;
        }
        .output {
            background: #f8f9fa;
            border: 1px solid #ddd;
            border-radius: 4px;
            padding: 15px;
            margin: 15px 0;
            max-height: 500px;
            overflow-y: auto;
        }
        pre {
            margin: 0;
            white-space: pre-wrap;
            word-wrap: break-word;
            font-family: 'Monaco', 'Courier New', monospace;
            font-size: 12px;
        }
        .success {
            color: #28a745;
            font-weight: bold;
        }
        .error {
            color: #dc3545;
            font-weight: bold;
        }
        .info-box {
            background: #e7f3ff;
            border-left: 4px solid #4A90E2;
            padding: 15px;
            margin: 20px 0;
        }
        .stats {
            display: grid;
            grid-template-columns: repeat(auto-fit, minmax(200px, 1fr));
            gap: 15px;
            margin: 20px 0;
        }
        .stat-card {
            background: #f8f9fa;
            padding: 15px;
            border-radius: 4px;
            border: 1px solid #dee2e6;
        }
        .stat-label {
            font-size: 12px;
            color: #6c757d;
            text-transform: uppercase;
        }
        .stat-value {
            font-size: 24px;
            font-weight: bold;
            color: #333;
            margin-top: 5px;
        }
        .cds-list {
            list-style: none;
            padding: 0;
        }
        .cds-item {
            background: #fff;
            border: 1px solid #dee2e6;
            border-radius: 4px;
            padding: 10px;
            margin: 8px 0;
        }
        .cds-gene {
            font-weight: bold;
            color: #4A90E2;
            font-size: 16px;
        }
        .cds-product {
            color: #666;
            margin: 5px 0;
        }
        .cds-coords {
            font-family: monospace;
            color: #999;
            font-size: 12px;
        }
    </style>
</head>
<body>
    <div class="container">
        <h1>GenBank File Parser Utility</h1>

        <div class="info-box">
            <strong>Purpose:</strong> This utility parses GenBank format files (.gb) and converts them to the reference genome JSON format used by Sealion viewer.
            You can use this to load reference genomes directly from GenBank files instead of manually creating JSON files.
        </div>

        <div class="input-section">
            <h2>Select GenBank File</h2>
            <div class="file-input">
                <input type="file" id="fileInput" accept=".gb,.gbk,.genbank" />
                <button id="parseBtn" disabled>Parse GenBank File</button>
                <button id="downloadBtn" disabled>Download as JSON</button>
            </div>
        </div>

        <div id="statusDiv"></div>

        <div id="statsDiv"></div>

        <div id="cdsDiv"></div>

        <div id="outputDiv"></div>

        <h2>Usage Example</h2>
        <div class="output">
            <pre>// In your code:
const fileInput = document.getElementById('myFileInput');
fileInput.addEventListener('change', async (e) => {
  const file = e.target.files[0];
  const text = await file.text();

  // Parse GenBank file
  const refGenome = SealionUtils.parseGenBankFile(text);

  if (refGenome) {
    // Add to alignment
    alignment.addReferenceGenome(refGenome);
    console.log('Loaded reference:', refGenome.accession);
  }
});</pre>
        </div>
    </div>

    <!-- Load the utility -->
    <script src="ui/js/utils.js"></script>

    <script>
        let parsedData = null;

        const fileInput = document.getElementById('fileInput');
        const parseBtn = document.getElementById('parseBtn');
        const downloadBtn = document.getElementById('downloadBtn');
        const statusDiv = document.getElementById('statusDiv');
        const statsDiv = document.getElementById('statsDiv');
        const cdsDiv = document.getElementById('cdsDiv');
        const outputDiv = document.getElementById('outputDiv');

        fileInput.addEventListener('change', (e) => {
            parseBtn.disabled = !e.target.files[0];
            downloadBtn.disabled = true;
            parsedData = null;
            statusDiv.innerHTML = '';
            statsDiv.innerHTML = '';
            cdsDiv.innerHTML = '';
            outputDiv.innerHTML = '';
        });

        parseBtn.addEventListener('click', async () => {
            const file = fileInput.files[0];
            if (!file) return;

            statusDiv.innerHTML = '<p>Parsing...</p>';

            try {
                const text = await file.text();
                parsedData = SealionUtils.parseGenBankFile(text);

                if (parsedData) {
                    statusDiv.innerHTML = '<p class="success">✓ Successfully parsed GenBank file!</p>';
                    downloadBtn.disabled = false;
                    displayResults(parsedData);
                } else {
                    statusDiv.innerHTML = '<p class="error">✗ Failed to parse GenBank file. See console for details.</p>';
                }
            } catch (e) {
                statusDiv.innerHTML = `<p class="error">✗ Error: ${e.message}</p>`;
                console.error(e);
            }
        });

        downloadBtn.addEventListener('click', () => {
            if (!parsedData) return;

            const json = JSON.stringify(parsedData, null, 2);
            const blob = new Blob([json], { type: 'application/json' });
            const url = URL.createObjectURL(blob);
            const a = document.createElement('a');
            a.href = url;
            a.download = `${parsedData.accession || 'reference'}.json`;
            document.body.appendChild(a);
            a.click();
            document.body.removeChild(a);
            URL.revokeObjectURL(url);
        });

        function displayResults(data) {
            // Display stats
            statsDiv.innerHTML = `
                <h2>Reference Genome Information</h2>
                <div class="stats">
                    <div class="stat-card">
                        <div class="stat-label">Accession</div>
                        <div class="stat-value">${data.accession || 'N/A'}</div>
                    </div>
                    <div class="stat-card">
                        <div class="stat-label">Length</div>
                        <div class="stat-value">${data.length.toLocaleString()} bp</div>
                    </div>
                    <div class="stat-card">
                        <div class="stat-label">CDS Features</div>
                        <div class="stat-value">${data.cds.length}</div>
                    </div>
                    <div class="stat-card">
                        <div class="stat-label">Organism</div>
                        <div class="stat-value" style="font-size: 14px;">${data.organism || 'N/A'}</div>
                    </div>
                </div>
                <div class="info-box">
                    <strong>Definition:</strong> ${data.definition || 'N/A'}
                </div>
            `;

            // Display CDS features
            if (data.cds.length > 0) {
                let cdsHTML = '<h2>CDS Features</h2><ul class="cds-list">';
                data.cds.forEach(cds => {
                    cdsHTML += `
                        <li class="cds-item">
                            <div class="cds-gene">${cds.gene || 'Unknown'}</div>
                            <div class="cds-product">${cds.product || ''}</div>
                            ${cds.function ? `<div class="cds-product"><em>${cds.function}</em></div>` : ''}
                            <div class="cds-coords">${cds.coordinates}</div>
                        </li>
                    `;
                });
                cdsHTML += '</ul>';
                cdsDiv.innerHTML = cdsHTML;
            }

            // Display JSON output
            outputDiv.innerHTML = `
                <h2>Generated JSON</h2>
                <div class="output">
                    <pre>${JSON.stringify(data, null, 2)}</pre>
                </div>
            `;
        }
    </script>
</body>
</html>