ChampuruOld/input.html at gh-pages · eeg-ebe/ChampuruOld · 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
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
<!Doctype html>
<html>
    <head>
        <meta charset="UTF-8" />
        <title>Champuru</title>
        <link rel="stylesheet" href="style.css"/>
        <script>
location.replace("https://eeg-ebe.github.io/ChampuruV1.5");
        </script>
    </head>
    <body>
        <a href="https://github.com/eeg-ebe/Champuru">
            <svg width="80" height="80" viewBox="0 0 250 250" style="fill:white; color:black; z-index: 51; position: absolute; top: 0; right: 0; border: 0;" aria-hidden="true"><path d="M0,0 L115,115 L130,115 L142,142 L250,250 L250,0 Z"></path><path d="M128.3,109.0 C113.8,99.7 119.0,89.6 119.0,89.6 C122.0,82.7 120.5,78.6 120.5,78.6 C119.2,72.0 123.4,76.3 123.4,76.3 C127.3,80.9 125.5,87.3 125.5,87.3 C122.9,97.6 130.6,101.9 134.4,103.2" fill="currentColor" style="transform-origin: 130px 106px;" class="octo-arm"></path><path d="M115.0,115.0 C114.9,115.1 118.7,116.5 119.8,115.4 L133.7,101.6 C136.9,99.2 139.9,98.4 142.2,98.6 C133.8,88.0 127.5,74.4 143.8,58.0 C148.5,53.4 154.0,51.2 159.7,51.0 C160.3,49.4 163.2,43.6 171.4,40.1 C171.4,40.1 176.1,42.5 178.8,56.2 C183.1,58.6 187.2,61.8 190.9,65.4 C194.5,69.0 197.7,73.2 200.1,77.6 C213.8,80.2 216.3,84.9 216.3,84.9 C212.7,93.1 206.9,96.0 205.4,96.6 C205.1,102.4 203.0,107.8 198.3,112.5 C181.9,128.9 168.3,122.5 157.7,114.1 C157.9,116.9 156.7,120.9 152.7,124.9 L141.0,136.5 C139.8,137.7 141.6,141.9 141.8,141.8 Z" fill="currentColor" class="octo-body"></path>
            </svg>
        </a>
        <div class="contentdiv">
            <h1>Champuru v1.1</h1>
            <p id="cite">Flot (2007) <strong>Champuru 1.0: a computer software for unraveling mixtures of two DNA sequences of unequal lengths.</strong> <em>Molecular Ecology Notes</em> <strong>7</strong> (6), 974-977 [<a href="http://dx.doi.org/10.1111/j.1471-8286.2007.01857.x">link</a>]</p>
            <div class="navigation">
                <a href="index.html">Back to startpage</a>
                <a href="faq.html">FAQ</a>
                <a href="tutorial.html">Tutorial</a>
                <a href="mailto: jflot@ulb.ac.be">E-Mail the author</a>
            </div>
            <h2></h2>
            <div class="importanttips">
                Champuru makes it possible to determine the haplotypes of heterozygous individuals without cloning, simply by analyzing the patterns of double peaks in the forward and reverse chromatograms.
            </div>
            <br>
            <table style="margin: 0 auto;">
                <tr class="option">
                    <td>Forward sequence:</td>
                    <td>&nbsp;&nbsp;&nbsp;</td>
                    <td><input id="forward" type="text" name="forward" style="width: 400px" autocomplete="off"/></td>
                </tr>
                <tr class="description">
                    <td colspan="3">
                        <p>The forward sequence (IUPAC one-letter code) of the heterozygous individual.</p>
                    </td>
                </tr>
                <tr class="option">
                    <td>Reverse sequence:</td>
                    <td>&nbsp;&nbsp;&nbsp;</td>
                    <td><input id="reverse" type="text" name="reverse" style="width: 400px" autocomplete="off"/></td>
                </tr>
                <tr class="description">
                    <td colspan="3">
                        <p>The reverse sequence (IUPAC one-letter code) of the heterozygous individual.<br>
                        <button onclick="reverse()">Reverse-complement</button>
                        </p>
                    </td>
                </tr>
                <tr class="option">
                    <td>Score calculation:</td>
                    <td>&nbsp;&nbsp;&nbsp;</td>
                    <td>
                        <select id="score" autocomplete="off">
                            <option value="0">Paper</option>
                            <option value="1" selected="selected">Ambiguity correction</option>
                            <option value="2">Longest length</option>
                        </select>
                    </td>
                </tr>
                <tr class="description">
                    <td colspan="3">
                        <p>Which score calculation method to use. Currently the following methods are implemented:</p>
                        <table class="descTable">
                            <tr class="even">
                                <td valign="top">Paper</td><td valign="top">The score correction method described in the Champuru 1.0 paper.</td>
                            </tr>
                            <tr class="odd">
                                <td valign="top">Ambiguity correction</td><td valign="top">A modification of the score correction method described in the Champuru 1.0 paper.
The score will get corrected for the fact that ambiguous characters (e.g. W) can match multiple other characters (e.g. A, T).
Preliminary results suggests that this score calculation method works better when the reconstructed consensus sequences contain a lot of ambiguities.
However this score correction method seems to work less good on short input sequences.
</td>
                            </tr>
                            <tr class="even">
                                <td valign="top">Longest Length</td><td valign="top">Take the longest number of consecutive matching nucleotides as score.</td>
                            </tr>
                        </table>
                    </td>
                </tr>
            </table>
            <span class="middle">
                <button onclick="calculate()">Calculate</button>
                <button onclick="resetForm()">Reset form</button>
            </span>
            <p><br></p>
            <div id="resultArea" style="display: none">
            </div>
            <p><br></p>
            <div id="exampleSection">
                <div class="noindent">
                    To get a quick feeling of how Champuru works, use the following data:<br>
                    Forward sequence: <span class="sequence" id="example1forward">ATSYKRMKY</span><br>
                    Reverse sequence: <span class="sequence" id="example1reverse">WWKCTGAST</span><br>
                    <button href="#" onclick="load(1)">Copy data to input fields</button><br>
                </div>
                <br>
                <div class="noindent">
                    This example may be used in order to explain how Champuru can resolve ambiguities in the consensus sequences (Step 3):<br>
                    Forward sequence: <span class="sequence" id="example2forward">CTRAATTCAAATCACACTCGCGAAAWYMWKRAA</span><br>
                    Reverse sequence: <span class="sequence" id="example2reverse">YWRAWTYMAAWYMMMMYYSSSRAAATCATGAA</span><br>
                    <button href="#" onclick="load(2)">Copy data to input fields</button><br>
                </div>
                <br>
                <div class="noindent">
                    A more complex example with lots of ambiguities in the consensus sequence:<br>
                    Forward sequence: <span class="sequence" id="example3forward">AAATSSYKRWTYMMMMMRSSRMSGSCCYWRSMWWMCCSRRGGRWYSGRARR</span><br>
                    Reverse sequence: <span class="sequence" id="example3reverse">MRMTGMTKMWYMMMRCRRCGRCSSYMSYAKMMYMSMSGRRKSRKMRGRRKA</span><br>
                    <button href="#" onclick="load(3)">Copy data to input fields</button><br>
                </div>
                <br>
                <div class="noindent">
                    And here is a 'real-life' example (original chromatograms: <a href="ExampleForward.ab1">Forward</a> and <a href="ExampleReverse.ab1">Reverse</a>):<br>
                    Forward sequence: <span class="sequence" id="example4forward">ATCGTGGGCGGCCGGCCCTGCCACAGACGGGGTTGTCACCCTCTGCGACGTGCCGTTCCAAGCAACTTAGGCAGGGCCCCTCCGCCTAGAAAGTGCTTCTCGCAACTACAACTCGCCGATGCAGGCATCGGAGATTTCAAATTTGAGCTCTTCCCGCTTCACTCGCCGTTACTGGGGGAATCCTTGTTAGTTTCTTTTCCTCCGCTTATTAATATGCTTAAATTCAGCGGGTAGCCTTGCCTGATCTGAGGTCTGGAAGGCGATTCCTTTTTTCCTTTGAGATGCCGCCACCGCTACCCGGCGGCAGCAGAAAAAAGAATCGAATGGAGAAAGATTTGTTCCGTCAAAGCGATAGAGCCGTGGCCGTTTGGGGTACATTGTTCTATGATCCCCGCGCGACACCGGATGTCGCTTGGCGGATCTTTCTCCCTGAATTTCAAGGGACGCGGTAAACCGACCGGTCGGGCCGAGCAGCACCAGGGCTGGCTAGCTAGCGCACGACCGGTCATCTCGACCGCGACCCTCAACGCCGCACGAACCCGTTCACGGCGGGCGCGYSYCSSSSCCMYMYSCKMYASASRSGGRSMMSRSGSRSRCGCGCRCRCGSRKWYKCRCRMKRKRKRTKTKWRWAKASACWCWSASASASAYRYKCYYSKGRGARMMCMMRAGMGCSMYWTKYGYKYWMARAKWYKMKRWKWYWCWSWRWWYTCYGCWWYTCACWCTWYWTMTCRSMMTCKMKCTGA</span><br>
                    Reverse sequence: <span class="sequence" id="example4reverse">GTGCRMTMTCAACACMCSASTCTCGMRACRCATMKYGKGSGSSSSSSSCYSYSMCASASRSGGKKKTSWCMCYCTSYGMSRYGYSSYKYYMMRMRMMWYWKRSRSRGSSCCYCYSCSYMKARARWGYKYYTCKCRMMWMYAMMWCKCSSMKRYRSRSRYMKSRGAKWTYWMAWWTKWGMKCTYYYCSCKYYWCWCKCSSYKWYWSKGGGRRWMYYYKTKWKWKTYTYTTYYYCYSCKYWTWWWWATRYKYWWAWWYWSMGSGKRKMSYYKYSYSWKMTSWGRKSTSKRRRRSGMKWYYYYTTTTYYYYTKWGAKRYSSCSMCMSCKMYMCSSSGSSRSMRSARAAAARARWMKMRWRKRGARARAKWTKTKYYSYSWMARMGMKAKAGMSSYGKSSSYKTKKGGKRYAYWKTKYTMTRWKMYCCSCGCGMSACMSSRKRTSKCKYKKSGSRKMTYTYTCYCYSWRWWTYWMRRGRSRCGSKRWAMMSMSMSSKSKSGSSSMGMRSMRCMMSRGSKSKSKMKMKMKMGCRCRMSMSSKSWYMTCKMSMSCGMSMCYCWMMRCSSCRCRMRMMCSYKYWCRSSGSGSGCGCGTCCCGGCCCCATCCGCTACAGACGGGGACCAGGCGGACGCGCGCACGCGGATTCGCACGATGGATGTTTGAATAGACACTCAGACAGACATGCTCCTGGGAGAACCCAAGAGCGCCATTTGCGTTCAAAGATTCGATGATTCACTGAAT</span><br>
                    <button href="#" onclick="load(4)">Copy data to input fields</button><br>
                </div>
                <br>
            </div>
            <div id="hiddenDiv" style="display: none"></div>
            <div class="navigation">
                <a href="index.html">Back to startpage</a>
                <a href="faq.html">FAQ</a>
                <a href="tutorial.html">Tutorial</a>
                <a href="mailto: jflot@ulb.ac.be">E-Mail the author</a>
            </div>
        </div>
        <script>

var reverseLookup = {
    'A' : 'T', 'T' : 'A', 'G' : 'C', 'C' : 'G',
    'R' : 'Y', 'Y' : 'R', 'M' : 'K', 'K' : 'M',
    'W' : 'W', 'S' : 'S', 'V' : 'B', 'B' : 'V',
    'H' : 'D', 'D' : 'H', 'N' : 'N'
};

function checkInput(s) {
    for (var i = 0; i < s.length; i++) {
        var character = s[i];
        var lookup = reverseLookup[character];
        if (lookup == "" || lookup == undefined) {
            return character;
        }
    }
    return null;
}

function calculate() {
    var fwd = document.getElementById('forward').value.trim().toUpperCase();
    var rev = document.getElementById('reverse').value.trim().toUpperCase();
    var score = parseInt(document.getElementById('score').value);

    if (fwd == "") {
        alert("Missing forward sequence input!");
        return;
    }
    if (rev == "") {
        alert("Missing reverse sequence input!");
        return;
    }
    if (fwd.length + rev.length <= 3) {
        alert("Sequences to short!");
        return;
    }
    var unknown1 = checkInput(fwd);
    if (unknown1 != null) {
        alert("Unknown base (" + unknown1 + ") in forward sequence!");
        return;
    }
    var unknown2 = checkInput(rev);
    if (unknown2 != null) {
        alert("Unknown base (" + unknown2 + ") in reverse sequence!");
        return;
    }

    var resultArea = document.getElementById("resultArea");
    resultArea.innerText = "Calculating ... Please wait ... Results will appear here!";
    resultArea.style.display = "block";
    document.getElementById('exampleSection').style.display = "none";

    var worker = new Worker("champuru.js");
    worker.addEventListener("message", function(e) {
        data = e.data;
        resultArea.innerHTML = data.result;
        worker.terminate();
    });
    worker.postMessage({"fwd" : fwd, "rev" : rev, "score" : score, "i" : 0, "j" : 0, "useOffsets" : false});
}

function askForOffset(title, fwd, rev) {
    var input = prompt(title);
    if (input == null || input == undefined) return NaN; // Cancel button
    var i = parseInt(input.trim());
    if (i == NaN) {
        alert("Invalid input!");
        return NaN;
    }
    if (!(-fwd.length + 1 <= i && i < rev.length)) {
        alert("Invalid offset for input sequences!");
        return NaN;
    }
    return i;
}
function rerunAnalysisWithDifferentOffsets(fwd, rev, method) {
    var i = askForOffset("Please enter first offset:", fwd, rev);
    if (isNaN(i)) return;
    var j = askForOffset("Please enter second offset:", fwd, rev);
    if (isNaN(j)) return;

    var worker = new Worker("champuru.js");
    worker.addEventListener("message", function(e) {
        data = e.data;
        resultArea.innerHTML = data.result;
        worker.terminate();
    });
    worker.postMessage({"fwd" : fwd, "rev" : rev, "score" : method, "i" : i, "j" : j, "useOffsets" : true});
}

function resetForm() {
    document.getElementById('forward').value = '';
    document.getElementById('reverse').value = '';
    document.getElementById('score').value = 1;
    document.getElementById('resultArea').style.display = "none";
    document.getElementById('exampleSection').style.display = "block";
}

function load(i) {
    document.getElementById('forward').value = document.getElementById('example' + i + 'forward').innerText;
    document.getElementById('reverse').value = document.getElementById('example' + i + 'reverse').innerText;
}

function reverse() {
    var s = document.getElementById('reverse').value;
    s = s.trim().toUpperCase();
    if (s == "") {
        alert("Please specify the sequence to reverse in the 'Reverse sequence' field.");
        return;
    }
    var result = s.split("").reverse();
    for (var i = 0; i < result.length; i++) {
        var character = result[i];
        result[i] = reverseLookup[character];
        if (result[i] == "" || result[i] == undefined) {
            alert("Illegal character '" + character + "' detected in 'Reverse sequence'!");
            return;
        }
    }
    result = result.join("");
    document.getElementById('reverse').value = result;
}

function addColorsIfUnderscore(s) {
    var result = []
    for (var i = 0; i < s.length; i++) {
        if (s[i] == "_") {
            result.push("<span class='bgred'>_</span>");
        } else {
            result.push(s[i]);
        }
    }
    return result.join("");
}
function colorConsensusByIncompatiblePositions() {
    var txt1 = document.getElementById('consensus1').innerText;
    var txt2 = document.getElementById('consensus2').innerText;
    document.getElementById('consensus1').innerHTML = addColorsIfUnderscore(txt1);
    document.getElementById('consensus2').innerHTML = addColorsIfUnderscore(txt2);
}
function addColorsIfAmb(s) {
    var result = []
    for (var i = 0; i < s.length; i++) {
        if (s[i] == "_" || s[i] == "A" || s[i] == "C" || s[i] == "T" || s[i] == "G") {
            result.push(s[i]);
        } else {
            result.push("<span class='bgred'>" + s[i] + "</span>");
        }
    }
    return result.join("");
}
function colorConsensusByAmbPositions() {
    var txt1 = document.getElementById('consensus1').innerText;
    var txt2 = document.getElementById('consensus2').innerText;
    document.getElementById('consensus1').innerHTML = addColorsIfAmb(txt1);
    document.getElementById('consensus2').innerHTML = addColorsIfAmb(txt2);
}
function removeColor() {
    var txt1 = document.getElementById('consensus1').innerText.trim();
    var txt2 = document.getElementById('consensus2').innerText.trim();
    document.getElementById('consensus1').innerText = txt1;
    document.getElementById('consensus2').innerText = txt2;
}
function colorProblems() {
    var txt1 = document.getElementById('reconstructed1').innerText;
    var txt2 = document.getElementById('reconstructed2').innerText;
    document.getElementById('reconstructed1').innerHTML = addColorsIfUnderscore(txt1);
    document.getElementById('reconstructed2').innerHTML = addColorsIfUnderscore(txt2);
}
function colorAmbPos() {
    var txt1 = document.getElementById('reconstructed1').innerText;
    var txt2 = document.getElementById('reconstructed2').innerText;
    document.getElementById('reconstructed1').innerHTML = addColorsIfAmb(txt1);
    document.getElementById('reconstructed2').innerHTML = addColorsIfAmb(txt2);
}
function removeColorFinal() {
    var txt1 = document.getElementById('reconstructed1').innerText.trim();
    var txt2 = document.getElementById('reconstructed2').innerText.trim();
    document.getElementById('reconstructed1').innerText = txt1;
    document.getElementById('reconstructed2').innerText = txt2;
}
function download() {
    var txt1 = document.getElementById('reconstructed1').innerText;
    var txt2 = document.getElementById('reconstructed2').innerText;
    var content = []
    content.push(">first")
    content.push(txt1);
    content.push(">second")
    content.push(txt2);
    var b64 = window.btoa(content.join('\n'));
    var link = "<a id='downloadLink' href-lang='text/fasta' href='data:text/fasta;base64,\n" + b64 + "' title='result.fasta' style='display:none' download='result.fasta'>Download</a>";
    document.getElementById("hiddenDiv").innerHTML = link;
    document.getElementById('downloadLink').click();
}
function highlight(id) {
    var circle = document.getElementById(id);
    var x = circle.getAttribute("cx");
    var y = circle.getAttribute("cy");
    var svg = document.getElementById("scorePlot");
    var newElement = document.createElementNS("http://www.w3.org/2000/svg", "circle");
    newElement.setAttribute("id", "addedCircle");
    newElement.setAttribute("cx", x);
    newElement.setAttribute("cy", y);
    newElement.setAttribute("stroke", "red");
    newElement.setAttribute("stroke-width", "2");
    newElement.setAttribute("fill", "none");
    newElement.setAttribute("r", "5");
    svg.appendChild(newElement);
}
function removeHighlight(id) {
    var svg = document.getElementById("scorePlot");
    var circle = document.getElementById("addedCircle");
    svg.removeChild(circle);
}
function toClipboard(id) {
    var text = document.getElementById(id).innerText;
    navigator.clipboard.writeText(text);
    return false;
}

        </script>
    </body>
</html>