Mercurial > repos > xuebing > sharplabtool

comparison tools/mutation/visualize.py @ 0:9071e359b9a3

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author xuebing
date Fri, 09 Mar 2012 19:37:19 -0500
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1 #!/usr/bin/env python
2
3 '''
4 Mutation Visualizer tool
5 '''
6
7 from __future__ import division
8
9 import sys, csv, os, math
10 import optparse
11
12 from galaxy import eggs
13 import pkg_resources
14 pkg_resources.require( "SVGFig" )
15 import svgfig as svg
16
17
18 SVGPan = """
19 /**
20 * SVGPan library 1.2
21 * ====================
22 *
23 * Given an unique existing element with id "viewport", including the
24 * the library into any SVG adds the following capabilities:
25 *
26 * - Mouse panning
27 * - Mouse zooming (using the wheel)
28 * - Object dargging
29 *
30 * Known issues:
31 *
32 * - Zooming (while panning) on Safari has still some issues
33 *
34 * Releases:
35 *
36 * 1.2, Sat Mar 20 08:42:50 GMT 2010, Zeng Xiaohui
37 * Fixed a bug with browser mouse handler interaction
38 *
39 * 1.1, Wed Feb 3 17:39:33 GMT 2010, Zeng Xiaohui
40 * Updated the zoom code to support the mouse wheel on Safari/Chrome
41 *
42 * 1.0, Andrea Leofreddi
43 * First release
44 *
45 * This code is licensed under the following BSD license:
46 *
47 * Copyright 2009-2010 Andrea Leofreddi (a.leofreddi@itcharm.com). All rights reserved.
48 *
49 * Redistribution and use in source and binary forms, with or without modification, are
50 * permitted provided that the following conditions are met:
51 *
52 * 1. Redistributions of source code must retain the above copyright notice, this list of
53 * conditions and the following disclaimer.
54 *
55 * 2. Redistributions in binary form must reproduce the above copyright notice, this list
56 * of conditions and the following disclaimer in the documentation and/or other materials
57 * provided with the distribution.
58 *
59 * THIS SOFTWARE IS PROVIDED BY Andrea Leofreddi ``AS IS'' AND ANY EXPRESS OR IMPLIED
60 * WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND
61 * FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL Andrea Leofreddi OR
62 * CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
63 * CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
64 * SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON
65 * ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING
66 * NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
67 * ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
68 *
69 * The views and conclusions contained in the software and documentation are those of the
70 * authors and should not be interpreted as representing official policies, either expressed
71 * or implied, of Andrea Leofreddi.
72 */
73
74 var root = document.documentElement;
75
76 var state = 'none', stateTarget, stateOrigin, stateTf;
77
78 setupHandlers(root);
79
80 /**
81 * Register handlers
82 */
83 function setupHandlers(root){
84 setAttributes(root, {
85 "onmouseup" : "add(evt)",
86 "onmousedown" : "handleMouseDown(evt)",
87 "onmousemove" : "handleMouseMove(evt)",
88 "onmouseup" : "handleMouseUp(evt)",
89 //"onmouseout" : "handleMouseUp(evt)", // Decomment this to stop the pan functionality when dragging out of the SVG element
90 });
91
92 if(navigator.userAgent.toLowerCase().indexOf('webkit') >= 0)
93 window.addEventListener('mousewheel', handleMouseWheel, false); // Chrome/Safari
94 else
95 window.addEventListener('DOMMouseScroll', handleMouseWheel, false); // Others
96 }
97
98 /**
99 * Instance an SVGPoint object with given event coordinates.
100 */
101 function getEventPoint(evt) {
102 var p = root.createSVGPoint();
103
104 p.x = evt.clientX;
105 p.y = evt.clientY;
106
107 return p;
108 }
109
110 /**
111 * Sets the current transform matrix of an element.
112 */
113 function setCTM(element, matrix) {
114 var s = "matrix(" + matrix.a + "," + matrix.b + "," + matrix.c + "," + matrix.d + "," + matrix.e + "," + matrix.f + ")";
115
116 element.setAttribute("transform", s);
117 }
118
119 /**
120 * Dumps a matrix to a string (useful for debug).
121 */
122 function dumpMatrix(matrix) {
123 var s = "[ " + matrix.a + ", " + matrix.c + ", " + matrix.e + "\\n " + matrix.b + ", " + matrix.d + ", " + matrix.f + "\\n 0, 0, 1 ]";
124
125 return s;
126 }
127
128 /**
129 * Sets attributes of an element.
130 */
131 function setAttributes(element, attributes){
132 for (i in attributes)
133 element.setAttributeNS(null, i, attributes[i]);
134 }
135
136 /**
137 * Handle mouse move event.
138 */
139 function handleMouseWheel(evt) {
140 if(evt.preventDefault)
141 evt.preventDefault();
142
143 evt.returnValue = false;
144
145 var svgDoc = evt.target.ownerDocument;
146
147 var delta;
148
149 if(evt.wheelDelta)
150 delta = evt.wheelDelta / 3600; // Chrome/Safari
151 else
152 delta = evt.detail / -90; // Mozilla
153
154 var z = 1 + delta; // Zoom factor: 0.9/1.1
155
156 var g = svgDoc.getElementById("viewport");
157
158 var p = getEventPoint(evt);
159
160 p = p.matrixTransform(g.getCTM().inverse());
161
162 // Compute new scale matrix in current mouse position
163 var k = root.createSVGMatrix().translate(p.x, p.y).scale(z).translate(-p.x, -p.y);
164
165 setCTM(g, g.getCTM().multiply(k));
166
167 stateTf = stateTf.multiply(k.inverse());
168 }
169
170 /**
171 * Handle mouse move event.
172 */
173 function handleMouseMove(evt) {
174 if(evt.preventDefault)
175 evt.preventDefault();
176
177 evt.returnValue = false;
178
179 var svgDoc = evt.target.ownerDocument;
180
181 var g = svgDoc.getElementById("viewport");
182
183 if(state == 'pan') {
184 // Pan mode
185 var p = getEventPoint(evt).matrixTransform(stateTf);
186
187 setCTM(g, stateTf.inverse().translate(p.x - stateOrigin.x, p.y - stateOrigin.y));
188 } else if(state == 'move') {
189 // Move mode
190 var p = getEventPoint(evt).matrixTransform(g.getCTM().inverse());
191
192 setCTM(stateTarget, root.createSVGMatrix().translate(p.x - stateOrigin.x, p.y - stateOrigin.y).multiply(g.getCTM().inverse()).multiply(stateTarget.getCTM()));
193
194 stateOrigin = p;
195 }
196 }
197
198 /**
199 * Handle click event.
200 */
201 function handleMouseDown(evt) {
202 if(evt.preventDefault)
203 evt.preventDefault();
204
205 evt.returnValue = false;
206
207 var svgDoc = evt.target.ownerDocument;
208
209 var g = svgDoc.getElementById("viewport");
210
211 if(evt.target.tagName == "svg") {
212 // Pan mode
213 state = 'pan';
214
215 stateTf = g.getCTM().inverse();
216
217 stateOrigin = getEventPoint(evt).matrixTransform(stateTf);
218 }
219 /*else {
220 // Move mode
221 state = 'move';
222
223 stateTarget = evt.target;
224
225 stateTf = g.getCTM().inverse();
226
227 stateOrigin = getEventPoint(evt).matrixTransform(stateTf);
228 }*/
229 }
230 /**
231 * Handle mouse button release event.
232 */
233 function handleMouseUp(evt) {
234 if(evt.preventDefault)
235 evt.preventDefault();
236
237 evt.returnValue = false;
238
239 var svgDoc = evt.target.ownerDocument;
240
241 if(state == 'pan' || state == 'move') {
242 // Quit pan mode
243 state = '';
244 }
245 }
246 """
247
248 COLS_PER_SAMPLE = 7
249 HEADER_COLS = 4
250
251 HEIGHT = 6
252 WIDTH = 12
253 BAR_WIDTH = 1.5
254 GAP = 2
255
256
257 colors = {'A':'blue', 'C':'green', 'G':'orange', 'T':'red'}
258 bases = ['A', 'C', 'G', 'T' ]
259
260 def stop_error(message):
261 print >> sys.stderr, message
262 sys.exit(1)
263
264 def validate_bases(n_a, n_c, n_g, n_t, total):
265 if n_a > total:
266 return 'A'
267 elif n_c > total:
268 return 'C'
269 elif n_g > total:
270 return 'G'
271 elif n_t > total:
272 return 'T'
273 return None
274
275 def main(opts, args):
276 s = svg.SVG('g', id='viewport')
277
278 # display legend
279 for i, b in enumerate( bases ):
280 bt = svg.SVG("tspan", b, style="font-family:Verdana;font-size:20%")
281 s.append(svg.SVG("text", bt, x=12+(i*10), y=3, stroke="none", fill="black"))
282 s.append(svg.SVG("rect", x=14+(i*10), y=0, width=4, height=3,
283 stroke="none", fill=colors[b], fill_opacity=0.5))
284
285 reader = open(opts.input_file, 'U')
286
287 samples = []
288 for i in range(int(len(args)/3)):
289 index = i*3
290 samples.append(dict(name=args[index],
291 a_col=args[index+1],
292 totals_col=args[index+2]))
293
294 if opts.zoom == 'interactive':
295 y = 35
296 else:
297 y = 25
298 for i, sample in enumerate(samples):
299 x = 23+(i*(WIDTH+GAP))
300 t = svg.SVG("text", svg.SVG("tspan", sample['name'], style="font-family:Verdana;font-size:25%"),
301 x=x, y=y, transform="rotate(-90 %i,%i)" % (x, y), stroke="none", fill="black")
302 s.append(t)
303
304 count=1
305 for line in reader:
306 row = line.split('\t')
307 highlighted_position = False
308 show_pos = True
309 position = row[int(opts.position_col)-1]
310 ref = row[int(opts.ref_col)-1].strip().upper()
311 # validate
312 if ref not in bases:
313 stop_error( "The reference column (col%s) contains invalid character '%s' at row %i of the dataset." % ( opts.ref_col, ref, count ) )
314 # display positions
315 if opts.zoom == 'interactive':
316 textx = 0
317 else:
318 textx = 7
319 bt = svg.SVG("tspan", str(position), style="font-family:Verdana;font-size:25%")
320 s.append(svg.SVG("text", bt, x=textx, y=34+(count*(HEIGHT+GAP)), stroke="none", fill="black"))
321 s.append(svg.SVG("rect", x=0, y=30+(count*(HEIGHT+GAP)), width=14, height=HEIGHT,
322 stroke='none', fill=colors[ref.upper()], fill_opacity=0.2))
323
324 for sample_index, sample in enumerate(samples):
325 n_a = int(row[int(sample['a_col'])-1])
326 n_c = int(row[int(sample['a_col'])+1-1])
327 n_g = int(row[int(sample['a_col'])+2-1])
328 n_t = int(row[int(sample['a_col'])+3-1])
329 total = int(row[int(sample['totals_col'])-1])
330 # validate
331 base_error = validate_bases(n_a, n_c, n_g, n_t, total)
332 if base_error:
333 stop_error("For sample %i (%s), the number of base %s reads is more than the coverage on row %i." % (sample_index+1,
334 sample['name'],
335 base_error,
336 count))
337
338 if total:
339 x = 16+(sample_index*(WIDTH+GAP))
340 y = 30+(count*(HEIGHT+GAP))
341 width = WIDTH
342 height = HEIGHT
343 if count%2:
344 s.append(svg.SVG("rect", x=x, y=y, width=width, height=height,
345 stroke='none', fill='grey', fill_opacity=0.25))
346 else:
347 s.append(svg.SVG("rect", x=x, y=y, width=width, height=height,
348 stroke='none', fill='grey', fill_opacity=0.25))
349
350 for base, value in enumerate([n_a, n_c, n_g, n_t]):
351 width = int(math.ceil(value / total * WIDTH))
352 s.append(svg.SVG("rect", x=x, y=y, width=width, height=BAR_WIDTH,
353 stroke='none', fill=colors[bases[base]], fill_opacity=0.6))
354 y = y + BAR_WIDTH
355
356 count=count+1
357
358 if opts.zoom == 'interactive':
359 canv = svg.canvas(s)
360 canv.save(opts.output_file)
361 import fileinput
362 flag = False
363 for line in fileinput.input(opts.output_file, inplace=1):
364 if line.startswith('<svg'):
365 print '<svg xmlns="http://www.w3.org/2000/svg" xmlns:xlink="http://www.w3.org/1999/xlink" version="1.1">'
366 flag = True
367 continue
368 else:
369 if flag:
370 print '<script type="text/javascript">%s</script>' % SVGPan
371 flag = False
372 print line,
373 else:
374 zoom = int(opts.zoom)
375 w = "%ipx" % (x*(10+zoom))
376 h = "%ipx" % (y*(2+zoom))
377 canv = svg.canvas(s, width=w, height=h, viewBox="0 0 %i %i" %(x+100, y+100))
378 canv.save(opts.output_file)
379
380 if __name__ == '__main__':
381 parser = optparse.OptionParser()
382 parser.add_option('-i', '--input-file', dest='input_file', action='store')
383 parser.add_option('-o', '--output-file', dest='output_file', action='store')
384 parser.add_option('-z', '--zoom', dest='zoom', action='store', default='1')
385 parser.add_option('-p', '--position_col', dest='position_col', action='store', default='c0')
386 parser.add_option('-r', '--ref_col', dest='ref_col', action='store', default='c1')
387 (opts, args) = parser.parse_args()
388 main(opts, args)
389 sys.exit(1)
390
391