/tools/mutation/visualize.py
https://bitbucket.org/cistrome/cistrome-harvard/ · Python · 391 lines · 357 code · 26 blank · 8 comment · 26 complexity · d82a8d907b004b44f87141ac629babfe MD5 · raw file
- #!/usr/bin/env python
- '''
- Mutation Visualizer tool
- '''
- from __future__ import division
- import sys, csv, os, math
- import optparse
- from galaxy import eggs
- import pkg_resources
- pkg_resources.require( "SVGFig" )
- import svgfig as svg
- SVGPan = """
- /**
- * SVGPan library 1.2
- * ====================
- *
- * Given an unique existing element with id "viewport", including the
- * the library into any SVG adds the following capabilities:
- *
- * - Mouse panning
- * - Mouse zooming (using the wheel)
- * - Object dargging
- *
- * Known issues:
- *
- * - Zooming (while panning) on Safari has still some issues
- *
- * Releases:
- *
- * 1.2, Sat Mar 20 08:42:50 GMT 2010, Zeng Xiaohui
- * Fixed a bug with browser mouse handler interaction
- *
- * 1.1, Wed Feb 3 17:39:33 GMT 2010, Zeng Xiaohui
- * Updated the zoom code to support the mouse wheel on Safari/Chrome
- *
- * 1.0, Andrea Leofreddi
- * First release
- *
- * This code is licensed under the following BSD license:
- *
- * Copyright 2009-2010 Andrea Leofreddi (a.leofreddi@itcharm.com). All rights reserved.
- *
- * Redistribution and use in source and binary forms, with or without modification, are
- * permitted provided that the following conditions are met:
- *
- * 1. Redistributions of source code must retain the above copyright notice, this list of
- * conditions and the following disclaimer.
- *
- * 2. Redistributions in binary form must reproduce the above copyright notice, this list
- * of conditions and the following disclaimer in the documentation and/or other materials
- * provided with the distribution.
- *
- * THIS SOFTWARE IS PROVIDED BY Andrea Leofreddi ``AS IS'' AND ANY EXPRESS OR IMPLIED
- * WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND
- * FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL Andrea Leofreddi OR
- * CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
- * CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
- * SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON
- * ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING
- * NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
- * ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
- *
- * The views and conclusions contained in the software and documentation are those of the
- * authors and should not be interpreted as representing official policies, either expressed
- * or implied, of Andrea Leofreddi.
- */
- var root = document.documentElement;
- var state = 'none', stateTarget, stateOrigin, stateTf;
- setupHandlers(root);
- /**
- * Register handlers
- */
- function setupHandlers(root){
- setAttributes(root, {
- "onmouseup" : "add(evt)",
- "onmousedown" : "handleMouseDown(evt)",
- "onmousemove" : "handleMouseMove(evt)",
- "onmouseup" : "handleMouseUp(evt)",
- //"onmouseout" : "handleMouseUp(evt)", // Decomment this to stop the pan functionality when dragging out of the SVG element
- });
- if(navigator.userAgent.toLowerCase().indexOf('webkit') >= 0)
- window.addEventListener('mousewheel', handleMouseWheel, false); // Chrome/Safari
- else
- window.addEventListener('DOMMouseScroll', handleMouseWheel, false); // Others
- }
- /**
- * Instance an SVGPoint object with given event coordinates.
- */
- function getEventPoint(evt) {
- var p = root.createSVGPoint();
- p.x = evt.clientX;
- p.y = evt.clientY;
- return p;
- }
- /**
- * Sets the current transform matrix of an element.
- */
- function setCTM(element, matrix) {
- var s = "matrix(" + matrix.a + "," + matrix.b + "," + matrix.c + "," + matrix.d + "," + matrix.e + "," + matrix.f + ")";
- element.setAttribute("transform", s);
- }
- /**
- * Dumps a matrix to a string (useful for debug).
- */
- function dumpMatrix(matrix) {
- var s = "[ " + matrix.a + ", " + matrix.c + ", " + matrix.e + "\\n " + matrix.b + ", " + matrix.d + ", " + matrix.f + "\\n 0, 0, 1 ]";
- return s;
- }
- /**
- * Sets attributes of an element.
- */
- function setAttributes(element, attributes){
- for (i in attributes)
- element.setAttributeNS(null, i, attributes[i]);
- }
- /**
- * Handle mouse move event.
- */
- function handleMouseWheel(evt) {
- if(evt.preventDefault)
- evt.preventDefault();
- evt.returnValue = false;
- var svgDoc = evt.target.ownerDocument;
- var delta;
- if(evt.wheelDelta)
- delta = evt.wheelDelta / 3600; // Chrome/Safari
- else
- delta = evt.detail / -90; // Mozilla
- var z = 1 + delta; // Zoom factor: 0.9/1.1
- var g = svgDoc.getElementById("viewport");
-
- var p = getEventPoint(evt);
- p = p.matrixTransform(g.getCTM().inverse());
- // Compute new scale matrix in current mouse position
- var k = root.createSVGMatrix().translate(p.x, p.y).scale(z).translate(-p.x, -p.y);
- setCTM(g, g.getCTM().multiply(k));
- stateTf = stateTf.multiply(k.inverse());
- }
- /**
- * Handle mouse move event.
- */
- function handleMouseMove(evt) {
- if(evt.preventDefault)
- evt.preventDefault();
- evt.returnValue = false;
- var svgDoc = evt.target.ownerDocument;
- var g = svgDoc.getElementById("viewport");
- if(state == 'pan') {
- // Pan mode
- var p = getEventPoint(evt).matrixTransform(stateTf);
- setCTM(g, stateTf.inverse().translate(p.x - stateOrigin.x, p.y - stateOrigin.y));
- } else if(state == 'move') {
- // Move mode
- var p = getEventPoint(evt).matrixTransform(g.getCTM().inverse());
- setCTM(stateTarget, root.createSVGMatrix().translate(p.x - stateOrigin.x, p.y - stateOrigin.y).multiply(g.getCTM().inverse()).multiply(stateTarget.getCTM()));
- stateOrigin = p;
- }
- }
- /**
- * Handle click event.
- */
- function handleMouseDown(evt) {
- if(evt.preventDefault)
- evt.preventDefault();
- evt.returnValue = false;
- var svgDoc = evt.target.ownerDocument;
- var g = svgDoc.getElementById("viewport");
- if(evt.target.tagName == "svg") {
- // Pan mode
- state = 'pan';
- stateTf = g.getCTM().inverse();
- stateOrigin = getEventPoint(evt).matrixTransform(stateTf);
- }
- /*else {
- // Move mode
- state = 'move';
- stateTarget = evt.target;
- stateTf = g.getCTM().inverse();
- stateOrigin = getEventPoint(evt).matrixTransform(stateTf);
- }*/
- }
- /**
- * Handle mouse button release event.
- */
- function handleMouseUp(evt) {
- if(evt.preventDefault)
- evt.preventDefault();
- evt.returnValue = false;
- var svgDoc = evt.target.ownerDocument;
- if(state == 'pan' || state == 'move') {
- // Quit pan mode
- state = '';
- }
- }
- """
- COLS_PER_SAMPLE = 7
- HEADER_COLS = 4
- HEIGHT = 6
- WIDTH = 12
- BAR_WIDTH = 1.5
- GAP = 2
- colors = {'A':'blue', 'C':'green', 'G':'orange', 'T':'red'}
- bases = ['A', 'C', 'G', 'T' ]
- def stop_error(message):
- print >> sys.stderr, message
- sys.exit(1)
- def validate_bases(n_a, n_c, n_g, n_t, total):
- if n_a > total:
- return 'A'
- elif n_c > total:
- return 'C'
- elif n_g > total:
- return 'G'
- elif n_t > total:
- return 'T'
- return None
- def main(opts, args):
- s = svg.SVG('g', id='viewport')
-
- # display legend
- for i, b in enumerate( bases ):
- bt = svg.SVG("tspan", b, style="font-family:Verdana;font-size:20%")
- s.append(svg.SVG("text", bt, x=12+(i*10), y=3, stroke="none", fill="black"))
- s.append(svg.SVG("rect", x=14+(i*10), y=0, width=4, height=3,
- stroke="none", fill=colors[b], fill_opacity=0.5))
- reader = open(opts.input_file, 'U')
- samples = []
- for i in range(int(len(args)/3)):
- index = i*3
- samples.append(dict(name=args[index],
- a_col=args[index+1],
- totals_col=args[index+2]))
- if opts.zoom == 'interactive':
- y = 35
- else:
- y = 25
- for i, sample in enumerate(samples):
- x = 23+(i*(WIDTH+GAP))
- t = svg.SVG("text", svg.SVG("tspan", sample['name'], style="font-family:Verdana;font-size:25%"),
- x=x, y=y, transform="rotate(-90 %i,%i)" % (x, y), stroke="none", fill="black")
- s.append(t)
-
- count=1
- for line in reader:
- row = line.split('\t')
- highlighted_position = False
- show_pos = True
- position = row[int(opts.position_col)-1]
- ref = row[int(opts.ref_col)-1].strip().upper()
- # validate
- if ref not in bases:
- stop_error( "The reference column (col%s) contains invalid character '%s' at row %i of the dataset." % ( opts.ref_col, ref, count ) )
- # display positions
- if opts.zoom == 'interactive':
- textx = 0
- else:
- textx = 7
- bt = svg.SVG("tspan", str(position), style="font-family:Verdana;font-size:25%")
- s.append(svg.SVG("text", bt, x=textx, y=34+(count*(HEIGHT+GAP)), stroke="none", fill="black"))
- s.append(svg.SVG("rect", x=0, y=30+(count*(HEIGHT+GAP)), width=14, height=HEIGHT,
- stroke='none', fill=colors[ref.upper()], fill_opacity=0.2))
-
- for sample_index, sample in enumerate(samples):
- n_a = int(row[int(sample['a_col'])-1])
- n_c = int(row[int(sample['a_col'])+1-1])
- n_g = int(row[int(sample['a_col'])+2-1])
- n_t = int(row[int(sample['a_col'])+3-1])
- total = int(row[int(sample['totals_col'])-1])
- # validate
- base_error = validate_bases(n_a, n_c, n_g, n_t, total)
- if base_error:
- stop_error("For sample %i (%s), the number of base %s reads is more than the coverage on row %i." % (sample_index+1,
- sample['name'],
- base_error,
- count))
-
- if total:
- x = 16+(sample_index*(WIDTH+GAP))
- y = 30+(count*(HEIGHT+GAP))
- width = WIDTH
- height = HEIGHT
- if count%2:
- s.append(svg.SVG("rect", x=x, y=y, width=width, height=height,
- stroke='none', fill='grey', fill_opacity=0.25))
- else:
- s.append(svg.SVG("rect", x=x, y=y, width=width, height=height,
- stroke='none', fill='grey', fill_opacity=0.25))
-
- for base, value in enumerate([n_a, n_c, n_g, n_t]):
- width = int(math.ceil(value / total * WIDTH))
- s.append(svg.SVG("rect", x=x, y=y, width=width, height=BAR_WIDTH,
- stroke='none', fill=colors[bases[base]], fill_opacity=0.6))
- y = y + BAR_WIDTH
- count=count+1
-
- if opts.zoom == 'interactive':
- canv = svg.canvas(s)
- canv.save(opts.output_file)
- import fileinput
- flag = False
- for line in fileinput.input(opts.output_file, inplace=1):
- if line.startswith('<svg'):
- print '<svg xmlns="http://www.w3.org/2000/svg" xmlns:xlink="http://www.w3.org/1999/xlink" version="1.1">'
- flag = True
- continue
- else:
- if flag:
- print '<script type="text/javascript">%s</script>' % SVGPan
- flag = False
- print line,
- else:
- zoom = int(opts.zoom)
- w = "%ipx" % (x*(10+zoom))
- h = "%ipx" % (y*(2+zoom))
- canv = svg.canvas(s, width=w, height=h, viewBox="0 0 %i %i" %(x+100, y+100))
- canv.save(opts.output_file)
- if __name__ == '__main__':
- parser = optparse.OptionParser()
- parser.add_option('-i', '--input-file', dest='input_file', action='store')
- parser.add_option('-o', '--output-file', dest='output_file', action='store')
- parser.add_option('-z', '--zoom', dest='zoom', action='store', default='1')
- parser.add_option('-p', '--position_col', dest='position_col', action='store', default='c0')
- parser.add_option('-r', '--ref_col', dest='ref_col', action='store', default='c1')
- (opts, args) = parser.parse_args()
- main(opts, args)
- sys.exit(1)