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galaxy/tools/mutation/visualize.py
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#!/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)
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