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