1 | # Draws a genealogical tree (generates a SVG file) based on parent-child relationship information.
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2 |
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3 | import json
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4 | import random
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5 | import math
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6 | import argparse
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7 |
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8 | TIME = "" # BIRTHS / GENERATIONAL / REAL
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9 | BALANCE = "" # MIN / DENSITY
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10 |
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11 | DOT_STYLE = "" # NONE / NORMAL / CLEAR
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12 |
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13 | JITTER = "" #
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14 |
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15 | # ------SVG---------
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16 | svg_file = 0
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17 |
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18 | svg_line_style = 'stroke="rgb(90%,10%,16%)" stroke-width="1" stroke-opacity="0.8"'
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19 | svg_dot_style = 'r="2" stroke="black" stroke-width="0.2" fill="red"'
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20 | svg_clear_dot_style = 'r="2" stroke="black" stroke-width="0.4" fill="none"'
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21 |
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22 | svg_spine_line_style = 'stroke="rgb(0%,0%,80%)" stroke-width="2" stroke-opacity="1"'
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23 | svg_spine_dot_style = 'r="1" stroke="black" stroke-width="0.2" fill="rgb(50%,50%,100%)"'
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24 |
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25 | def svg_add_line(from_pos, to_pos, style=svg_line_style):
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26 | svg_file.write('<line ' + style + ' x1="' + str(from_pos[0]) + '" x2="' + str(to_pos[0]) + '" y1="' + str(from_pos[1]) + '" y2="' + str(to_pos[1]) + '" />')
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27 |
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28 | def svg_add_dot(pos, style=svg_dot_style):
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29 | svg_file.write('<circle ' + style + ' cx="' + str(pos[0]) + '" cy="' + str(pos[1]) + '" />')
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30 |
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31 | def svg_generate_line_style(percent):
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32 | # hotdog
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33 | from_col = [100, 70, 0]
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34 | to_col = [60, 0, 0]
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35 | # lava
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36 | # from_col = [100, 80, 0]
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37 | # to_col = [100, 0, 0]
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38 | # neon
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39 | # from_col = [30, 200, 255]
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40 | # to_col = [240, 0, 220]
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41 |
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42 | from_opa = 0.2
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43 | to_opa = 1.0
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44 | from_stroke = 1
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45 | to_stroke = 3
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46 |
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47 | opa = from_opa*(1-percent) + to_opa*percent
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48 | stroke = from_stroke*(1-percent) + to_stroke*percent
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49 |
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50 | percent = 1 - ((1-percent)**20)
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51 |
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52 | return 'stroke="rgb(' + str(from_col[0]*(1-percent) + to_col[0]*percent) + '%,' \
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53 | + str(from_col[1]*(1-percent) + to_col[1]*percent) + '%,' \
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54 | + str(from_col[2]*(1-percent) + to_col[2]*percent) + '%)" stroke-width="' + str(stroke) + '" stroke-opacity="' + str(opa) + '"'
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55 |
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56 | def svg_generate_dot_style(percent):
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57 | from_col = [100, 70, 0]
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58 | to_col = [60, 0, 0]
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59 | # neon
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60 | # from_col = [30, 200, 255]
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61 | # to_col = [240, 0, 220]
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62 |
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63 | from_opa = 0.2
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64 | to_opa = 1.0
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65 |
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66 | opa = from_opa*(1-percent) + to_opa*percent
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67 |
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68 | percent = 1 - ((1-percent)**20)
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69 |
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70 | return 'fill="rgb(' + str(from_col[0]*(1-percent) + to_col[0]*percent) + '%,' \
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71 | + str(from_col[1]*(1-percent) + to_col[1]*percent) + '%,' \
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72 | + str(from_col[2]*(1-percent) + to_col[2]*percent) + '%)" r="1.5" stroke="black" stroke-width="0.2" fill-opacity="' + str(opa) + '" ' \
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73 | 'stroke-opacity="' + str(opa) + '"'
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74 |
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75 | # -------------------
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76 |
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77 | def load_data(dir):
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78 | global firstnode, nodes, inv_nodes, time
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79 | f = open(dir)
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80 | for line in f:
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81 | sline = line.split(' ', 1)
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82 | if len(sline) == 2:
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83 | if sline[0] == "[OFFSPRING]":
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84 | creature = json.loads(sline[1])
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85 | #print("B" +str(creature))
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86 | if "FromIDs" in creature:
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87 | if not creature["ID"] in nodes:
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88 | nodes[creature["ID"]] = {}
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89 | # we assign to each parent its contribution to the genotype of the child
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90 | for i in range(0, len(creature["FromIDs"])):
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91 | inherited = 1 #(creature["Inherited"][i] if 'Inherited' in creature else 1) #ONLY FOR NOW
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92 | nodes[creature["ID"]][creature["FromIDs"][i]] = inherited
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93 | else:
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94 | print("Doubled entry for " + creature["ID"])
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95 | quit()
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96 |
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97 | if not creature["FromIDs"][0] in nodes:
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98 | firstnode = creature["FromIDs"][0]
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99 |
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100 | if "Time" in creature:
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101 | time[creature["ID"]] = creature["Time"]
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102 |
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103 | for k, v in sorted(nodes.items()):
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104 | for val in sorted(v):
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105 | inv_nodes[val] = inv_nodes.get(val, [])
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106 | inv_nodes[val].append(k)
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107 |
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108 |
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109 | def load_simple_data(dir):
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110 | global firstnode, nodes, inv_nodes
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111 | f = open(dir)
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112 | for line in f:
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113 | sline = line.split()
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114 | if len(sline) > 1:
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115 | #if int(sline[0]) > 15000:
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116 | # break
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117 | if sline[0] == firstnode:
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118 | continue
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119 | nodes[sline[0]] = str(max(int(sline[1]), int(firstnode)))
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120 | else:
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121 | firstnode = sline[0]
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122 |
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123 | for k, v in sorted(nodes.items()):
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124 | inv_nodes[v] = inv_nodes.get(v, [])
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125 | inv_nodes[v].append(k)
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126 |
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127 | #print(str(inv_nodes))
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128 | #quit()
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129 |
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130 | def compute_depth(node):
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131 | my_depth = 0
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132 | if node in inv_nodes:
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133 | for c in inv_nodes[node]:
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134 | my_depth = max(my_depth, compute_depth(c)+1)
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135 | depth[node] = my_depth
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136 | return my_depth
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137 |
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138 | # ------------------------------------
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139 |
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140 | def xmin_crowd(x1, x2, y):
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141 | if BALANCE == "RANDOM":
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142 | return (x1 if random.randrange(2) == 0 else x2)
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143 | elif BALANCE == "MIN":
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144 | x1_closest = 999999
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145 | x2_closest = 999999
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146 | for pos in positions:
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147 | pos = positions[pos]
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148 | if pos[1] == y:
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149 | x1_closest = min(x1_closest, abs(x1-pos[0]))
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150 | x2_closest = min(x2_closest, abs(x2-pos[0]))
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151 | return (x1 if x1_closest > x2_closest else x2)
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152 | elif BALANCE == "DENSITY":
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153 | x1_dist = 0
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154 | x2_dist = 0
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155 | for pos in positions:
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156 | pos = positions[pos]
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157 | if pos[1] > y-10 or pos[1] < y+10:
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158 | dy = pos[1]-y
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159 | dx1 = pos[0]-x1
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160 | dx2 = pos[0]-x2
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161 |
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162 | x1_dist += math.sqrt(dy**2 + dx1**2)
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163 | x2_dist += math.sqrt(dy**2 + dx2**2)
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164 | return (x1 if x1_dist > x2_dist else x2)
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165 |
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166 | # ------------------------------------
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167 |
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168 | def prepos_children_reccurent(node):
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169 | global visited
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170 | for c in inv_nodes[node]:
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171 |
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172 | # we want to visit the node just once, after all of its parents
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173 | if not all_parents_visited(c):
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174 | continue
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175 | else:
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176 | visited[c] = True
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177 |
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178 | # if JITTER == True:
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179 | # dissimilarity = random.gauss(0,1)
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180 | # else:
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181 | # dissimilarity = 1
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182 | # #TODO take this info from proper fields
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183 |
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184 | cy = 0
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185 | if TIME == "BIRTHS":
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186 | if c[0] == "c":
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187 | cy = int(c[1:])
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188 | else:
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189 | cy = int(c)
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190 | elif TIME == "GENERATIONAL":
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191 | cy = positions[node][1]+1
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192 | elif TIME == "REAL":
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193 | cy = time[c]
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194 |
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195 | if len(nodes[c]) == 1:
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196 | dissimilarity = 0
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197 | if JITTER == True:
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198 | dissimilarity = random.gauss(0,1)
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199 | else:
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200 | dissimilarity = 1
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201 | positions[c] = [xmin_crowd(positions[node][0]-dissimilarity, positions[node][0]+dissimilarity, cy), cy]
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202 | else:
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203 | vsum = sum([v for k, v in nodes[c].items()])
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204 | cx = sum([positions[k][0]*v/vsum for k, v in nodes[c].items()])
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205 |
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206 | if JITTER == True:
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207 | positions[c] = [cx + random.gauss(0, 0.1), cy]
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208 | else:
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209 | positions[c] = [cx, cy]
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210 |
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211 |
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212 | if c in inv_nodes:
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213 | prepos_children_reccurent(c)
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214 |
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215 | def prepos_children():
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216 | global max_height, max_width, min_width, visited
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217 |
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218 | if not bool(time):
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219 | print("REAL time requested, but no real time data provided. Assuming BIRTHS time instead.")
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220 | TIME = "BIRTHS"
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221 |
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222 | positions[firstnode] = [0, 0]
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223 |
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224 | visited = {}
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225 | visited[firstnode] = True
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226 | prepos_children_reccurent(firstnode)
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227 |
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228 | for pos in positions:
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229 | max_height = max(max_height, positions[pos][1])
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230 | max_width = max(max_width, positions[pos][0])
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231 | min_width = min(min_width, positions[pos][0])
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232 |
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233 | # ------------------------------------
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234 |
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235 | def all_parents_visited(node):
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236 | apv = True
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237 | for k, v in sorted(nodes[node].items()):
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238 | if not k in visited:
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239 | apv = False
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240 | break
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241 | return apv
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242 | # ------------------------------------
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243 |
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244 | def draw_children_recurrent(node, max_depth):
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245 | global visited
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246 |
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247 | for c in inv_nodes[node]:
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248 |
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249 | # we want to draw the node just once
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250 | if not all_parents_visited(c):
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251 | continue
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252 | else:
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253 | visited[c] = True
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254 |
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255 | if c in inv_nodes:
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256 | draw_children_recurrent(c, max_depth)
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257 |
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258 | line_style = (svg_line_style if args.mono_tree else svg_generate_line_style(depth[c]/max_depth))
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259 | for k, v in sorted(nodes[c].items()):
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260 | svg_add_line( (w_margin+w_no_margs*(positions[k][0]-min_width)/(max_width-min_width), h_margin+h_no_margs*positions[k][1]/max_height),
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261 | (w_margin+w_no_margs*(positions[c][0]-min_width)/(max_width-min_width), h_margin+h_no_margs*positions[c][1]/max_height), line_style)
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262 |
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263 | if DOT_STYLE == "NONE":
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264 | continue
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265 | elif DOT_STYLE == "CLEAR":
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266 | dot_style = svg_clear_dot_style
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267 | else: # NORMAL, default
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268 | dot_style = svg_generate_dot_style(depth[c]/max_depth)
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269 | svg_add_dot( (w_margin+w_no_margs*(positions[c][0]-min_width)/(max_width-min_width), h_margin+h_no_margs*positions[c][1]/max_height), dot_style)
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270 | def draw_children():
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271 | global visited
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272 | visited = {}
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273 | visited[firstnode] = True
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274 |
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275 | max_depth = 0
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276 | for k, v in depth.items():
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277 | max_depth = max(max_depth, v)
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278 | draw_children_recurrent(firstnode, max_depth)
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279 |
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280 | if DOT_STYLE == "NONE":
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281 | return
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282 | elif DOT_STYLE == "CLEAR":
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283 | dot_style = svg_clear_dot_style
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284 | else: # NORMAL, default
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285 | dot_style = svg_generate_dot_style(depth[firstnode]/max_depth)
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286 | svg_add_dot( (w_margin+w_no_margs*(positions[firstnode][0]-min_width)/(max_width-min_width), h_margin+h_no_margs*positions[firstnode][1]/max_height), dot_style)
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287 |
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288 | def draw_spine_recurrent(node):
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289 | for c in inv_nodes[node]:
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290 | if depth[c] == depth[node] - 1:
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291 | if c in inv_nodes:
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292 | draw_spine_recurrent(c)
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293 |
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294 | line_style = svg_spine_line_style
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295 | svg_add_line( (w_margin+w_no_margs*(positions[node][0]-min_width)/(max_width-min_width), h_margin+h_no_margs*positions[node][1]/max_height),
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296 | (w_margin+w_no_margs*(positions[c][0]-min_width)/(max_width-min_width), h_margin+h_no_margs*positions[c][1]/max_height), line_style)
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297 | #svg_add_dot( (w_margin+w_no_margs*(positions[c][0]-min_width)/(max_width-min_width), h_margin+h_no_margs*positions[c][1]/max_height), svg_spine_dot_style)
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298 | def draw_spine():
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299 | draw_spine_recurrent(firstnode)
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300 | #svg_add_dot( (w_margin+w_no_margs*(positions[firstnode][0]-min_width)/(max_width-min_width), h_margin+h_no_margs*positions[firstnode][1]/max_height), svg_spine_dot_style)
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301 |
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302 | def draw_skeleton_reccurent(node, max_depth):
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303 | for c in inv_nodes[node]:
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304 | if depth[c] >= min_skeleton_depth or depth[c] == max([depth[q] for q in inv_nodes[node]]):
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305 | if c in inv_nodes:
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306 | draw_skeleton_reccurent(c, max_depth)
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307 |
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308 | line_style = svg_spine_line_style
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309 | svg_add_line( (w_margin+w_no_margs*(positions[node][0]-min_width)/(max_width-min_width), h_margin+h_no_margs*positions[node][1]/max_height),
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310 | (w_margin+w_no_margs*(positions[c][0]-min_width)/(max_width-min_width), h_margin+h_no_margs*positions[c][1]/max_height), line_style)
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311 | #svg_add_dot( (w_margin+w_no_margs*(positions[c][0]-min_width)/(max_width-min_width), h_margin+h_no_margs*positions[c][1]/max_height),
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312 | # svg_spine_dot_style)
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313 | def draw_skeleton():
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314 | max_depth = 0
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315 | for k, v in depth.items():
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316 | max_depth = max(max_depth, v)
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317 |
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318 | draw_skeleton_reccurent(firstnode, max_depth)
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319 | #svg_add_dot( (w_margin+w_no_margs*(positions[firstnode][0]-min_width)/(max_width-min_width), h_margin+h_no_margs*positions[firstnode][1]/max_height),
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320 | # svg_spine_dot_style)
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321 |
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322 |
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323 |
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324 | ##################################################### main #####################################################
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325 |
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326 | args = 0
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327 |
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328 | h = 800
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329 | w = 600
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330 | h_margin = 10
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331 | w_margin = 10
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332 | h_no_margs = h - 2* h_margin
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333 | w_no_margs = w - 2* w_margin
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334 |
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335 | max_height = 0
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336 | max_width = 0
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337 | min_width = 9999999999
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338 |
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339 | min_skeleton_depth = 0
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340 |
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341 | firstnode = ""
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342 | nodes = {}
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343 | inv_nodes = {}
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344 | positions = {}
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345 | visited= {}
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346 | depth = {}
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347 | time = {}
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348 |
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349 | def main():
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350 | global svg_file, min_skeleton_depth, args, TIME, BALANCE, DOT_STYLE, JITTER
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351 |
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352 | parser = argparse.ArgumentParser(description='Process some integers.')
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353 | parser.add_argument('--in', dest='input', required=True, help='input file with stuctured evolutionary data')
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354 | parser.add_argument('--out', dest='output', required=True, help='output file for the evolutionary tree')
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355 | draw_tree_parser = parser.add_mutually_exclusive_group(required=False)
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356 | draw_tree_parser.add_argument('--draw-tree', dest='draw_tree', action='store_true', help='whether drawing the full tree should be skipped')
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357 | draw_tree_parser.add_argument('--no-draw-tree', dest='draw_tree', action='store_false')
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358 |
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359 | draw_skeleton_parser = parser.add_mutually_exclusive_group(required=False)
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360 | draw_skeleton_parser.add_argument('--draw-skeleton', dest='draw_skeleton', action='store_true', help='whether the skeleton of the tree should be drawn')
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361 | draw_skeleton_parser.add_argument('--no-draw-skeleton', dest='draw_skeleton', action='store_false')
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362 |
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363 | draw_spine_parser = parser.add_mutually_exclusive_group(required=False)
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364 | draw_spine_parser.add_argument('--draw-spine', dest='draw_spine', action='store_true', help='whether the spine of the tree should be drawn')
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365 | draw_spine_parser.add_argument('--no-draw-spine', dest='draw_spine', action='store_false')
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366 |
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367 | #TODO: better names for those parameters
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368 | parser.add_argument('--time', default='BIRTHS', dest='time', help='values on vertical axis (BIRTHS/GENERATIONAL/REAL); '
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369 | 'BIRTHS: time measured as the number of births since the beggining; '
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370 | 'GENERATIONAL: time measured as number of ancestors; '
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371 | 'REAL: real time of the simulation')
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372 | parser.add_argument('--balance', default='MIN', dest='balance', help='method of placing node in the tree (RANDOM/MIN/DENSITY)')
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373 |
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374 | parser.add_argument('--dots', default='NORMAL', dest='dots', help='method of drawing dots (individuals) (NONE/NORMAL/CLEAR)')
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375 |
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376 | parser.add_argument('-j', '--jitter', dest="jitter", action='store_true', help='draw horizontal positions of children from the normal distribution')
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377 |
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378 | mono_tree_parser = parser.add_mutually_exclusive_group(required=False)
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379 | mono_tree_parser.add_argument('--mono-tree', dest='mono_tree', action='store_true', help='whether the tree should be drawn with a single color')
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380 | mono_tree_parser.add_argument('--no-mono-tree', dest='mono_tree', action='store_false')
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381 |
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382 | parser.add_argument('--min-skeleton-depth', type=int, default=2, dest='min_skeleton_depth', help='minimal distance from the leafs for the nodes in the skeleton')
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383 | parser.add_argument('--seed', type=int, dest='seed', help='seed for the random number generator (-1 for random)')
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384 |
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385 | parser.add_argument('--simple-data', type=bool, dest='simple_data', help='input data are given in a simple format (#child #parent)')
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386 |
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387 | parser.set_defaults(mono_tree=False)
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388 | parser.set_defaults(draw_tree=True)
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389 | parser.set_defaults(draw_skeleton=False)
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390 | parser.set_defaults(draw_spine=False)
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391 |
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392 | parser.set_defaults(seed=-1)
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393 |
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394 | args = parser.parse_args()
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395 |
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396 | TIME = args.time
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397 | BALANCE = args.balance
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398 | DOT_STYLE = args.dots
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399 | JITTER = args.jitter
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400 |
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401 | dir = args.input
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402 | min_skeleton_depth = args.min_skeleton_depth
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403 | seed = args.seed
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404 | if seed == -1:
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405 | seed = random.randint(0, 10000)
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406 | random.seed(seed)
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407 | print("seed:", seed)
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408 |
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409 | if args.simple_data:
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410 | load_simple_data(dir)
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411 | else:
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412 | load_data(dir)
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413 |
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414 | compute_depth(firstnode)
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415 |
|
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416 | svg_file = open(args.output, "w")
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417 | svg_file.write('<svg xmlns:svg="http://www.w3.org/2000/svg" xmlns="http://www.w3.org/2000/svg" xmlns:xlink="http://www.w3.org/1999/xlink" version="1.0" '
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418 | 'width="' + str(w) + '" height="' + str(h) + '">')
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419 |
|
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420 | prepos_children()
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421 |
|
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422 | if args.draw_tree:
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423 | draw_children()
|
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424 | if args.draw_skeleton:
|
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425 | draw_skeleton()
|
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426 | if args.draw_spine:
|
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427 | draw_spine()
|
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428 |
|
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429 | svg_file.write("</svg>")
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430 | svg_file.close()
|
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431 |
|
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432 | main()
|
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433 |
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