Mercurial > repos > shellac > guppy_basecaller

annotate env/lib/python3.7/site-packages/networkx/readwrite/graph6.py @ 4:79f47841a781 draft

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"planemo upload commit 2a0fe2cc28b09e101d37293e53e82f61762262ec"
author shellac
date Thu, 14 May 2020 16:47:39 -0400
parents 26e78fe6e8c4
children
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1 # Original author: D. Eppstein, UC Irvine, August 12, 2003.
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2 # The original code at http://www.ics.uci.edu/~eppstein/PADS/ is public domain.
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3 # Copyright (C) 2004-2019 by
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4 # Aric Hagberg <hagberg@lanl.gov>
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5 # Dan Schult <dschult@colgate.edu>
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6 # Pieter Swart <swart@lanl.gov>
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7 # Tomas Gavenciak <gavento@ucw.cz>
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8 # All rights reserved.
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9 # BSD license.
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10 #
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11 # Authors: Tomas Gavenciak <gavento@ucw.cz>
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12 # Aric Hagberg <aric.hagberg@lanl.gov>
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13 """Functions for reading and writing graphs in the *graph6* format.
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14
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15 The *graph6* file format is suitable for small graphs or large dense
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16 graphs. For large sparse graphs, use the *sparse6* format.
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17
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18 For more information, see the `graph6`_ homepage.
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19
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20 .. _graph6: http://users.cecs.anu.edu.au/~bdm/data/formats.html
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21
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22 """
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23 from itertools import islice
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24 import sys
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25
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26 import networkx as nx
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27 from networkx.exception import NetworkXError
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28 from networkx.utils import open_file, not_implemented_for
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29
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30 __all__ = ['from_graph6_bytes', 'read_graph6', 'to_graph6_bytes',
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31 'write_graph6']
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32
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33
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34 def _generate_graph6_bytes(G, nodes, header):
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35 """Yield bytes in the graph6 encoding of a graph.
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36
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37 `G` is an undirected simple graph. `nodes` is the list of nodes for
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38 which the node-induced subgraph will be encoded; if `nodes` is the
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39 list of all nodes in the graph, the entire graph will be
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40 encoded. `header` is a Boolean that specifies whether to generate
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41 the header ``b'>>graph6<<'`` before the remaining data.
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42
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43 This function generates `bytes` objects in the following order:
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44
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45 1. the header (if requested),
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46 2. the encoding of the number of nodes,
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47 3. each character, one-at-a-time, in the encoding of the requested
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48 node-induced subgraph,
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49 4. a newline character.
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50
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51 This function raises :exc:`ValueError` if the graph is too large for
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52 the graph6 format (that is, greater than ``2 ** 36`` nodes).
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53
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54 """
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55 n = len(G)
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56 if n >= 2 ** 36:
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57 raise ValueError('graph6 is only defined if number of nodes is less '
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58 'than 2 ** 36')
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59 if header:
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60 yield b'>>graph6<<'
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61 for d in n_to_data(n):
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62 yield str.encode(chr(d + 63))
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63 # This generates the same as `(v in G[u] for u, v in combinations(G, 2))`,
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64 # but in "column-major" order instead of "row-major" order.
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65 bits = (nodes[j] in G[nodes[i]] for j in range(1, n) for i in range(j))
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66 chunk = list(islice(bits, 6))
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67 while chunk:
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68 d = sum(b << 5 - i for i, b in enumerate(chunk))
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69 yield str.encode(chr(d + 63))
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70 chunk = list(islice(bits, 6))
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71 yield b'\n'
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72
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73
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74 def from_graph6_bytes(string):
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75 """Read a simple undirected graph in graph6 format from string.
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76
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77 Parameters
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78 ----------
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79 string : string
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80 Data in graph6 format, without a trailing newline.
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81
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82 Returns
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83 -------
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84 G : Graph
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85
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86 Raises
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87 ------
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88 NetworkXError
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89 If the string is unable to be parsed in graph6 format
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90
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91 ValueError
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92 If any character ``c`` in the input string does not satisfy
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93 ``63 <= ord(c) < 127``.
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94
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95 Examples
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96 --------
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97 >>> G = nx.from_graph6_bytes(b'A_')
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98 >>> sorted(G.edges())
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99 [(0, 1)]
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100
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101 See Also
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102 --------
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103 read_graph6, write_graph6
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104
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105 References
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106 ----------
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107 .. [1] Graph6 specification
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108 <http://users.cecs.anu.edu.au/~bdm/data/formats.html>
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109
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110 """
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111 def bits():
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112 """Returns sequence of individual bits from 6-bit-per-value
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113 list of data values."""
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114 for d in data:
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115 for i in [5, 4, 3, 2, 1, 0]:
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116 yield (d >> i) & 1
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117
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118 if string.startswith(b'>>graph6<<'):
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119 string = string[10:]
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120
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121 if sys.version_info < (3, ):
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122 data = [ord(c) - 63 for c in string]
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123 else:
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124 data = [c - 63 for c in string]
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125 if any(c > 63 for c in data):
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126 raise ValueError('each input character must be in range(63, 127)')
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127
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128 n, data = data_to_n(data)
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129 nd = (n * (n - 1) // 2 + 5) // 6
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130 if len(data) != nd:
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131 raise NetworkXError(
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132 'Expected %d bits but got %d in graph6' % (n * (n - 1) // 2, len(data) * 6))
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133
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134 G = nx.Graph()
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135 G.add_nodes_from(range(n))
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136 for (i, j), b in zip([(i, j) for j in range(1, n) for i in range(j)], bits()):
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137 if b:
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138 G.add_edge(i, j)
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139
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140 return G
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141
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142
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143 def to_graph6_bytes(G, nodes=None, header=True):
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144 """Convert a simple undirected graph to bytes in graph6 format.
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145
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146 Parameters
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147 ----------
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148 G : Graph (undirected)
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149
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150 nodes: list or iterable
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151 Nodes are labeled 0...n-1 in the order provided. If None the ordering
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152 given by ``G.nodes()`` is used.
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153
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154 header: bool
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155 If True add '>>graph6<<' bytes to head of data.
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156
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157 Raises
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158 ------
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159 NetworkXNotImplemented
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160 If the graph is directed or is a multigraph.
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161
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162 ValueError
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163 If the graph has at least ``2 ** 36`` nodes; the graph6 format
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164 is only defined for graphs of order less than ``2 ** 36``.
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165
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166 Examples
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167 --------
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168 >>> nx.to_graph6_bytes(nx.path_graph(2)) # doctest: +SKIP
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169 b'>>graph6<<A_\\n'
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170
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171 See Also
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172 --------
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173 from_graph6_bytes, read_graph6, write_graph6_bytes
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174
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175 Notes
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176 -----
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177 The returned bytes end with a newline character.
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178
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179 The format does not support edge or node labels, parallel edges or
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180 self loops. If self loops are present they are silently ignored.
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181
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182 References
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183 ----------
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184 .. [1] Graph6 specification
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185 <http://users.cecs.anu.edu.au/~bdm/data/formats.html>
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186
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187 """
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188 if nodes is not None:
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189 G = G.subgraph(nodes)
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190 H = nx.convert_node_labels_to_integers(G)
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191 nodes = sorted(H.nodes())
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192 return b''.join(_generate_graph6_bytes(H, nodes, header))
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193
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194
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195 @open_file(0, mode='rb')
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196 def read_graph6(path):
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197 """Read simple undirected graphs in graph6 format from path.
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198
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199 Parameters
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200 ----------
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201 path : file or string
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202 File or filename to write.
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203
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204 Returns
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205 -------
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206 G : Graph or list of Graphs
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207 If the file contains multiple lines then a list of graphs is returned
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208
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209 Raises
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210 ------
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211 NetworkXError
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212 If the string is unable to be parsed in graph6 format
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213
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214 Examples
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215 --------
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216 You can read a graph6 file by giving the path to the file::
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217
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218 >>> import tempfile
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219 >>> with tempfile.NamedTemporaryFile() as f:
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220 ... _ = f.write(b'>>graph6<<A_\\n')
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221 ... _ = f.seek(0)
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222 ... G = nx.read_graph6(f.name)
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223 >>> list(G.edges())
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224 [(0, 1)]
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225
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226 You can also read a graph6 file by giving an open file-like object::
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227
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228 >>> import tempfile
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229 >>> with tempfile.NamedTemporaryFile() as f:
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230 ... _ = f.write(b'>>graph6<<A_\\n')
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231 ... _ = f.seek(0)
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232 ... G = nx.read_graph6(f)
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233 >>> list(G.edges())
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234 [(0, 1)]
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235
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236 See Also
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237 --------
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238 from_graph6_bytes, write_graph6
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239
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240 References
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241 ----------
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242 .. [1] Graph6 specification
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243 <http://users.cecs.anu.edu.au/~bdm/data/formats.html>
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244
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245 """
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246 glist = []
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247 for line in path:
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248 line = line.strip()
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249 if not len(line):
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250 continue
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251 glist.append(from_graph6_bytes(line))
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252 if len(glist) == 1:
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253 return glist[0]
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254 else:
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255 return glist
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256
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257
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258 @not_implemented_for('directed')
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259 @not_implemented_for('multigraph')
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260 @open_file(1, mode='wb')
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261 def write_graph6(G, path, nodes=None, header=True):
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262 """Write a simple undirected graph to a path in graph6 format.
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263
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264 Parameters
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265 ----------
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266 G : Graph (undirected)
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267
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268 path : str
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269 The path naming the file to which to write the graph.
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270
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271 nodes: list or iterable
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272 Nodes are labeled 0...n-1 in the order provided. If None the ordering
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273 given by ``G.nodes()`` is used.
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274
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275 header: bool
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276 If True add '>>graph6<<' string to head of data
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277
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278 Raises
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279 ------
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280 NetworkXNotImplemented
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281 If the graph is directed or is a multigraph.
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282
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283 ValueError
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284 If the graph has at least ``2 ** 36`` nodes; the graph6 format
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285 is only defined for graphs of order less than ``2 ** 36``.
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286
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287 Examples
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288 --------
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289 You can write a graph6 file by giving the path to a file::
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290
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291 >>> import tempfile
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292 >>> with tempfile.NamedTemporaryFile() as f:
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293 ... nx.write_graph6(nx.path_graph(2), f.name)
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294 ... _ = f.seek(0)
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295 ... print(f.read()) # doctest: +SKIP
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296 b'>>graph6<<A_\\n'
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297
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298 See Also
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299 --------
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300 from_graph6_bytes, read_graph6
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301
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302 Notes
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303 -----
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304 The function writes a newline character after writing the encoding
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305 of the graph.
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306
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307 The format does not support edge or node labels, parallel edges or
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308 self loops. If self loops are present they are silently ignored.
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309
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310 References
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311 ----------
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312 .. [1] Graph6 specification
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313 <http://users.cecs.anu.edu.au/~bdm/data/formats.html>
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314
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315 """
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316 return write_graph6_file(G, path, nodes=nodes, header=header)
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317
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318
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319 @not_implemented_for('directed')
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320 @not_implemented_for('multigraph')
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321 def write_graph6_file(G, f, nodes=None, header=True):
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322 """Write a simple undirected graph to a file-like object in graph6 format.
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323
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324 Parameters
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325 ----------
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326 G : Graph (undirected)
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327
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328 f : file-like object
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329 The file to write.
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330
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331 nodes: list or iterable
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332 Nodes are labeled 0...n-1 in the order provided. If None the ordering
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333 given by ``G.nodes()`` is used.
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334
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335 header: bool
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336 If True add '>>graph6<<' string to head of data
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337
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338 Raises
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339 ------
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340 NetworkXNotImplemented
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341 If the graph is directed or is a multigraph.
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342
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343 ValueError
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344 If the graph has at least ``2 ** 36`` nodes; the graph6 format
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345 is only defined for graphs of order less than ``2 ** 36``.
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346
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347 Examples
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348 --------
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349 You can write a graph6 file by giving an open file-like object::
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350
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351 >>> import tempfile
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352 >>> with tempfile.NamedTemporaryFile() as f:
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353 ... nx.write_graph6(nx.path_graph(2), f)
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354 ... _ = f.seek(0)
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355 ... print(f.read()) # doctest: +SKIP
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356 b'>>graph6<<A_\\n'
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357
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358 See Also
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359 --------
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360 from_graph6_bytes, read_graph6
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361
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362 Notes
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363 -----
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364 The function writes a newline character after writing the encoding
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365 of the graph.
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366
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367 The format does not support edge or node labels, parallel edges or
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368 self loops. If self loops are present they are silently ignored.
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369
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370 References
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371 ----------
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372 .. [1] Graph6 specification
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373 <http://users.cecs.anu.edu.au/~bdm/data/formats.html>
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374
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375 """
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376 if nodes is not None:
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377 G = G.subgraph(nodes)
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378 H = nx.convert_node_labels_to_integers(G)
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379 nodes = sorted(H.nodes())
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380 for b in _generate_graph6_bytes(H, nodes, header):
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381 f.write(b)
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382
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383
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384 def data_to_n(data):
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385 """Read initial one-, four- or eight-unit value from graph6
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386 integer sequence.
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387
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388 Return (value, rest of seq.)"""
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389 if data[0] <= 62:
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390 return data[0], data[1:]
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391 if data[1] <= 62:
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392 return (data[1] << 12) + (data[2] << 6) + data[3], data[4:]
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393 return ((data[2] << 30) + (data[3] << 24) + (data[4] << 18) +
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394 (data[5] << 12) + (data[6] << 6) + data[7], data[8:])
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395
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396
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397 def n_to_data(n):
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398 """Convert an integer to one-, four- or eight-unit graph6 sequence.
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399
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400 This function is undefined if `n` is not in ``range(2 ** 36)``.
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401
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402 """
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403 if n <= 62:
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404 return [n]
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405 elif n <= 258047:
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406 return [63, (n >> 12) & 0x3f, (n >> 6) & 0x3f, n & 0x3f]
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407 else: # if n <= 68719476735:
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408 return [63, 63,
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409 (n >> 30) & 0x3f, (n >> 24) & 0x3f, (n >> 18) & 0x3f,
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410 (n >> 12) & 0x3f, (n >> 6) & 0x3f, n & 0x3f]