Mercurial > repos > shellac > guppy_basecaller

annotate env/lib/python3.7/site-packages/networkx/readwrite/pajek.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 # Copyright (C) 2008-2014 by
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2 # Aric Hagberg <hagberg@lanl.gov>
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3 # Dan Schult <dschult@colgate.edu>
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4 # Pieter Swart <swart@lanl.gov>
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5 # All rights reserved.
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6 # BSD license.
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7 #
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8 # Authors: Aric Hagberg (hagberg@lanl.gov)
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9 """
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10 *****
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11 Pajek
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12 *****
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13 Read graphs in Pajek format.
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14
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15 This implementation handles directed and undirected graphs including
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16 those with self loops and parallel edges.
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17
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18 Format
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19 ------
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20 See http://vlado.fmf.uni-lj.si/pub/networks/pajek/doc/draweps.htm
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21 for format information.
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22
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23 """
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24
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25 import warnings
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26
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27 import networkx as nx
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28 from networkx.utils import is_string_like, open_file, make_str
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29
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30 __all__ = ['read_pajek', 'parse_pajek', 'generate_pajek', 'write_pajek']
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31
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32
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33 def generate_pajek(G):
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34 """Generate lines in Pajek graph format.
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35
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36 Parameters
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37 ----------
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38 G : graph
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39 A Networkx graph
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40
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41 References
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42 ----------
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43 See http://vlado.fmf.uni-lj.si/pub/networks/pajek/doc/draweps.htm
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44 for format information.
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45 """
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46 if G.name == '':
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47 name = 'NetworkX'
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48 else:
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49 name = G.name
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50 # Apparently many Pajek format readers can't process this line
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51 # So we'll leave it out for now.
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52 # yield '*network %s'%name
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53
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54 # write nodes with attributes
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55 yield '*vertices %s' % (G.order())
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56 nodes = list(G)
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57 # make dictionary mapping nodes to integers
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58 nodenumber = dict(zip(nodes, range(1, len(nodes) + 1)))
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59 for n in nodes:
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60 # copy node attributes and pop mandatory attributes
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61 # to avoid duplication.
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62 na = G.nodes.get(n, {}).copy()
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63 x = na.pop('x', 0.0)
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64 y = na.pop('y', 0.0)
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65 id = int(na.pop('id', nodenumber[n]))
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66 nodenumber[n] = id
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67 shape = na.pop('shape', 'ellipse')
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68 s = ' '.join(map(make_qstr, (id, n, x, y, shape)))
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69 # only optional attributes are left in na.
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70 for k, v in na.items():
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71 if is_string_like(v) and v.strip() != '':
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72 s += ' %s %s' % (make_qstr(k), make_qstr(v))
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73 else:
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74 warnings.warn('Node attribute %s is not processed. %s.' %
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75 (k,
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76 'Empty attribute' if is_string_like(v) else
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77 'Non-string attribute'))
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78 yield s
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79
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80 # write edges with attributes
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81 if G.is_directed():
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82 yield '*arcs'
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83 else:
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84 yield '*edges'
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85 for u, v, edgedata in G.edges(data=True):
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86 d = edgedata.copy()
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87 value = d.pop('weight', 1.0) # use 1 as default edge value
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88 s = ' '.join(map(make_qstr, (nodenumber[u], nodenumber[v], value)))
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89 for k, v in d.items():
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90 if is_string_like(v) and v.strip() != '':
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91 s += ' %s %s' % (make_qstr(k), make_qstr(v))
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92 else:
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93 warnings.warn('Edge attribute %s is not processed. %s.' %
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94 (k,
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95 'Empty attribute' if is_string_like(v) else
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96 'Non-string attribute'))
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97 yield s
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98
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99
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100 @open_file(1, mode='wb')
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101 def write_pajek(G, path, encoding='UTF-8'):
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102 """Write graph in Pajek format to path.
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103
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104 Parameters
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105 ----------
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106 G : graph
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107 A Networkx graph
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108 path : file or string
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109 File or filename to write.
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110 Filenames ending in .gz or .bz2 will be compressed.
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111
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112 Examples
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113 --------
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114 >>> G=nx.path_graph(4)
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115 >>> nx.write_pajek(G, "test.net")
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116
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117 Warnings
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118 --------
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119 Optional node attributes and edge attributes must be non-empty strings.
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120 Otherwise it will not be written into the file. You will need to
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121 convert those attributes to strings if you want to keep them.
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122
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123 References
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124 ----------
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125 See http://vlado.fmf.uni-lj.si/pub/networks/pajek/doc/draweps.htm
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126 for format information.
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127 """
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128 for line in generate_pajek(G):
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parents:
diff changeset
129 line += '\n'
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parents:
diff changeset
130 path.write(line.encode(encoding))
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parents:
diff changeset
131
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parents:
diff changeset
132
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parents:
diff changeset
133 @open_file(0, mode='rb')
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parents:
diff changeset
134 def read_pajek(path, encoding='UTF-8'):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
135 """Read graph in Pajek format from path.
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parents:
diff changeset
136
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parents:
diff changeset
137 Parameters
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parents:
diff changeset
138 ----------
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parents:
diff changeset
139 path : file or string
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shellac
parents:
diff changeset
140 File or filename to write.
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parents:
diff changeset
141 Filenames ending in .gz or .bz2 will be uncompressed.
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parents:
diff changeset
142
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parents:
diff changeset
143 Returns
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shellac
parents:
diff changeset
144 -------
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
145 G : NetworkX MultiGraph or MultiDiGraph.
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parents:
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146
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shellac
parents:
diff changeset
147 Examples
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parents:
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148 --------
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parents:
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149 >>> G=nx.path_graph(4)
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parents:
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150 >>> nx.write_pajek(G, "test.net")
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parents:
diff changeset
151 >>> G=nx.read_pajek("test.net")
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parents:
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152
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parents:
diff changeset
153 To create a Graph instead of a MultiGraph use
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parents:
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154
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
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155 >>> G1=nx.Graph(G)
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parents:
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156
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shellac
parents:
diff changeset
157 References
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parents:
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158 ----------
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parents:
diff changeset
159 See http://vlado.fmf.uni-lj.si/pub/networks/pajek/doc/draweps.htm
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parents:
diff changeset
160 for format information.
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parents:
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161 """
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
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162 lines = (line.decode(encoding) for line in path)
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parents:
diff changeset
163 return parse_pajek(lines)
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parents:
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164
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parents:
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165
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
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166 def parse_pajek(lines):
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parents:
diff changeset
167 """Parse Pajek format graph from string or iterable.
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parents:
diff changeset
168
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parents:
diff changeset
169 Parameters
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
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170 ----------
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
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171 lines : string or iterable
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
172 Data in Pajek format.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
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173
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shellac
parents:
diff changeset
174 Returns
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
175 -------
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
176 G : NetworkX graph
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
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177
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parents:
diff changeset
178 See Also
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
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179 --------
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
180 read_pajek()
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
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181
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
182 """
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
183 import shlex
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
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184 # multigraph=False
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
185 if is_string_like(lines):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
186 lines = iter(lines.split('\n'))
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
187 lines = iter([line.rstrip('\n') for line in lines])
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
188 G = nx.MultiDiGraph() # are multiedges allowed in Pajek? assume yes
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
189 labels = [] # in the order of the file, needed for matrix
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parents:
diff changeset
190 while lines:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
191 try:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
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192 l = next(lines)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
193 except: # EOF
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
194 break
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
195 if l.lower().startswith("*network"):
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shellac
parents:
diff changeset
196 try:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
197 label, name = l.split(None, 1)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
198 except ValueError:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
199 # Line was not of the form: *network NAME
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shellac
parents:
diff changeset
200 pass
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
201 else:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
202 G.graph['name'] = name
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
203 elif l.lower().startswith("*vertices"):
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parents:
diff changeset
204 nodelabels = {}
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
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parents:
diff changeset
205 l, nnodes = l.split()
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
206 for i in range(int(nnodes)):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
207 l = next(lines)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
208 try:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
209 splitline = [x.decode('utf-8') for x in
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
210 shlex.split(make_str(l).encode('utf-8'))]
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
211 except AttributeError:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
212 splitline = shlex.split(str(l))
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
213 id, label = splitline[0:2]
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
214 labels.append(label)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
215 G.add_node(label)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
216 nodelabels[id] = label
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
217 G.nodes[label]['id'] = id
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
218 try:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
219 x, y, shape = splitline[2:5]
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
220 G.nodes[label].update({'x': float(x),
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
221 'y': float(y),
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
222 'shape': shape})
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
223 except:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
224 pass
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
225 extra_attr = zip(splitline[5::2], splitline[6::2])
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
226 G.nodes[label].update(extra_attr)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
227 elif l.lower().startswith("*edges") or l.lower().startswith("*arcs"):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
228 if l.lower().startswith("*edge"):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
229 # switch from multidigraph to multigraph
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
230 G = nx.MultiGraph(G)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
231 if l.lower().startswith("*arcs"):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
232 # switch to directed with multiple arcs for each existing edge
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
233 G = G.to_directed()
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
234 for l in lines:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
235 try:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
236 splitline = [x.decode('utf-8') for x in
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
237 shlex.split(make_str(l).encode('utf-8'))]
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
238 except AttributeError:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
239 splitline = shlex.split(str(l))
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
240
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
241 if len(splitline) < 2:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
242 continue
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
243 ui, vi = splitline[0:2]
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
244 u = nodelabels.get(ui, ui)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
245 v = nodelabels.get(vi, vi)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
246 # parse the data attached to this edge and put in a dictionary
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shellac
parents:
diff changeset
247 edge_data = {}
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
248 try:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
249 # there should always be a single value on the edge?
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
250 w = splitline[2:3]
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
251 edge_data.update({'weight': float(w[0])})
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
252 except:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
253 pass
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
254 # if there isn't, just assign a 1
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
255 # edge_data.update({'value':1})
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
256 extra_attr = zip(splitline[3::2], splitline[4::2])
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
257 edge_data.update(extra_attr)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
parents:
diff changeset
258 # if G.has_edge(u,v):
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
shellac
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259 # multigraph=True
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260 G.add_edge(u, v, **edge_data)
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261 elif l.lower().startswith("*matrix"):
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262 G = nx.DiGraph(G)
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263 adj_list = ((labels[row], labels[col], {'weight': int(data)})
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264 for (row, line) in enumerate(lines)
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265 for (col, data) in enumerate(line.split())
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266 if int(data) != 0)
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267 G.add_edges_from(adj_list)
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268
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269 return G
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270
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271
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272 def make_qstr(t):
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273 """Returns the string representation of t.
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274 Add outer double-quotes if the string has a space.
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275 """
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276 if not is_string_like(t):
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277 t = str(t)
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278 if " " in t:
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279 t = r'"%s"' % t
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280 return t
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281
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282
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283 # fixture for pytest
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284 def teardown_module(module):
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285 import os
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286 os.unlink('test.net')