Mercurial > repos > shellac > sam_consensus_v3
annotate env/lib/python3.9/site-packages/networkx/algorithms/bipartite/edgelist.py @ 0:4f3585e2f14b draft default tip
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author | shellac |
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date | Mon, 22 Mar 2021 18:12:50 +0000 |
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1 """ |
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2 ******************** |
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3 Bipartite Edge Lists |
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4 ******************** |
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5 Read and write NetworkX graphs as bipartite edge lists. |
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6 |
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7 Format |
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8 ------ |
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9 You can read or write three formats of edge lists with these functions. |
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10 |
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11 Node pairs with no data:: |
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12 |
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13 1 2 |
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14 |
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15 Python dictionary as data:: |
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16 |
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17 1 2 {'weight':7, 'color':'green'} |
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18 |
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19 Arbitrary data:: |
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20 |
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21 1 2 7 green |
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22 |
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23 For each edge (u, v) the node u is assigned to part 0 and the node v to part 1. |
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24 """ |
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25 __all__ = ["generate_edgelist", "write_edgelist", "parse_edgelist", "read_edgelist"] |
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26 |
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27 import networkx as nx |
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28 from networkx.utils import open_file, not_implemented_for |
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29 |
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30 |
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31 @open_file(1, mode="wb") |
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32 def write_edgelist(G, path, comments="#", delimiter=" ", data=True, encoding="utf-8"): |
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33 """Write a bipartite graph as a list of edges. |
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34 |
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35 Parameters |
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36 ---------- |
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37 G : Graph |
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38 A NetworkX bipartite graph |
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39 path : file or string |
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40 File or filename to write. If a file is provided, it must be |
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41 opened in 'wb' mode. Filenames ending in .gz or .bz2 will be compressed. |
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42 comments : string, optional |
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43 The character used to indicate the start of a comment |
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44 delimiter : string, optional |
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45 The string used to separate values. The default is whitespace. |
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46 data : bool or list, optional |
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47 If False write no edge data. |
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48 If True write a string representation of the edge data dictionary.. |
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49 If a list (or other iterable) is provided, write the keys specified |
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50 in the list. |
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51 encoding: string, optional |
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52 Specify which encoding to use when writing file. |
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53 |
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54 Examples |
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55 -------- |
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56 >>> G = nx.path_graph(4) |
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57 >>> G.add_nodes_from([0, 2], bipartite=0) |
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58 >>> G.add_nodes_from([1, 3], bipartite=1) |
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59 >>> nx.write_edgelist(G, "test.edgelist") |
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60 >>> fh = open("test.edgelist", "wb") |
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61 >>> nx.write_edgelist(G, fh) |
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62 >>> nx.write_edgelist(G, "test.edgelist.gz") |
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63 >>> nx.write_edgelist(G, "test.edgelist.gz", data=False) |
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64 |
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65 >>> G = nx.Graph() |
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66 >>> G.add_edge(1, 2, weight=7, color="red") |
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67 >>> nx.write_edgelist(G, "test.edgelist", data=False) |
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68 >>> nx.write_edgelist(G, "test.edgelist", data=["color"]) |
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69 >>> nx.write_edgelist(G, "test.edgelist", data=["color", "weight"]) |
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70 |
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71 See Also |
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72 -------- |
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73 write_edgelist() |
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74 generate_edgelist() |
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75 """ |
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76 for line in generate_edgelist(G, delimiter, data): |
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77 line += "\n" |
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78 path.write(line.encode(encoding)) |
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79 |
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80 |
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81 @not_implemented_for("directed") |
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82 def generate_edgelist(G, delimiter=" ", data=True): |
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83 """Generate a single line of the bipartite graph G in edge list format. |
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84 |
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85 Parameters |
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86 ---------- |
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87 G : NetworkX graph |
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88 The graph is assumed to have node attribute `part` set to 0,1 representing |
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89 the two graph parts |
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90 |
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91 delimiter : string, optional |
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92 Separator for node labels |
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93 |
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94 data : bool or list of keys |
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95 If False generate no edge data. If True use a dictionary |
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96 representation of edge data. If a list of keys use a list of data |
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97 values corresponding to the keys. |
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98 |
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99 Returns |
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100 ------- |
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101 lines : string |
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102 Lines of data in adjlist format. |
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103 |
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104 Examples |
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105 -------- |
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106 >>> from networkx.algorithms import bipartite |
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107 >>> G = nx.path_graph(4) |
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108 >>> G.add_nodes_from([0, 2], bipartite=0) |
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109 >>> G.add_nodes_from([1, 3], bipartite=1) |
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110 >>> G[1][2]["weight"] = 3 |
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111 >>> G[2][3]["capacity"] = 12 |
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112 >>> for line in bipartite.generate_edgelist(G, data=False): |
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113 ... print(line) |
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114 0 1 |
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115 2 1 |
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116 2 3 |
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117 |
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118 >>> for line in bipartite.generate_edgelist(G): |
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119 ... print(line) |
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120 0 1 {} |
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121 2 1 {'weight': 3} |
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122 2 3 {'capacity': 12} |
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123 |
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124 >>> for line in bipartite.generate_edgelist(G, data=["weight"]): |
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125 ... print(line) |
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126 0 1 |
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127 2 1 3 |
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128 2 3 |
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129 """ |
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130 try: |
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131 part0 = [n for n, d in G.nodes.items() if d["bipartite"] == 0] |
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132 except BaseException as e: |
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133 raise AttributeError("Missing node attribute `bipartite`") from e |
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134 if data is True or data is False: |
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135 for n in part0: |
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136 for e in G.edges(n, data=data): |
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137 yield delimiter.join(map(str, e)) |
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138 else: |
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139 for n in part0: |
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140 for u, v, d in G.edges(n, data=True): |
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141 e = [u, v] |
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142 try: |
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143 e.extend(d[k] for k in data) |
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144 except KeyError: |
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145 pass # missing data for this edge, should warn? |
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146 yield delimiter.join(map(str, e)) |
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147 |
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148 |
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149 def parse_edgelist( |
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150 lines, comments="#", delimiter=None, create_using=None, nodetype=None, data=True |
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151 ): |
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152 """Parse lines of an edge list representation of a bipartite graph. |
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153 |
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154 Parameters |
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155 ---------- |
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156 lines : list or iterator of strings |
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157 Input data in edgelist format |
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158 comments : string, optional |
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159 Marker for comment lines |
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160 delimiter : string, optional |
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161 Separator for node labels |
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162 create_using: NetworkX graph container, optional |
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163 Use given NetworkX graph for holding nodes or edges. |
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164 nodetype : Python type, optional |
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165 Convert nodes to this type. |
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166 data : bool or list of (label,type) tuples |
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167 If False generate no edge data or if True use a dictionary |
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168 representation of edge data or a list tuples specifying dictionary |
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169 key names and types for edge data. |
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170 |
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171 Returns |
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172 ------- |
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173 G: NetworkX Graph |
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174 The bipartite graph corresponding to lines |
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175 |
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176 Examples |
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177 -------- |
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178 Edgelist with no data: |
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179 |
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180 >>> from networkx.algorithms import bipartite |
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181 >>> lines = ["1 2", "2 3", "3 4"] |
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182 >>> G = bipartite.parse_edgelist(lines, nodetype=int) |
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183 >>> sorted(G.nodes()) |
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184 [1, 2, 3, 4] |
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185 >>> sorted(G.nodes(data=True)) |
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186 [(1, {'bipartite': 0}), (2, {'bipartite': 0}), (3, {'bipartite': 0}), (4, {'bipartite': 1})] |
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187 >>> sorted(G.edges()) |
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188 [(1, 2), (2, 3), (3, 4)] |
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189 |
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190 Edgelist with data in Python dictionary representation: |
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191 |
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192 >>> lines = ["1 2 {'weight':3}", "2 3 {'weight':27}", "3 4 {'weight':3.0}"] |
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193 >>> G = bipartite.parse_edgelist(lines, nodetype=int) |
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194 >>> sorted(G.nodes()) |
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195 [1, 2, 3, 4] |
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196 >>> sorted(G.edges(data=True)) |
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197 [(1, 2, {'weight': 3}), (2, 3, {'weight': 27}), (3, 4, {'weight': 3.0})] |
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198 |
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199 Edgelist with data in a list: |
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200 |
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201 >>> lines = ["1 2 3", "2 3 27", "3 4 3.0"] |
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202 >>> G = bipartite.parse_edgelist(lines, nodetype=int, data=(("weight", float),)) |
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203 >>> sorted(G.nodes()) |
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204 [1, 2, 3, 4] |
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205 >>> sorted(G.edges(data=True)) |
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206 [(1, 2, {'weight': 3.0}), (2, 3, {'weight': 27.0}), (3, 4, {'weight': 3.0})] |
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207 |
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208 See Also |
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209 -------- |
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210 """ |
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211 from ast import literal_eval |
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212 |
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213 G = nx.empty_graph(0, create_using) |
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214 for line in lines: |
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215 p = line.find(comments) |
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216 if p >= 0: |
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217 line = line[:p] |
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218 if not len(line): |
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219 continue |
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220 # split line, should have 2 or more |
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221 s = line.strip().split(delimiter) |
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222 if len(s) < 2: |
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223 continue |
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224 u = s.pop(0) |
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225 v = s.pop(0) |
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226 d = s |
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227 if nodetype is not None: |
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228 try: |
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229 u = nodetype(u) |
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230 v = nodetype(v) |
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231 except BaseException as e: |
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232 raise TypeError( |
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233 f"Failed to convert nodes {u},{v} " f"to type {nodetype}." |
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234 ) from e |
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235 |
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236 if len(d) == 0 or data is False: |
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237 # no data or data type specified |
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238 edgedata = {} |
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239 elif data is True: |
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240 # no edge types specified |
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241 try: # try to evaluate as dictionary |
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242 edgedata = dict(literal_eval(" ".join(d))) |
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243 except BaseException as e: |
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244 raise TypeError( |
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245 f"Failed to convert edge data ({d})" f"to dictionary." |
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246 ) from e |
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247 else: |
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248 # convert edge data to dictionary with specified keys and type |
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249 if len(d) != len(data): |
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250 raise IndexError( |
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251 f"Edge data {d} and data_keys {data} are not the same length" |
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252 ) |
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253 edgedata = {} |
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254 for (edge_key, edge_type), edge_value in zip(data, d): |
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255 try: |
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256 edge_value = edge_type(edge_value) |
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257 except BaseException as e: |
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258 raise TypeError( |
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259 f"Failed to convert {edge_key} data " |
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260 f"{edge_value} to type {edge_type}." |
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261 ) from e |
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262 edgedata.update({edge_key: edge_value}) |
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263 G.add_node(u, bipartite=0) |
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264 G.add_node(v, bipartite=1) |
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265 G.add_edge(u, v, **edgedata) |
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266 return G |
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267 |
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268 |
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269 @open_file(0, mode="rb") |
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270 def read_edgelist( |
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271 path, |
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272 comments="#", |
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273 delimiter=None, |
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274 create_using=None, |
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275 nodetype=None, |
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276 data=True, |
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277 edgetype=None, |
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278 encoding="utf-8", |
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279 ): |
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280 """Read a bipartite graph from a list of edges. |
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281 |
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282 Parameters |
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283 ---------- |
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284 path : file or string |
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285 File or filename to read. If a file is provided, it must be |
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286 opened in 'rb' mode. |
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287 Filenames ending in .gz or .bz2 will be uncompressed. |
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288 comments : string, optional |
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289 The character used to indicate the start of a comment. |
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290 delimiter : string, optional |
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291 The string used to separate values. The default is whitespace. |
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292 create_using : Graph container, optional, |
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293 Use specified container to build graph. The default is networkx.Graph, |
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294 an undirected graph. |
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295 nodetype : int, float, str, Python type, optional |
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296 Convert node data from strings to specified type |
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297 data : bool or list of (label,type) tuples |
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298 Tuples specifying dictionary key names and types for edge data |
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299 edgetype : int, float, str, Python type, optional OBSOLETE |
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300 Convert edge data from strings to specified type and use as 'weight' |
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301 encoding: string, optional |
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302 Specify which encoding to use when reading file. |
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303 |
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304 Returns |
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305 ------- |
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306 G : graph |
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307 A networkx Graph or other type specified with create_using |
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308 |
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309 Examples |
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310 -------- |
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311 >>> from networkx.algorithms import bipartite |
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312 >>> G = nx.path_graph(4) |
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313 >>> G.add_nodes_from([0, 2], bipartite=0) |
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314 >>> G.add_nodes_from([1, 3], bipartite=1) |
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315 >>> bipartite.write_edgelist(G, "test.edgelist") |
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316 >>> G = bipartite.read_edgelist("test.edgelist") |
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317 |
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318 >>> fh = open("test.edgelist", "rb") |
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319 >>> G = bipartite.read_edgelist(fh) |
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320 >>> fh.close() |
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321 |
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322 >>> G = bipartite.read_edgelist("test.edgelist", nodetype=int) |
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323 |
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324 Edgelist with data in a list: |
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325 |
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326 >>> textline = "1 2 3" |
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327 >>> fh = open("test.edgelist", "w") |
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328 >>> d = fh.write(textline) |
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329 >>> fh.close() |
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330 >>> G = bipartite.read_edgelist( |
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331 ... "test.edgelist", nodetype=int, data=(("weight", float),) |
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332 ... ) |
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333 >>> list(G) |
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334 [1, 2] |
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335 >>> list(G.edges(data=True)) |
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336 [(1, 2, {'weight': 3.0})] |
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337 |
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338 See parse_edgelist() for more examples of formatting. |
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339 |
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340 See Also |
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341 -------- |
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342 parse_edgelist |
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343 |
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344 Notes |
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345 ----- |
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346 Since nodes must be hashable, the function nodetype must return hashable |
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347 types (e.g. int, float, str, frozenset - or tuples of those, etc.) |
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348 """ |
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349 lines = (line.decode(encoding) for line in path) |
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350 return parse_edgelist( |
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351 lines, |
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352 comments=comments, |
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353 delimiter=delimiter, |
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354 create_using=create_using, |
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355 nodetype=nodetype, |
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356 data=data, |
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357 ) |