Mercurial > repos > shellac > sam_consensus_v3
annotate env/lib/python3.9/site-packages/networkx/readwrite/adjlist.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 Adjacency List |
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4 ************** |
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5 Read and write NetworkX graphs as adjacency lists. |
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6 |
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7 Adjacency list format is useful for graphs without data associated |
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8 with nodes or edges and for nodes that can be meaningfully represented |
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9 as strings. |
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10 |
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11 Format |
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12 ------ |
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13 The adjacency list format consists of lines with node labels. The |
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14 first label in a line is the source node. Further labels in the line |
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15 are considered target nodes and are added to the graph along with an edge |
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16 between the source node and target node. |
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17 |
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18 The graph with edges a-b, a-c, d-e can be represented as the following |
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19 adjacency list (anything following the # in a line is a comment):: |
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20 |
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21 a b c # source target target |
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22 d e |
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23 """ |
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24 |
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25 __all__ = ["generate_adjlist", "write_adjlist", "parse_adjlist", "read_adjlist"] |
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26 |
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27 from networkx.utils import open_file |
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28 import networkx as nx |
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29 |
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30 |
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31 def generate_adjlist(G, delimiter=" "): |
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32 """Generate a single line of the graph G in adjacency list format. |
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33 |
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34 Parameters |
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35 ---------- |
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36 G : NetworkX graph |
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37 |
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38 delimiter : string, optional |
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39 Separator for node labels |
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40 |
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41 Returns |
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42 ------- |
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43 lines : string |
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44 Lines of data in adjlist format. |
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45 |
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46 Examples |
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47 -------- |
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48 >>> G = nx.lollipop_graph(4, 3) |
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49 >>> for line in nx.generate_adjlist(G): |
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50 ... print(line) |
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51 0 1 2 3 |
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52 1 2 3 |
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53 2 3 |
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54 3 4 |
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55 4 5 |
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56 5 6 |
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57 6 |
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58 |
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59 See Also |
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60 -------- |
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61 write_adjlist, read_adjlist |
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62 |
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63 """ |
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64 directed = G.is_directed() |
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65 seen = set() |
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66 for s, nbrs in G.adjacency(): |
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67 line = str(s) + delimiter |
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68 for t, data in nbrs.items(): |
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69 if not directed and t in seen: |
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70 continue |
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71 if G.is_multigraph(): |
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72 for d in data.values(): |
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73 line += str(t) + delimiter |
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74 else: |
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75 line += str(t) + delimiter |
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76 if not directed: |
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77 seen.add(s) |
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78 yield line[: -len(delimiter)] |
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79 |
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80 |
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81 @open_file(1, mode="wb") |
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82 def write_adjlist(G, path, comments="#", delimiter=" ", encoding="utf-8"): |
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83 """Write graph G in single-line adjacency-list format to path. |
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84 |
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85 |
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86 Parameters |
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87 ---------- |
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88 G : NetworkX graph |
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89 |
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90 path : string or file |
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91 Filename or file handle for data output. |
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92 Filenames ending in .gz or .bz2 will be compressed. |
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93 |
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94 comments : string, optional |
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95 Marker for comment lines |
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96 |
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97 delimiter : string, optional |
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98 Separator for node labels |
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99 |
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100 encoding : string, optional |
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101 Text encoding. |
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102 |
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103 Examples |
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104 -------- |
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105 >>> G = nx.path_graph(4) |
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106 >>> nx.write_adjlist(G, "test.adjlist") |
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107 |
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108 The path can be a filehandle or a string with the name of the file. If a |
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109 filehandle is provided, it has to be opened in 'wb' mode. |
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110 |
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111 >>> fh = open("test.adjlist", "wb") |
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112 >>> nx.write_adjlist(G, fh) |
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113 |
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114 Notes |
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115 ----- |
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116 This format does not store graph, node, or edge data. |
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117 |
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118 See Also |
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119 -------- |
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120 read_adjlist, generate_adjlist |
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121 """ |
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122 import sys |
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123 import time |
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124 |
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125 pargs = comments + " ".join(sys.argv) + "\n" |
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126 header = ( |
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127 pargs |
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128 + comments |
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129 + f" GMT {time.asctime(time.gmtime())}\n" |
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130 + comments |
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131 + f" {G.name}\n" |
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132 ) |
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133 path.write(header.encode(encoding)) |
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134 |
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135 for line in generate_adjlist(G, delimiter): |
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136 line += "\n" |
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137 path.write(line.encode(encoding)) |
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138 |
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139 |
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140 def parse_adjlist( |
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141 lines, comments="#", delimiter=None, create_using=None, nodetype=None |
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142 ): |
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143 """Parse lines of a graph adjacency list representation. |
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144 |
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145 Parameters |
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146 ---------- |
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147 lines : list or iterator of strings |
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148 Input data in adjlist format |
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149 |
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150 create_using : NetworkX graph constructor, optional (default=nx.Graph) |
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151 Graph type to create. If graph instance, then cleared before populated. |
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152 |
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153 nodetype : Python type, optional |
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154 Convert nodes to this type. |
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155 |
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156 comments : string, optional |
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157 Marker for comment lines |
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158 |
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159 delimiter : string, optional |
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160 Separator for node labels. The default is whitespace. |
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161 |
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162 Returns |
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163 ------- |
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164 G: NetworkX graph |
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165 The graph corresponding to the lines in adjacency list format. |
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166 |
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167 Examples |
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168 -------- |
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169 >>> lines = ["1 2 5", "2 3 4", "3 5", "4", "5"] |
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170 >>> G = nx.parse_adjlist(lines, nodetype=int) |
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171 >>> nodes = [1, 2, 3, 4, 5] |
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172 >>> all(node in G for node in nodes) |
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173 True |
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174 >>> edges = [(1, 2), (1, 5), (2, 3), (2, 4), (3, 5)] |
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175 >>> all((u, v) in G.edges() or (v, u) in G.edges() for (u, v) in edges) |
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176 True |
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177 |
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178 See Also |
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179 -------- |
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180 read_adjlist |
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181 |
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182 """ |
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183 G = nx.empty_graph(0, create_using) |
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184 for line in lines: |
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185 p = line.find(comments) |
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186 if p >= 0: |
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187 line = line[:p] |
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188 if not len(line): |
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189 continue |
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190 vlist = line.strip().split(delimiter) |
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191 u = vlist.pop(0) |
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192 # convert types |
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193 if nodetype is not None: |
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194 try: |
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195 u = nodetype(u) |
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196 except BaseException as e: |
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197 raise TypeError( |
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198 f"Failed to convert node ({u}) to type " f"{nodetype}" |
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199 ) from e |
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200 G.add_node(u) |
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201 if nodetype is not None: |
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202 try: |
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203 vlist = list(map(nodetype, vlist)) |
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204 except BaseException as e: |
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205 raise TypeError( |
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206 f"Failed to convert nodes ({','.join(vlist)}) " |
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207 f"to type {nodetype}" |
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208 ) from e |
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209 G.add_edges_from([(u, v) for v in vlist]) |
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210 return G |
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211 |
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212 |
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213 @open_file(0, mode="rb") |
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214 def read_adjlist( |
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215 path, |
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216 comments="#", |
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217 delimiter=None, |
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218 create_using=None, |
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219 nodetype=None, |
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220 encoding="utf-8", |
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221 ): |
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222 """Read graph in adjacency list format from path. |
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223 |
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224 Parameters |
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225 ---------- |
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226 path : string or file |
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227 Filename or file handle to read. |
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228 Filenames ending in .gz or .bz2 will be uncompressed. |
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229 |
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230 create_using : NetworkX graph constructor, optional (default=nx.Graph) |
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231 Graph type to create. If graph instance, then cleared before populated. |
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232 |
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233 nodetype : Python type, optional |
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234 Convert nodes to this type. |
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235 |
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236 comments : string, optional |
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237 Marker for comment lines |
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238 |
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239 delimiter : string, optional |
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240 Separator for node labels. The default is whitespace. |
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241 |
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242 Returns |
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243 ------- |
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244 G: NetworkX graph |
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245 The graph corresponding to the lines in adjacency list format. |
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246 |
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247 Examples |
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248 -------- |
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249 >>> G = nx.path_graph(4) |
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250 >>> nx.write_adjlist(G, "test.adjlist") |
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251 >>> G = nx.read_adjlist("test.adjlist") |
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252 |
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253 The path can be a filehandle or a string with the name of the file. If a |
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254 filehandle is provided, it has to be opened in 'rb' mode. |
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255 |
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256 >>> fh = open("test.adjlist", "rb") |
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257 >>> G = nx.read_adjlist(fh) |
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258 |
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259 Filenames ending in .gz or .bz2 will be compressed. |
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260 |
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261 >>> nx.write_adjlist(G, "test.adjlist.gz") |
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262 >>> G = nx.read_adjlist("test.adjlist.gz") |
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263 |
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264 The optional nodetype is a function to convert node strings to nodetype. |
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265 |
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266 For example |
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267 |
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268 >>> G = nx.read_adjlist("test.adjlist", nodetype=int) |
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269 |
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270 will attempt to convert all nodes to integer type. |
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271 |
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272 Since nodes must be hashable, the function nodetype must return hashable |
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273 types (e.g. int, float, str, frozenset - or tuples of those, etc.) |
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274 |
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275 The optional create_using parameter indicates the type of NetworkX graph |
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276 created. The default is `nx.Graph`, an undirected graph. |
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277 To read the data as a directed graph use |
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278 |
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279 >>> G = nx.read_adjlist("test.adjlist", create_using=nx.DiGraph) |
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280 |
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281 Notes |
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282 ----- |
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283 This format does not store graph or node data. |
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284 |
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285 See Also |
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286 -------- |
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287 write_adjlist |
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288 """ |
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289 lines = (line.decode(encoding) for line in path) |
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290 return parse_adjlist( |
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291 lines, |
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292 comments=comments, |
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293 delimiter=delimiter, |
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294 create_using=create_using, |
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295 nodetype=nodetype, |
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296 ) |