Mercurial > repos > shellac > guppy_basecaller

annotate env/lib/python3.7/site-packages/networkx/readwrite/p2g.py @ 3:758bc20232e8 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
"planemo upload commit 2a0fe2cc28b09e101d37293e53e82f61762262ec"
author shellac
date Thu, 14 May 2020 16:20:52 -0400
parents 26e78fe6e8c4
children
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0
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1 """
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2 This module provides the following: read and write of p2g format
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3 used in metabolic pathway studies.
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4
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5 See https://web.archive.org/web/20080626113807/http://www.cs.purdue.edu/homes/koyuturk/pathway/ for a description.
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6
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7 The summary is included here:
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8
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9 A file that describes a uniquely labeled graph (with extension ".gr")
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10 format looks like the following:
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11
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12
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13 name
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14 3 4
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15 a
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16 1 2
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17 b
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18
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19 c
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20 0 2
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21
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22 "name" is simply a description of what the graph corresponds to. The
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23 second line displays the number of nodes and number of edges,
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24 respectively. This sample graph contains three nodes labeled "a", "b",
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25 and "c". The rest of the graph contains two lines for each node. The
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26 first line for a node contains the node label. After the declaration
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27 of the node label, the out-edges of that node in the graph are
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28 provided. For instance, "a" is linked to nodes 1 and 2, which are
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29 labeled "b" and "c", while the node labeled "b" has no outgoing
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30 edges. Observe that node labeled "c" has an outgoing edge to
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31 itself. Indeed, self-loops are allowed. Node index starts from 0.
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32
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33 """
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34 # Copyright (C) 2008-2012 by
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35 # Aric Hagberg <hagberg@lanl.gov>
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36 # Dan Schult <dschult@colgate.edu>
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37 # Pieter Swart <swart@lanl.gov>
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38 # All rights reserved.
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39 # BSD license.
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40 import networkx
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41 from networkx.utils import is_string_like, open_file
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42 __author__ = '\n'.join(['Willem Ligtenberg (w.p.a.ligtenberg@tue.nl)',
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43 'Aric Hagberg (aric.hagberg@gmail.com)'])
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44
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45
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46 @open_file(1, mode='w')
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47 def write_p2g(G, path, encoding='utf-8'):
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48 """Write NetworkX graph in p2g format.
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49
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50 Notes
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51 -----
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52 This format is meant to be used with directed graphs with
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53 possible self loops.
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54 """
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55 path.write(("%s\n" % G.name).encode(encoding))
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56 path.write(("%s %s\n" % (G.order(), G.size())).encode(encoding))
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57 nodes = list(G)
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58 # make dictionary mapping nodes to integers
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59 nodenumber = dict(zip(nodes, range(len(nodes))))
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60 for n in nodes:
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61 path.write(("%s\n" % n).encode(encoding))
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62 for nbr in G.neighbors(n):
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63 path.write(("%s " % nodenumber[nbr]).encode(encoding))
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64 path.write("\n".encode(encoding))
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65
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66
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67 @open_file(0, mode='r')
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68 def read_p2g(path, encoding='utf-8'):
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69 """Read graph in p2g format from path.
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70
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71 Returns
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72 -------
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73 MultiDiGraph
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74
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75 Notes
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76 -----
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77 If you want a DiGraph (with no self loops allowed and no edge data)
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78 use D=networkx.DiGraph(read_p2g(path))
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79 """
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80 lines = (line.decode(encoding) for line in path)
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81 G = parse_p2g(lines)
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82 return G
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83
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84
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85 def parse_p2g(lines):
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86 """Parse p2g format graph from string or iterable.
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87
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88 Returns
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89 -------
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90 MultiDiGraph
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91 """
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92 description = next(lines).strip()
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93 # are multiedges (parallel edges) allowed?
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94 G = networkx.MultiDiGraph(name=description, selfloops=True)
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95 nnodes, nedges = map(int, next(lines).split())
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96 nodelabel = {}
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97 nbrs = {}
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98 # loop over the nodes keeping track of node labels and out neighbors
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99 # defer adding edges until all node labels are known
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100 for i in range(nnodes):
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101 n = next(lines).strip()
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102 nodelabel[i] = n
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103 G.add_node(n)
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104 nbrs[n] = map(int, next(lines).split())
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105 # now we know all of the node labels so we can add the edges
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106 # with the correct labels
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107 for n in G:
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108 for nbr in nbrs[n]:
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109 G.add_edge(n, nodelabel[nbr])
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110 return G