ioftools / networkxMiCe / networkxmaster / networkx / readwrite / p2g.py @ 5cef0f13
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"""


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This module provides the following: read and write of p2g format

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used in metabolic pathway studies.

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See https://web.archive.org/web/20080626113807/http://www.cs.purdue.edu/homes/koyuturk/pathway/ for a description.

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The summary is included here:

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A file that describes a uniquely labeled graph (with extension ".gr")

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format looks like the following:

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name

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3 4

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a

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1 2

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b

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c

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0 2

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"name" is simply a description of what the graph corresponds to. The

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second line displays the number of nodes and number of edges,

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respectively. This sample graph contains three nodes labeled "a", "b",

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and "c". The rest of the graph contains two lines for each node. The

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first line for a node contains the node label. After the declaration

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of the node label, the outedges of that node in the graph are

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provided. For instance, "a" is linked to nodes 1 and 2, which are

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labeled "b" and "c", while the node labeled "b" has no outgoing

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edges. Observe that node labeled "c" has an outgoing edge to

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itself. Indeed, selfloops are allowed. Node index starts from 0.

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"""

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# Copyright (C) 20082012 by

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# Aric Hagberg <hagberg@lanl.gov>

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# Dan Schult <dschult@colgate.edu>

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# Pieter Swart <swart@lanl.gov>

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# All rights reserved.

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# BSD license.

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import networkx 
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from networkx.utils import is_string_like, open_file 
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__author__ = '\n'.join(['Willem Ligtenberg (w.p.a.ligtenberg@tue.nl)', 
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'Aric Hagberg (aric.hagberg@gmail.com)'])

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@open_file(1, mode='w') 
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def write_p2g(G, path, encoding='utf8'): 
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"""Write NetworkX graph in p2g format.

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Notes

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This format is meant to be used with directed graphs with

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possible self loops.

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"""

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path.write(("%s\n" % G.name).encode(encoding))

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path.write(("%s %s\n" % (G.order(), G.size())).encode(encoding))

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nodes = list(G)

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# make dictionary mapping nodes to integers

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nodenumber = dict(zip(nodes, range(len(nodes)))) 
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for n in nodes: 
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path.write(("%s\n" % n).encode(encoding))

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for nbr in G.neighbors(n): 
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path.write(("%s " % nodenumber[nbr]).encode(encoding))

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path.write("\n".encode(encoding))

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@open_file(0, mode='r') 
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def read_p2g(path, encoding='utf8'): 
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"""Read graph in p2g format from path.

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Returns

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MultiDiGraph

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Notes

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If you want a DiGraph (with no self loops allowed and no edge data)

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use D=networkx.DiGraph(read_p2g(path))

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"""

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lines = (line.decode(encoding) for line in path) 
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G = parse_p2g(lines) 
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return G

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def parse_p2g(lines): 
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"""Parse p2g format graph from string or iterable.

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Returns

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MultiDiGraph

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"""

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description = next(lines).strip()

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# are multiedges (parallel edges) allowed?

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G = networkx.MultiDiGraph(name=description, selfloops=True)

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nnodes, nedges = map(int, next(lines).split()) 
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nodelabel = {} 
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nbrs = {} 
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# loop over the nodes keeping track of node labels and out neighbors

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# defer adding edges until all node labels are known

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for i in range(nnodes): 
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n = next(lines).strip()

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nodelabel[i] = n 
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G.add_node(n) 
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nbrs[n] = map(int, next(lines).split()) 
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# now we know all of the node labels so we can add the edges

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# with the correct labels

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for n in G: 
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for nbr in nbrs[n]: 
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G.add_edge(n, nodelabel[nbr]) 
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return G
