103 lines
2.9 KiB
Python
103 lines
2.9 KiB
Python
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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 out-edges 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, self-loops are allowed. Node index starts from 0.
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"""
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import networkx
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from networkx.utils import open_file
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@open_file(1, mode="w")
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def write_p2g(G, path, encoding="utf-8"):
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"""Write NetworkX graph in p2g format.
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Notes
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-----
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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((f"{G.name}\n").encode(encoding))
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path.write((f"{G.order()} {G.size()}\n").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((f"{n}\n").encode(encoding))
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for nbr in G.neighbors(n):
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path.write((f"{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="utf-8"):
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"""Read graph in p2g format from path.
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Returns
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-------
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MultiDiGraph
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Notes
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-----
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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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-------
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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
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