forked from 170010011/fr
103 lines
2.9 KiB
Python
103 lines
2.9 KiB
Python
|
"""
|
||
|
This module provides the following: read and write of p2g format
|
||
|
used in metabolic pathway studies.
|
||
|
|
||
|
See https://web.archive.org/web/20080626113807/http://www.cs.purdue.edu/homes/koyuturk/pathway/ for a description.
|
||
|
|
||
|
The summary is included here:
|
||
|
|
||
|
A file that describes a uniquely labeled graph (with extension ".gr")
|
||
|
format looks like the following:
|
||
|
|
||
|
|
||
|
name
|
||
|
3 4
|
||
|
a
|
||
|
1 2
|
||
|
b
|
||
|
|
||
|
c
|
||
|
0 2
|
||
|
|
||
|
"name" is simply a description of what the graph corresponds to. The
|
||
|
second line displays the number of nodes and number of edges,
|
||
|
respectively. This sample graph contains three nodes labeled "a", "b",
|
||
|
and "c". The rest of the graph contains two lines for each node. The
|
||
|
first line for a node contains the node label. After the declaration
|
||
|
of the node label, the out-edges of that node in the graph are
|
||
|
provided. For instance, "a" is linked to nodes 1 and 2, which are
|
||
|
labeled "b" and "c", while the node labeled "b" has no outgoing
|
||
|
edges. Observe that node labeled "c" has an outgoing edge to
|
||
|
itself. Indeed, self-loops are allowed. Node index starts from 0.
|
||
|
|
||
|
"""
|
||
|
import networkx
|
||
|
from networkx.utils import open_file
|
||
|
|
||
|
|
||
|
@open_file(1, mode="w")
|
||
|
def write_p2g(G, path, encoding="utf-8"):
|
||
|
"""Write NetworkX graph in p2g format.
|
||
|
|
||
|
Notes
|
||
|
-----
|
||
|
This format is meant to be used with directed graphs with
|
||
|
possible self loops.
|
||
|
"""
|
||
|
path.write((f"{G.name}\n").encode(encoding))
|
||
|
path.write((f"{G.order()} {G.size()}\n").encode(encoding))
|
||
|
nodes = list(G)
|
||
|
# make dictionary mapping nodes to integers
|
||
|
nodenumber = dict(zip(nodes, range(len(nodes))))
|
||
|
for n in nodes:
|
||
|
path.write((f"{n}\n").encode(encoding))
|
||
|
for nbr in G.neighbors(n):
|
||
|
path.write((f"{nodenumber[nbr]} ").encode(encoding))
|
||
|
path.write("\n".encode(encoding))
|
||
|
|
||
|
|
||
|
@open_file(0, mode="r")
|
||
|
def read_p2g(path, encoding="utf-8"):
|
||
|
"""Read graph in p2g format from path.
|
||
|
|
||
|
Returns
|
||
|
-------
|
||
|
MultiDiGraph
|
||
|
|
||
|
Notes
|
||
|
-----
|
||
|
If you want a DiGraph (with no self loops allowed and no edge data)
|
||
|
use D=networkx.DiGraph(read_p2g(path))
|
||
|
"""
|
||
|
lines = (line.decode(encoding) for line in path)
|
||
|
G = parse_p2g(lines)
|
||
|
return G
|
||
|
|
||
|
|
||
|
def parse_p2g(lines):
|
||
|
"""Parse p2g format graph from string or iterable.
|
||
|
|
||
|
Returns
|
||
|
-------
|
||
|
MultiDiGraph
|
||
|
"""
|
||
|
description = next(lines).strip()
|
||
|
# are multiedges (parallel edges) allowed?
|
||
|
G = networkx.MultiDiGraph(name=description, selfloops=True)
|
||
|
nnodes, nedges = map(int, next(lines).split())
|
||
|
nodelabel = {}
|
||
|
nbrs = {}
|
||
|
# loop over the nodes keeping track of node labels and out neighbors
|
||
|
# defer adding edges until all node labels are known
|
||
|
for i in range(nnodes):
|
||
|
n = next(lines).strip()
|
||
|
nodelabel[i] = n
|
||
|
G.add_node(n)
|
||
|
nbrs[n] = map(int, next(lines).split())
|
||
|
# now we know all of the node labels so we can add the edges
|
||
|
# with the correct labels
|
||
|
for n in G:
|
||
|
for nbr in nbrs[n]:
|
||
|
G.add_edge(n, nodelabel[nbr])
|
||
|
return G
|