#!/usr/bin/python
# Load required modules
import networkx as nx
def parse_args(input_list=None):
# Parse arguments
import argparse
class Args: pass
args = Args()
description = 'Creates permuted networks for the given network.'
parser = argparse.ArgumentParser(description=description)
parser.add_argument('-n', '--network_edgelist', required=True,
help='PPI edgelist location.')
parser.add_argument('-o', '--output_dir', required=True,
help='Name of output directory.')
parser.add_argument('-q', '--Q', default=100, type=int,
help='Edge swap constant.')
parser.add_argument('-c', '--num_networks', default=100, type=int,
help='Number of permuted networks to create.')
parser.add_argument('-s', '--start_index', default=1, type=int,
help='Start index for name of permuted networks.')
parser.add_argument('-v', '--verbose', default=False, action='store_true',
help='Flag verbose mode.')
# If called from the command line, parse command line args.
if input_list: parser.parse_args(input_list, namespace=args)
else: parser.parse_args(namespace=args)
return args
[docs]def load_network(network_file):
"""Wrapper for the NetworkX `read_edgelist <http://goo.gl/xfDPS>`_ function."""
return nx.read_edgelist(network_file)
[docs]def permute_network(G, Q):
"""Permutes the given graph G=(V, E) by performing | E | * Q edge swaps.
:type G: NetworkX Graph
:param G: PPI network.
:type Q: int
:type Q: int
:param Q: constant multiplier for number Q * | E | of edge swaps to perform (default and suggested value: 100). See `Milo et al. (2003) <http://goo.gl/d723i>`_ for details on choosing Q.
:returns: a permuted version of H (G is not modified)
**Examples:**
A view of example input:
>>> import networkx as nx
>>> G = nx.Graph()
>>> G.add_edges_from([["G1", "G2"], ["G2", "G3"], ["G2", "G4"], ["G1", "G4"],
["G2", "G5"], ["G5", "G6"], ["G5", "G7"]])
>>> nx.draw_spectral(G, node_size=125, font_size=8)
.. image:: /_static/ppi_network.png
Permuting the network by performing | E | * 10 edge swaps.
>>> permute_network(G, 10)
.. image:: /_static/permuted_ppi_network.png
**See also:** :func:`load_network`, :func:`permute_mutation_data.permute_mutation_data`.
**Notes:** Uses the NetworkX `double_edge_swap <http://goo.gl/wWxBD>`_ function.
"""
H = G.copy()
nx.double_edge_swap(H, nswap=Q*len( G.edges() ), max_tries=1e75)
return H
def run(args):
"""Permutes the given PPI network the specified number of times."""
import sys, os
# Load network
G = load_network(args.network_edgelist)
if args.verbose:
print 'Input network has', len( G.edges() ), 'edges among', len(G.nodes()),
print 'nodes.\nPerforming', len( G.edges() ) * args.Q, 'edge swaps.'
# Make sure output directory exists
os.system('mkdir -p ' + args.output_dir)
# Permute network and output files
for i in range(args.num_networks):
if args.verbose:
sys.stdout.write('+')
sys.stdout.flush()
# Permute graph and output as an edge list
H = permute_network(G, args.Q)
filename = args.output_dir + "/" + str(i + args.start_index) + ".txt"
nx.write_edgelist(H, filename)
if args.verbose: print
if __name__ == "__main__": run(parse_args())
