"""
Main script for running tissue-specific graph walk experiments, to convergence.
"""
import sys
import argparse
from walker import Walker
def generate_seed_list(seed_file):
""" Read seed file into a list. """
seed_list = []
try:
fp = open(seed_file, "r")
except IOError:
sys.exit("Error opening file {}".format(seed_file))
for line in fp.readlines():
info = line.rstrip().split()
if len(info) > 1:
seed_list.append(info[1])
else:
seed_list.append(info[0])
fp.close()
return seed_list
def get_node_list(node_file):
node_list = []
try:
fp = open(node_file, 'r')
except IOError:
sys.exit('Could not open file: {}'.format(node_file))
# read the first (i.e. largest) connected component
cur_line = fp.readline()
while cur_line and not cur_line.isspace():
if cur_line:
node_list.append(cur_line.rstrip())
cur_line = fp.readline()
fp.close()
return node_list
def main(argv):
# set up argument parsing
parser = argparse.ArgumentParser()
parser.add_argument('input_graph', help='Original graph input file, in\
edge list format')
parser.add_argument('seed', help='Seed file, to pull start nodes from')
parser.add_argument('-e', '--restart_prob', type=float, default=0.7,
help='Restart probability for random walk')
parser.add_argument('-l', '--low_list', nargs='?', default=None,
help='<Optional> List of genes expressed and\
unexpressed in the current tissue, if applicable')
parser.add_argument('-n', '--node_list', nargs='?', default=None,
help='<Optional> Order of output probs')
parser.add_argument('-o', '--original_graph_prob', type=float, default=0.1,
help='Probability of walking on the original (non-\
tissue specific) graph, if applicable')
parser.add_argument('-r', '--remove', nargs='+',
help='<Optional> Nodes to remove from the graph, if any')
opts = parser.parse_args()
seed_list = generate_seed_list(opts.seed)
node_list = get_node_list(opts.node_list) if opts.node_list else []
# filter nodes we want to remove out of the starting seed, if any
remove_list = opts.remove if opts.remove else []
if remove_list:
seed_list = [s for s in seed_list if s not in remove_list]
# run the experiments, and write a rank list to stdout
wk = Walker(opts.input_graph, opts.low_list, remove_list)
wk.run_exp(seed_list, opts.restart_prob,
opts.original_graph_prob, node_list)
if __name__ == '__main__':
main(sys.argv)
# main(testdata/test_network.ppi,testdata/test_seed.txt)
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