regList

#!/usr/bin/python

import sys
import networkx as nx

def getOptions():
    import argparse

    # create the top-level parser
    description = ("Build list of regulated genes from a regulatory network")
    parser = argparse.ArgumentParser(description = description)
    parser.add_argument('GML_FILE', action='store',
                            help='Pangenome regulatory network')
    return parser.parse_args()

options = getOptions()

infile = options.GML_FILE
n = nx.read_gml(infile)

# Inspect the proportion of conserved and variable regulatory links
regulators = filter(lambda x: 'name' in n.node[x], n.nodes())

for r in regulators:
    tree = nx.depth_first_search.dfs_tree(n, r)

    for g in sorted(tree.nodes(), key=lambda x: n.node[x]['label']):
        if g == r: continue

        if 'operon' in n.node[g]:
            print('\t'.join( [n.node[r]['name'], n.node[r]['label'],
                              n.node[g]['label'], 'operon'] ))
        else:
            print('\t'.join( [n.node[r]['name'], n.node[r]['label'],
                              n.node[g]['label'], 'regulated'] ))