test_index_cliques.py

import argparse
import networkx as nx
from itertools import combinations
from multiprocessing import Pool


def parse_arguments():
    parser = argparse.ArgumentParser(description='Transform a 10X barcode graph into a d2 graph. The program dig for the d-graphs and then merge them into a d2-graph.')
    parser.add_argument('barcode_graph', help='The barcode graph file. Must be a gefx formated file.')
    parser.add_argument('--threads',       '-t', default=8, type=int, help='Number of thread to use for dgraph computation')

    args = parser.parse_args()
    return args


def main():
    args = parse_arguments()
    print(args.barcode_graph)

    graph = nx.read_gexf(args.barcode_graph)

    for node in graph.nodes():
        neighbors = list(graph.neighbors(node))
        subgraph = nx.Graph(graph.subgraph(neighbors))

        index_cliques(subgraph, node)


def index_cliques(graph, node):
    clique_index = {}

    nb_cliques = 0
    nb_unfiltered_cliques = 0
    for clique in nx.find_cliques(graph):
        nb_cliques += 1
        if len(clique) > 3:
            # print(clique)
            nb_unfiltered_cliques += 1
    print(nb_unfiltered_cliques, '/', nb_cliques)


if __name__ == "__main__":
    main()