bfs_subgraph_extractor.py

import sys
import os
from functions import write_gfa, bfs
from Graph import Graph

if len(sys.argv) < 5:
    print("You need to give 4 arguments, [input_gfa] [size_of_neighborhood] "
          "[output_file] [one or several starting points]")
    sys.exit(0)

if os.path.isfile(sys.argv[1]):
    print("reading file...\n")
    new_graph = Graph()
    new_graph.read_gfa(sys.argv[1])
    starting_points = []
    output_g = []

    for arg in sys.argv[4:]:
        starting_points.append(int(arg))

    for start in starting_points:
        path = bfs(new_graph.nodes, start, int(sys.argv[2]))
        output_g += path

    write_gfa(nodes=new_graph.nodes, list_of_nodes=output_g, output_file=sys.argv[3])

else:
    print("The file doesn't exist")
    sys.exit()