remove_lonely_nodes.py

import sys
from Graph import Graph
import find_components
import functions

if len(sys.argv) != 4:
    print("You need to give the following arguments <input_gfa> <k> <output_file>")
    sys.exit(0)

print("reading files")
new_graph = Graph()
new_graph.read_gfa(sys.argv[1])
new_graph.k = int(sys.argv[2])

nodes_to_remove = []
for n in new_graph.nodes.values():
    if (len(n.start) == 0) and (len(n.end) == 0):
        nodes_to_remove.append(n.id)

for i in nodes_to_remove:
    del new_graph.nodes[i]

functions.write_gfa(nodes=new_graph.nodes, k = new_graph.k, output_file=str(sys.argv[3]))