clip_tips.py

import Graph
import functions
import sys


if len(sys.argv) < 4:
    print("You need to give the following arguments <graph.gfa> <k> <output_file>")
    sys.exit()

new_graph = Graph.Graph()
new_graph.read_gfa(sys.argv[1])
new_graph.k = int(sys.argv[2])


nodes_to_remove = []
for node in new_graph.nodes.values():
    if (len(node.start) == 0) or (len(node.end) == 0):
        if node.seq_len < (2*new_graph.k - 1):
            nodes_to_remove.append(node.id)

functions.remove_nodes(new_graph, nodes_to_remove)

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