compress.py

#!/usr/bin/env python3


import pygfa
import networkx as nx
import matplotlib.pyplot as plt
import argparse

import logging

logging.basicConfig(level=logging.DEBUG)

if __name__ == "__main__":
    # -------------------------CLI-ARGUMENT-MANAGEMENT-------------------------------- #
    parser = argparse.ArgumentParser(description="Compute graph structure from GFA file.")
    parser.add_argument("-f", "--file", metavar="file", type=str, nargs=1, required=True)
    parser.add_argument("-d", "--display", action="store_true", default=False)
    parser.add_argument("-c", "--convert", metavar=("gfa_version", "output_file"), type=str, nargs=2, required=False)
    # -------------------------------------------------------------------------------- #

    try:
        args = parser.parse_args()

        tmp_pygfa = pygfa.gfa.GFA.from_gfa(args.file[0])
        node_color = "r"

        if args.display:
            edge_labels = dict([((node1, node2), key) for node1, node2, key in tmp_pygfa.edges(keys=True)])
            layout = nx.spring_layout(tmp_pygfa._graph)
            nx.draw(tmp_pygfa._graph, layout, with_labels=True, node_color=node_color)
            # nx.draw_networkx_edge_labels (tmp_pygfa, layout, edge_labels = edge_labels)
            plt.show()

        if args.convert:
            version = 1
            if args.convert[0] in ("1", "gfa1", "GFA1"):
                version = 1
            else:
                raise ValueError("Only GFA1 conversion is supported")

            tmp_pygfa.dump(gfa_version=version, out=args.convert[1])
    except SystemExit:
        pass
    except EnvironmentError as env_error:
        print(repr(env_error))