#!/opt/conda/conda-bld/goatools_1659831752154/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_plac/bin/python
# -*- coding: UTF-8 -*-

"""
Plot AMIGO style Gene Ontology graph using Graphviz.
"""

import os
import os.path as op
import sys

sys.path.insert(0, op.join(op.dirname(__file__), ".."))
from goatools.obo_parser import GODag, GraphEngines


if __name__ == "__main__":

    import optparse

    p = optparse.OptionParser("%prog [obo_file]", description=__doc__)
    p.add_option(
        "--description",
        dest="desc",
        help="Write term descriptions to stdout from the obo file specified in args",
        action="store_true",
    )
    p.add_option(
        "--term",
        dest="term",
        help="Write the parents and children of the query term",
        action="store",
        type="string",
        default=None,
    )
    p.add_option(
        "--engine",
        default="pygraphviz",
        choices=GraphEngines,
        help="Graph plot engine, must be one of {} [default: %default]".format(
            "|".join(GraphEngines)
        ),
    )
    p.add_option(
        "--gml",
        action="store_true",
        help="Write GML output (for Cytoscape) [default: %default]",
    )
    p.add_option(
        "--disable-draw-parents",
        action="store_false",
        dest="draw_parents",
        help="Do not draw parents of the query term",
    )
    p.add_option(
        "--disable-draw-children",
        action="store_false",
        dest="draw_children",
        help="Do not draw children of the query term",
    )
    p.add_option(
        "--output",
        "-o",
        default="GO_lineage.pdf",
        help="Output filename, suffix is image format, common formats e.g. pdf|svg|png|jpg|... [default: %default]",
    )
    p.add_option(
        "--dpi",
        default=96,
        type="int",
        help="Output figure dpi, ignored by vector image formats like svg and pdf [default: %default]",
    )

    p.set_defaults(draw_parents=True)
    p.set_defaults(draw_children=True)

    opts, args = p.parse_args()

    if not args:
        obo_file = "go-basic.obo"
    else:
        obo_file = args[0]
        assert os.path.exists(obo_file), "file %s not found!" % obo_file

    g = GODag(obo_file)

    if opts.desc:
        g.write_dag()

    # run a test case
    if opts.term is not None:
        rec = g.query_term(opts.term, verbose=True)
        g.draw_lineage(
            [rec],
            dpi=opts.dpi,
            engine=opts.engine,
            gml=opts.gml,
            output=opts.output,
            draw_parents=opts.draw_parents,
            draw_children=opts.draw_children,
        )
