#!/Users/runner/bioconda/conda-bld/pybedtools_1595591469880/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_/bin/python
from __future__ import print_function
import time
import os
import pybedtools
from pybedtools.contrib import plotting

try:
    from matplotlib import pyplot as plt
except ImportError:
    raise ImportError("Matplotlib needs to be installed for example plotting")

colors = ["r", "b", "g"]


def plot_a_b_tool(a, b, method, **kwargs):
    """
    Use for BEDTools programs that use -a and -b input arguments.  Filenames
    `a` and `b` are used for `method` of the BedTool class, and `kwargs` are
    sent to that method.

    The result is a plot of `a`, `b`, and the result, with the commandline
    argument as the plot title.
    """
    a = pybedtools.BedTool(a)
    b = pybedtools.BedTool(b)
    kwargs["b"] = b
    result = getattr(a, method)(**kwargs)

    fig = plt.figure(figsize=(8, 2))
    ax = fig.add_subplot(111)
    ybase = 0
    yheight = 1
    ylabels = []
    yticks = []
    for color, bt, label in zip(
        colors,
        [result, b, a],
        ["result", os.path.basename(b.fn), os.path.basename(a.fn)],
    ):
        ylabels.append(label)
        track = plotting.Track(
            bt, visibility="squish", alpha=0.5, ybase=ybase, color=color
        )
        yticks.append(track.midpoint)
        ybase = track.ymax + 0.1
        ax.add_collection(track)
    ax.set_yticklabels(ylabels)
    ax.set_yticks(yticks)
    ax.set_title(" ".join([os.path.basename(i) for i in result._cmds]))
    ax.axis("tight")
    fig.subplots_adjust(top=0.8, bottom=0.15)
    return ax


def plot_i_tool(i, method, **kwargs):
    a = pybedtools.BedTool(i)
    result = getattr(a, method)(**kwargs)
    fig = plt.figure(figsize=(8, 2))
    ax = fig.add_subplot(111)
    res_track = plotting.Track(
        result, color="r", alpha=0.5, ybase=0, visibility="squish"
    )
    a_track = plotting.Track(a, color="b", alpha=0.5, ybase=1.1, visibility="squish")
    ax.add_collection(res_track)
    ax.add_collection(a_track)
    ax.set_yticks([res_track.midpoint, a_track.midpoint])
    ax.set_yticklabels(["result", os.path.basename(a.fn)])
    ax.axis("tight")
    ax.set_title(" ".join([os.path.basename(k) for k in result._cmds]))
    fig.subplots_adjust(top=0.8, bottom=0.15)
    return ax


if __name__ == "__main__":
    a = pybedtools.example_filename("a.bed")
    b = pybedtools.example_filename("b.bed")

    plot_a_b_tool(a, b, "intersect", u=True)
    plot_a_b_tool(a, b, "intersect")
    plot_a_b_tool(a, b, "subtract")

    plot_i_tool(a, "merge")

    # Check performance -- should be <2s for 15k features
    t0 = time.time()
    fig = plt.figure(figsize=(8, 2))
    ax = fig.add_subplot(111)
    big = pybedtools.example_bedtool("dm3-chr2L-5M.gff.gz")
    gene_track = plotting.Track(
        big.filter(lambda x: x[2] == "gene"),
        color="k",
        visibility="squish",
        alpha=0.5,
        label="genes",
    )
    exon_track = plotting.Track(
        big.filter(lambda x: x[2] == "exon"),
        color="r",
        visibility="squish",
        alpha=0.5,
        ybase=gene_track.ymax,
        label="exons",
    )
    ax.add_collection(gene_track)
    ax.add_collection(exon_track)

    ax.legend(loc="best")
    ax.axis("tight")

    print("%.2fs" % (time.time() - t0))

    plt.show()
