annotate hist_plot.py @ 3:76d4cbefff85 draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit 5d56aa02b0f905507e1d98a2d74f0629b7591cd3"

#!/usr/bin/env python3
# read depth histogram plot

# imported from https://github.com/dfguan/purge_dups/blob/master/scripts/hist_plot.py

import argparse

import matplotlib as mpl
import matplotlib.pyplot as plt

mpl.use("Agg")


def col_hist(stat_fn, delim):
    hists = []
    # we consider the coverage histogram start with 0
    with open(stat_fn) as f:
        for ln in f:
            lnlist = ln.strip().split(delim)
            hists.append(int(lnlist[1]))
    return hists


def get_cutoffs(con):
    if con:
        lnlst = []
        with open(con) as f:
            lnlst = f.readline().strip().split("\t")
        if len(lnlst):
            return [int(lnlst[0]), int(lnlst[3]), int(lnlst[5])]
        else:
            return []
    else:
        return []


def mk_plot(hists, cutoffs, ttle, xm, xM, ym, yM, out_fl):

    if ttle is None:
        ttle = "read depth histogram"
    if xm is None:
        xm = 0
    if xM is None:
        xM = len(hists) - 2  # ignore the last read depth count
    if ym is None:
        ym = 0
    if yM is None:
        yM = 1.2 * max(hists)
    x = [t for t in range(xm, xM)]
    plt.axis([xm, xM, ym, yM])
    width = 8
    height = 6
    plt.figure(num=None, figsize=(width, height))
    plt.plot(x, hists[xm:xM], label="l", color="blue")  #
    plt.xticks([z for z in range(xm, xM, 10)], fontsize=3)
    # cutoffs
    colors = ["r", "g", "c"]
    if len(cutoffs):
        for i in range(len(cutoffs)):
            plt.text(cutoffs[i], 0, str(cutoffs[i]), fontsize=5, color=colors[i])
            plt.axvline(x=cutoffs[i], linewidth=1, color=colors[i])

    plt.title(ttle)
    plt.gca().xaxis.grid(True, color="black", alpha=0.2)

    # plt.grid(True, color="black", alpha=0.2)
    # plt.gca().get_legend().remove()

    plt.tight_layout()
    plt.savefig(out_fl, dpi=300)


if __name__ == "__main__":
    parser = argparse.ArgumentParser(description="read depth histogram plot")

    parser.add_argument(
        "-c",
        "--cutoffs",
        type=str,
        action="store",
        dest="con",
        help="read depth cutoffs",
    )
    parser.add_argument(
        "-y", "--ymin", type=int, action="store", dest="ymin", help="set ymin"
    )
    parser.add_argument(
        "-x", "--xmin", type=int, action="store", dest="xmin", help="set xmin"
    )
    parser.add_argument(
        "-Y", "--ymax", type=int, action="store", dest="ymax", help="set ymax"
    )
    parser.add_argument(
        "-X", "--xmax", type=int, action="store", dest="xmax", help="set xmax"
    )
    parser.add_argument(
        "-t",
        "--title",
        type=str,
        action="store",
        dest="title",
        help="figure title [NULL]",
        default="",
    )
    parser.add_argument(
        "-d",
        "--delim",
        type=str,
        action="store",
        dest="delim",
        help="delimiter",
        default="\t",
    )
    parser.add_argument("-v", "--version", action="version", version="hist_plot 0.0.0")
    parser.add_argument("stat_fn", type=str, action="store", help="stat file")
    parser.add_argument("out_fn", type=str, action="store", help="output file")
    opts = parser.parse_args()
    hists = col_hist(opts.stat_fn, opts.delim)
    cutoffs = get_cutoffs(opts.con)
    mk_plot(
        hists,
        cutoffs,
        opts.title,
        opts.xmin,
        opts.xmax,
        opts.ymin,
        opts.ymax,
        opts.out_fn,
    )