diff hist_plot.py @ 3:76d4cbefff85 draft

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

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/hist_plot.py	Mon Jun 14 18:01:05 2021 +0000
@@ -0,0 +1,129 @@
+#!/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,
+    )