| Previous changeset 2:17b378303f2d (2021-04-27) Next changeset 4:a315c25dc813 (2021-10-12) |
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Commit message:
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit 5d56aa02b0f905507e1d98a2d74f0629b7591cd3" |
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modified:
purge_dups.xml |
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added:
hist_plot.py test-data/hist.png test-data/hist_options.png test-data/out_hist_options.cov test-data/out_hist_options.wig test-data/pbcstats.tabular test-data/pbcstats2.tabular test-data/pbcstats_hist_options.tabular test-data/tx_stats.tabular |
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| diff -r 17b378303f2d -r 76d4cbefff85 hist_plot.py --- /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, + ) |
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| diff -r 17b378303f2d -r 76d4cbefff85 purge_dups.xml --- a/purge_dups.xml Tue Apr 27 20:48:51 2021 +0000 +++ b/purge_dups.xml Mon Jun 14 18:01:05 2021 +0000 |
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| b'@@ -2,13 +2,72 @@\n <description>and haplotigs in an assembly based on read depth (purge_dups)</description>\n <macros>\n <token name="@TOOL_VERSION@">1.2.5</token>\n- <token name="@VERSION_SUFFIX@">2</token>\n+ <token name="@VERSION_SUFFIX@">3</token>\n+ <xml name="trimmers">\n+ <section name="section_hist" title="Histogram plot options" >\n+ <!--<param name="cutoffs_his" type="data" optional="true" format="txt" label="Read depth cutoffs file" />-->\n+ <param argument="--ymin" type="integer" optional="true" min="0" label="Specify a minimum for the Y axis"/>\n+ <param argument="--ymax" type="integer" optional="true" label="Specify a maximum for the Y axis"/>\n+ <param argument="--xmin" type="integer" optional="true" min="0" label="Specify a minimum for the X axis"/>\n+ <param argument="--xmax" type="integer" optional="true" label="Specify a maximum for the X axis"/>\n+ <param argument="--title" type="text" value="Read depth histogram plot" label="Histogram title"/>\n+ </section>\n+ </xml>\n+ <token name="@HIST_PLOT@"><![CDATA[\n+ python \'$__tool_directory__/hist_plot.py\' \n+ --cutoffs cutoffs.tsv\n+ #if $function_select.section_hist.ymin\n+ --ymin $function_select.section_hist.ymin\n+ #end if\n+ #if $function_select.section_hist.ymax\n+ --ymax $function_select.section_hist.ymax\n+ #end if\n+ #if $function_select.section_hist.xmin\n+ --xmin $function_select.section_hist.xmin\n+ #end if\n+ #if $function_select.section_hist.xmax\n+ --xmax $function_select.section_hist.xmax\n+ #end if\n+ #if $function_select.section_hist.title\n+ --title \'${function_select.section_hist.title}\'\n+ #end if\n+ depth.stat hist.png\n+ ]]></token>\n+ <token name="@CALCUTS@"><![CDATA[\n+ calcuts\n+ #if $function_select.section_calcuts.min_depth:\n+ -f $function_select.section_calcuts.min_depth\n+ #end if\n+ #if $function_select.section_calcuts.low_depth:\n+ -l $function_select.section_calcuts.low_depth\n+ #end if\n+ #if $function_select.section_calcuts.transition:\n+ -m $function_select.section_calcuts.transition\n+ #end if\n+ #if $function_select.section_calcuts.upper_depth:\n+ -u $function_select.section_calcuts.upper_depth\n+ #end if\n+ $function_select.section_calcuts.ploidy\n+ ]]></token>\n+ <xml name="calcuts">\n+ <section name="section_calcuts" title="Calcuts options">\n+ <param name="min_depth" type="float" label="Minimum depth count fraction to maximum depth coun" min="0" max="1" argument="-f" optional="true" help="Default = 0.1"/>\n+ <param name="low_depth" label="Lower bound for read depth" type="integer" argument="-l" optional="true"/>\n+ <param name="transition" label="Transition between haploid and diploid" type="integer" argument="-m" optional="true"/>\n+ <param name="upper_depth" label="Upper bound for read depth" type="integer" argument="-u" optional="true"/>\n+ <param name="ploidy" argument="-d" type="select" label="Ploidy">\n+ <option value="-d 0" selected="true">Diploid [0]</option>\n+ <option value="-d 1">Haploid [1]</option>\n+ </param>\n+ </section>\n+ </xml>\n </macros>\n <requirements>\n <requirement type="package" version="@TOOL_VERSION@">purge_dups</requirement>\n+ <requirement type="package" version="3.4.2">matplotlib-base</requirement>\n </requirements>\n <command detect_errors="exit_code"><
