# HG changeset patch # User iuc # Date 1623693665 0 # Node ID 76d4cbefff854b2a3c3eeb26235b1cc7b02d1930 # Parent 17b378303f2de3d4f7ed5548d32725c1d7ec8421 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/purge_dups commit 5d56aa02b0f905507e1d98a2d74f0629b7591cd3" 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, + ) 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 @@ -2,13 +2,72 @@ and haplotigs in an assembly based on read depth (purge_dups) 1.2.5 - 2 + 3 + +
+ + + + + + +
+ + + + +
+ + + + + + + + +
+ purge_dups + matplotlib-base '${i}.gz' && @@ -18,10 +77,10 @@ #end for purge_dups #if $function_select.coverage: - -c '$function_select.coverage' + -c '${function_select.coverage}' #end if #if $function_select.cutoffs: - -T '$function_select.cutoffs' + -T '${function_select.cutoffs}' #end if #if $function_select.min_bad: -f $function_select.min_bad @@ -38,7 +97,7 @@ #if $function_select.max_gap: -M $function_select.max_gap #end if - #if $function_select.double_chain.chaining_rounds == "two": + #if $function_select.double_chain.chaining_rounds == 'two': -2 #if $function_select.double_chain.max_gap_2: -G $function_select.double_chain.max_gap_2 @@ -54,15 +113,15 @@ '${i}.gz' #end for > dups.bed 2> purge_dups.log - #else if $function_select.functions == "split_fa": + #else if $function_select.functions == 'split_fa': split_fa #if $function_select.split: -n $function_select.split #end if - '$function_select.input' > split.fasta - #else if $function_select.functions == "pbcstat": + '${function_select.input}' > split.fasta + #else if $function_select.functions == 'pbcstat': #for $i, $file in enumerate($function_select.input): - #if $file.is_of_type("paf"): + #if $file.is_of_type('paf'): gzip -c '${file}' > '${i}.gz' && #else ln -s '${file}' '${i}.gz' && @@ -82,10 +141,15 @@ -l $function_select.flank #end if $function_select.primary_alignments + #for $i, $file in enumerate($function_select.input): '${i}.gz' - #end for - #else if $function_select.functions == "ngscstat": + #end for + && mv PB.stat depth.stat + && @CALCUTS@ depth.stat > cutoffs.tsv 2>calcuts.log + && @HIST_PLOT@ + + #else if $function_select.functions == 'ngscstat': ngscstat #if $function_select.min_align_qual: -q $function_select.min_align_qual @@ -96,24 +160,15 @@ #if $function_select.max_insert: -L $function_select.max_insert #end if - '$function_select.input' - #else if $function_select.functions == "calcuts": - calcuts - #if $function_select.min_depth: - -f $function_select.min_depth - #end if - #if $function_select.low_depth: - -l $function_select.low_depth - #end if - #if $function_select.transition: - -m $function_select.transition - #end if - #if $function_select.upper_depth: - -u $function_select.upper_depth - #end if - $function_select.ploidy - '$function_select.input' > cutoffs.tsv 2>calcuts.log - #else if $function_select.functions == "get_seqs": + '${function_select.input}' + && mv TX.stat depth.stat + && @CALCUTS@ depth.stat > cutoffs.tsv 2>calcuts.log + && @HIST_PLOT@ + + #else if $function_select.functions == 'calcuts': + @CALCUTS@ '${function_select.input}' > cutoffs.tsv 2>calcuts.log + + #else if $function_select.functions == 'get_seqs': get_seqs $function_select.coverage $function_select.haplotigs @@ -128,18 +183,18 @@ #if $function_select.min_gap: -g $function_select.min_gap #end if - '$function_select.bed_input' '$function_select.fasta_input' + '${function_select.bed_input}' '${function_select.fasta_input}' #end if ]]> - - - - - - + + + + + + @@ -174,6 +229,8 @@ + + @@ -181,18 +238,15 @@ + + + - - - - - - - - + + @@ -222,8 +276,8 @@ function_select['functions'] == 'ngscstat' - - function_select['functions'] == 'ngscstat' + + function_select['functions'] == 'ngscstat' or function_select['functions'] == 'pbcstat' @@ -232,15 +286,17 @@ function_select['functions'] == 'pbcstat' - - function_select['functions'] == 'pbcstat' + + + function_select['functions'] == 'pbcstat' or function_select['functions'] == 'ngscstat' + - function_select['functions'] == 'calcuts' + function_select['functions'] in ('pbcstat', 'ngscstat', 'calcuts') - function_select['functions'] == 'calcuts' + function_select['functions'] in ('pbcstat', 'ngscstat', 'calcuts') @@ -311,7 +367,7 @@ - + @@ -320,12 +376,22 @@ +
+ + + + + +
+ + + - + @@ -334,39 +400,68 @@ +
+ + + + + +
+ - - + + +
+ + + + + +
+ - + + - + +
+ + + + + +
+ + + - - - - - +
+ + + + + +
@@ -386,6 +481,35 @@ + + + + + + + + + + +
+ + + + + +
+
+ + + +
+ + + + + + + gi|528476637:29857558-29915771 58214 +1 29093 0 +29094 29356 2 +29357 33376 0 +33377 41951 1 +41952 58214 0 +>gi|157734152:29655295-29712160 56866 +1 29214 0 +29215 29477 1 +29478 33498 0 +33499 42073 1 +42074 48471 0 +48472 56865 1 +56866 56866 0 diff -r 17b378303f2d -r 76d4cbefff85 test-data/out_hist_options.wig --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/out_hist_options.wig Mon Jun 14 18:01:05 2021 +0000 @@ -0,0 +1,116 @@ +track type="wiggle_0" name="PB" +fixedStep chrom=gi|528476637:29857558-29915771 start=1 step=1024 span=1024 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +1 +1 +1 +1 +1 +1 +1 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +variableStep chrom=gi|528476637:29857558-29915771 span=1894 +56321 0 +fixedStep chrom=gi|157734152:29655295-29712160 start=1 step=1024 span=1024 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +0 +1 +1 +1 +1 +1 +1 +1 +1 +0 +0 +0 +0 +0 +0 +0 +1 +1 +1 +1 +1 +1 +variableStep chrom=gi|157734152:29655295-29712160 span=1570 +55297 0 diff -r 17b378303f2d -r 76d4cbefff85 test-data/pbcstats.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/pbcstats.tabular Mon Jun 14 18:01:05 2021 +0000 @@ -0,0 +1,1001 @@ +0 89010 +1 25807 +2 263 +3 0 +4 0 +5 0 +6 0 +7 0 +8 0 +9 0 +10 0 +11 0 +12 0 +13 0 +14 0 +15 0 +16 0 +17 0 +18 0 +19 0 +20 0 +21 0 +22 0 +23 0 +24 0 +25 0 +26 0 +27 0 +28 0 +29 0 +30 0 +31 0 +32 0 +33 0 +34 0 +35 0 +36 0 +37 0 +38 0 +39 0 +40 0 +41 0 +42 0 +43 0 +44 0 +45 0 +46 0 +47 0 +48 0 +49 0 +50 0 +51 0 +52 0 +53 0 +54 0 +55 0 +56 0 +57 0 +58 0 +59 0 +60 0 +61 0 +62 0 +63 0 +64 0 +65 0 +66 0 +67 0 +68 0 +69 0 +70 0 +71 0 +72 0 +73 0 +74 0 +75 0 +76 0 +77 0 +78 0 +79 0 +80 0 +81 0 +82 0 +83 0 +84 0 +85 0 +86 0 +87 0 +88 0 +89 0 +90 0 +91 0 +92 0 +93 0 +94 0 +95 0 +96 0 +97 0 +98 0 +99 0 +100 0 +101 0 +102 0 +103 0 +104 0 +105 0 +106 0 +107 0 +108 0 +109 0 +110 0 +111 0 +112 0 +113 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