Mercurial > repos > iuc > bigwig_outlier_bed
diff bigwig_outlier_bed.py @ 1:8377a6abb4da draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigwig_outlier_bed commit 92ffe42a6ad6e81f3f157bbc9b942c000d450416
| author | iuc |
|---|---|
| date | Sun, 21 Jul 2024 11:03:36 +0000 |
| parents | ebcd48f183b3 |
| children | 61946b8bd43b |
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--- a/bigwig_outlier_bed.py Fri Jul 05 06:00:15 2024 +0000 +++ b/bigwig_outlier_bed.py Sun Jul 21 11:03:36 2024 +0000 @@ -28,8 +28,6 @@ self.bwnames = args.bigwig self.bwlabels = args.bigwiglabels self.bedwin = args.minwin - self.qlo = args.qlo - self.qhi = args.qhi self.outbeds = args.outbeds self.bedouthi = args.bedouthi self.bedoutlo = args.bedoutlo @@ -37,7 +35,13 @@ self.tableoutfile = args.tableoutfile self.bedwin = args.minwin self.qhi = args.qhi - self.qlo = args.qlo + self.qlo = None + try: + f = float(args.qlo) + self.qlo = f + except Exception as e: + s = str(e) + print(s, ' qlo=', args.qlo) nbw = len(args.bigwig) nlab = len(args.bigwiglabels) if nlab < nbw: @@ -90,13 +94,13 @@ bwmax, ) if self.qhi is not None: - row += "\t%f" % self.bwtop + row += "\t%.2f" % self.bwtop else: - row += "\t" + row += "\tnoqhi" if self.qlo is not None: - row += "\t%f" % self.bwbot + row += "\t%.2f" % self.bwbot else: - row += "\t" + row += "\tnoqlo" return row def makeBed(self): @@ -125,13 +129,31 @@ bwhi = self.processVals(bw, isTop=True) for j, seg in enumerate(bwhi): if seg[1] - seg[0] >= self.bedwin: - bedhi.append((chr, seg[0], seg[1], "%s_hi" % (bwlabel), 1)) + score = np.sum(bw[seg[0]:seg[1]]) + bedhi.append( + ( + chr, + seg[0], + seg[1], + "%s_%d" % (bwlabel, score), + score, + ) + ) if self.qlo is not None: self.bwbot = np.quantile(bw, self.qlo) bwlo = self.processVals(bw, isTop=False) for j, seg in enumerate(bwlo): if seg[1] - seg[0] >= self.bedwin: - bedlo.append((chr, seg[0], seg[1], "%s_lo" % (bwlabel), -1)) + score = -1 * np.sum(bw[seg[0]:seg[1]]) + bedlo.append( + ( + chr, + seg[0], + seg[1], + "%s_%d" % (bwlabel, score), + score, + ) + ) if self.tableoutfile: row = self.makeTableRow(bw, bwlabel, chr) restab.append(copy.copy(row)) @@ -164,7 +186,7 @@ parser = argparse.ArgumentParser() a = parser.add_argument a("-m", "--minwin", default=10, type=int) - a("-l", "--qlo", default=None, type=float) + a("-l", "--qlo", default=None) a("-i", "--qhi", default=None, type=float) a("--bedouthi", default=None) a("--bedoutlo", default=None)