diff --git a/tools/bigwig_outlier_bed/bigwig_outlier_bed.py b/tools/bigwig_outlier_bed/bigwig_outlier_bed.py index 1d69597ed76..4393a790988 100644 --- a/tools/bigwig_outlier_bed/bigwig_outlier_bed.py +++ b/tools/bigwig_outlier_bed/bigwig_outlier_bed.py @@ -28,8 +28,6 @@ def __init__(self, args): 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 @@ def __init__(self, args): 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 @@ def makeTableRow(self, bw, bwlabel, chr): 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 @@ def makeBed(self): 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 @@ def makeBed(self): 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) diff --git a/tools/bigwig_outlier_bed/bigwig_outlier_bed.xml b/tools/bigwig_outlier_bed/bigwig_outlier_bed.xml index 8ce52d258e3..8743fca3b60 100644 --- a/tools/bigwig_outlier_bed/bigwig_outlier_bed.xml +++ b/tools/bigwig_outlier_bed/bigwig_outlier_bed.xml @@ -1,5 +1,10 @@ - + Writes high and low bigwig runs as features in a bed file + + 0.2.0 + 2.0.0 + 3.12.3 + topic_0157 topic_0092 @@ -11,9 +16,9 @@ bigtools - python - numpy - pybigtools + python + numpy + pybigtools @@ -102,15 +107,25 @@ + + + + + + + + + + - + - - - + + + @@ -120,9 +135,9 @@ - - - + + + diff --git a/tools/bigwig_outlier_bed/test-data/bedouthi2_sample b/tools/bigwig_outlier_bed/test-data/bedouthi2_sample index d333b1a646b..93ce2ed013a 100644 --- a/tools/bigwig_outlier_bed/test-data/bedouthi2_sample +++ b/tools/bigwig_outlier_bed/test-data/bedouthi2_sample @@ -1,73 +1,1347 @@ -Merlin 20 30 bigwig_sample_hi 1 -Merlin 190 200 bigwig_sample_hi 1 -Merlin 1570 1580 bigwig_sample_hi 1 -Merlin 1730 1740 bigwig_sample_hi 1 -Merlin 1850 1860 bigwig_sample_hi 1 -Merlin 1880 1890 bigwig_sample_hi 1 -Merlin 3400 3410 bigwig_sample_hi 1 -Merlin 4030 4040 bigwig_sample_hi 1 -Merlin 7120 7130 bigwig_sample_hi 1 -Merlin 7860 7870 bigwig_sample_hi 1 -Merlin 8280 8290 bigwig_sample_hi 1 -Merlin 10820 10830 bigwig_sample_hi 1 -Merlin 13310 13320 bigwig_sample_hi 1 -Merlin 17570 17580 bigwig_sample_hi 1 -Merlin 17940 17950 bigwig_sample_hi 1 -Merlin 18340 18350 bigwig_sample_hi 1 -Merlin 18810 18820 bigwig_sample_hi 1 -Merlin 22310 22320 bigwig_sample_hi 1 -Merlin 23760 23770 bigwig_sample_hi 1 -Merlin 24580 24590 bigwig_sample_hi 1 -Merlin 24860 24870 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66219 66229 bigwig_sample_326610 326610 +Merlin 66519 66529 bigwig_sample_327310 327310 +Merlin 66859 66869 bigwig_sample_325520 325520 +Merlin 67249 67259 bigwig_sample_323350 323350 +Merlin 67699 67709 bigwig_sample_326970 326970 +Merlin 68649 68659 bigwig_sample_323020 323020 +Merlin 68769 68789 bigwig_sample_648580 648580 +Merlin 68989 68999 bigwig_sample_319610 319610 +Merlin 69259 69269 bigwig_sample_320570 320570 +Merlin 69579 69589 bigwig_sample_320980 320980 +Merlin 69819 69829 bigwig_sample_320470 320470 +Merlin 69859 69869 bigwig_sample_326630 326630 +Merlin 69889 69899 bigwig_sample_319940 319940 +Merlin 70049 180929 bigwig_sample_0 0 diff --git a/tools/bigwig_outlier_bed/test-data/bedoutlo2_sample b/tools/bigwig_outlier_bed/test-data/bedoutlo2_sample index c787b04b6b7..b2fcf71a9f9 100644 --- a/tools/bigwig_outlier_bed/test-data/bedoutlo2_sample +++ b/tools/bigwig_outlier_bed/test-data/bedoutlo2_sample @@ -1,91 +1,110 @@ -Merlin 80 90 bigwig_sample_lo -1 -Merlin 430 440 bigwig_sample_lo -1 -Merlin 1230 1240 bigwig_sample_lo -1 -Merlin 2670 2680 bigwig_sample_lo -1 -Merlin 3740 3750 bigwig_sample_lo -1 -Merlin 4700 4710 bigwig_sample_lo -1 -Merlin 5870 5890 bigwig_sample_lo -1 -Merlin 6290 6300 bigwig_sample_lo -1 -Merlin 8860 8870 bigwig_sample_lo -1 -Merlin 10520 10530 bigwig_sample_lo -1 -Merlin 11190 11200 bigwig_sample_lo -1 -Merlin 11380 11390 bigwig_sample_lo -1 -Merlin 11810 11820 bigwig_sample_lo -1 -Merlin 12660 12670 bigwig_sample_lo -1 -Merlin 14160 14170 bigwig_sample_lo -1 -Merlin 14750 14760 bigwig_sample_lo -1 -Merlin 16270 16280 bigwig_sample_lo -1 -Merlin 17240 17250 bigwig_sample_lo -1 -Merlin 18290 18300 bigwig_sample_lo -1 -Merlin 19080 19090 bigwig_sample_lo -1 -Merlin 19220 19230 bigwig_sample_lo -1 -Merlin 20240 20250 bigwig_sample_lo -1 -Merlin 21650 21660 bigwig_sample_lo -1 -Merlin 21810 21820 bigwig_sample_lo -1 -Merlin 23630 23640 bigwig_sample_lo -1 -Merlin 25030 25040 bigwig_sample_lo -1 -Merlin 26260 26270 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bigwig_sample_lo -1 -Merlin 52460 52470 bigwig_sample_lo -1 -Merlin 52740 52750 bigwig_sample_lo -1 -Merlin 52770 52780 bigwig_sample_lo -1 -Merlin 53150 53160 bigwig_sample_lo -1 -Merlin 54830 54840 bigwig_sample_lo -1 -Merlin 56020 56030 bigwig_sample_lo -1 -Merlin 57220 57230 bigwig_sample_lo -1 -Merlin 61250 61260 bigwig_sample_lo -1 -Merlin 63190 63200 bigwig_sample_lo -1 -Merlin 63290 63300 bigwig_sample_lo -1 -Merlin 64660 64670 bigwig_sample_lo -1 -Merlin 65050 65060 bigwig_sample_lo -1 -Merlin 66660 66670 bigwig_sample_lo -1 -Merlin 66900 66910 bigwig_sample_lo -1 -Merlin 67150 67160 bigwig_sample_lo -1 -Merlin 68790 68800 bigwig_sample_lo -1 -Merlin 69660 69670 bigwig_sample_lo -1 -chr21 610 625 1.bigwig_lo -1 -chr21 1010 1020 1.bigwig_lo -1 -chr21 1060 1070 1.bigwig_lo -1 -chr21 1170 1180 1.bigwig_lo -1 -chr21 1210 1225 1.bigwig_lo -1 -chr21 1250 1265 1.bigwig_lo -1 -chr21 1280 1290 1.bigwig_lo -1 -chr21 1450 1460 1.bigwig_lo -1 -chr21 1500 1510 1.bigwig_lo -1 -chr21 1865 1875 1.bigwig_lo -1 -chr21 1980 1990 1.bigwig_lo -1 -chr21 2960 2970 1.bigwig_lo -1 -chr21 3025 3035 1.bigwig_lo -1 -chr21 3465 3475 1.bigwig_lo -1 -chr21 3490 3500 1.bigwig_lo -1 -chr21 3670 3680 1.bigwig_lo -1 -chr21 3850 3865 1.bigwig_lo -1 -chr21 3875 3885 1.bigwig_lo -1 -chr21 3915 3925 1.bigwig_lo -1 -chr21 4495 4510 1.bigwig_lo -1 -chr21 4630 4640 1.bigwig_lo -1 -chr21 4975 4985 1.bigwig_lo -1 +Merlin 0 9 bigwig_sample_0 0 +Merlin 70049 180929 bigwig_sample_0 0 +chr21 0 9411190 1.bigwig_0 0 +chr21 9411785 9411790 1.bigwig_0 0 +chr21 9411800 9411815 1.bigwig_0 0 +chr21 9411860 9411865 1.bigwig_0 0 +chr21 9411900 9411905 1.bigwig_0 0 +chr21 9412005 9412010 1.bigwig_0 0 +chr21 9412050 9412055 1.bigwig_0 0 +chr21 9412065 9412070 1.bigwig_0 0 +chr21 9412080 9412085 1.bigwig_0 0 +chr21 9412100 9412105 1.bigwig_0 0 +chr21 9412120 9412125 1.bigwig_0 0 +chr21 9412130 9412135 1.bigwig_0 0 +chr21 9412140 9412145 1.bigwig_0 0 +chr21 9412180 9412185 1.bigwig_0 0 +chr21 9412200 9412210 1.bigwig_0 0 +chr21 9412225 9412230 1.bigwig_0 0 +chr21 9412250 9412260 1.bigwig_0 0 +chr21 9412305 9412310 1.bigwig_0 0 +chr21 9412360 9412370 1.bigwig_0 0 +chr21 9412385 9412390 1.bigwig_0 0 +chr21 9412400 9412415 1.bigwig_0 0 +chr21 9412440 9412455 1.bigwig_0 0 +chr21 9412460 9412465 1.bigwig_0 0 +chr21 9412470 9412480 1.bigwig_0 0 +chr21 9412485 9412490 1.bigwig_0 0 +chr21 9412510 9412515 1.bigwig_0 0 +chr21 9412565 9412570 1.bigwig_0 0 +chr21 9412590 9412595 1.bigwig_0 0 +chr21 9412640 9412650 1.bigwig_0 0 +chr21 9412670 9412675 1.bigwig_0 0 +chr21 9412690 9412700 1.bigwig_0 0 +chr21 9412770 9412775 1.bigwig_0 0 +chr21 9412815 9412820 1.bigwig_0 0 +chr21 9412835 9412840 1.bigwig_0 0 +chr21 9412845 9412850 1.bigwig_0 0 +chr21 9412900 9412905 1.bigwig_0 0 +chr21 9412970 9412975 1.bigwig_0 0 +chr21 9412990 9412995 1.bigwig_0 0 +chr21 9413040 9413045 1.bigwig_0 0 +chr21 9413055 9413065 1.bigwig_0 0 +chr21 9413095 9413100 1.bigwig_0 0 +chr21 9413130 9413135 1.bigwig_0 0 +chr21 9413155 9413160 1.bigwig_0 0 +chr21 9413170 9413180 1.bigwig_0 0 +chr21 9413205 9413210 1.bigwig_0 0 +chr21 9413250 9413255 1.bigwig_0 0 +chr21 9413280 9413285 1.bigwig_0 0 +chr21 9413310 9413315 1.bigwig_0 0 +chr21 9413345 9413350 1.bigwig_0 0 +chr21 9413400 9413405 1.bigwig_0 0 +chr21 9413510 9413515 1.bigwig_0 0 +chr21 9413665 9413670 1.bigwig_0 0 +chr21 9414040 9414045 1.bigwig_0 0 +chr21 9414055 9414060 1.bigwig_0 0 +chr21 9414100 9414105 1.bigwig_0 0 +chr21 9414150 9414160 1.bigwig_0 0 +chr21 9414175 9414180 1.bigwig_0 0 +chr21 9414215 9414225 1.bigwig_0 0 +chr21 9414255 9414260 1.bigwig_0 0 +chr21 9414265 9414270 1.bigwig_0 0 +chr21 9414280 9414285 1.bigwig_0 0 +chr21 9414305 9414310 1.bigwig_0 0 +chr21 9414435 9414440 1.bigwig_0 0 +chr21 9414525 9414530 1.bigwig_0 0 +chr21 9414585 9414590 1.bigwig_0 0 +chr21 9414595 9414600 1.bigwig_0 0 +chr21 9414655 9414665 1.bigwig_0 0 +chr21 9414680 9414690 1.bigwig_0 0 +chr21 9414695 9414700 1.bigwig_0 0 +chr21 9414705 9414710 1.bigwig_0 0 +chr21 9414720 9414725 1.bigwig_0 0 +chr21 9414755 9414760 1.bigwig_0 0 +chr21 9414775 9414780 1.bigwig_0 0 +chr21 9414785 9414790 1.bigwig_0 0 +chr21 9414820 9414825 1.bigwig_0 0 +chr21 9414835 9414840 1.bigwig_0 0 +chr21 9414850 9414855 1.bigwig_0 0 +chr21 9414860 9414870 1.bigwig_0 0 +chr21 9414905 9414910 1.bigwig_0 0 +chr21 9414925 9414930 1.bigwig_0 0 +chr21 9414955 9414960 1.bigwig_0 0 +chr21 9414975 9414980 1.bigwig_0 0 +chr21 9414995 9415000 1.bigwig_0 0 +chr21 9415040 9415055 1.bigwig_0 0 +chr21 9415065 9415075 1.bigwig_0 0 +chr21 9415095 9415100 1.bigwig_0 0 +chr21 9415105 9415115 1.bigwig_0 0 +chr21 9415135 9415140 1.bigwig_0 0 +chr21 9415150 9415155 1.bigwig_0 0 +chr21 9415170 9415175 1.bigwig_0 0 +chr21 9415270 9415275 1.bigwig_0 0 +chr21 9415320 9415325 1.bigwig_0 0 +chr21 9415385 9415390 1.bigwig_0 0 +chr21 9415470 9415475 1.bigwig_0 0 +chr21 9415535 9415540 1.bigwig_0 0 +chr21 9415595 9415600 1.bigwig_0 0 +chr21 9415665 9415670 1.bigwig_0 0 +chr21 9415685 9415700 1.bigwig_0 0 +chr21 9415710 9415715 1.bigwig_0 0 +chr21 9415820 9415830 1.bigwig_0 0 +chr21 9415880 9415885 1.bigwig_0 0 +chr21 9416020 9416025 1.bigwig_0 0 +chr21 9416080 9416085 1.bigwig_0 0 +chr21 9416095 9416100 1.bigwig_0 0 +chr21 9416130 9416135 1.bigwig_0 0 +chr21 9416150 9416155 1.bigwig_0 0 +chr21 9416165 9416175 1.bigwig_0 0 +chr21 9416185 48129895 1.bigwig_0 0 diff --git a/tools/bigwig_outlier_bed/test-data/bedoutlo_sample b/tools/bigwig_outlier_bed/test-data/bedoutlo_sample index 75b1c6ef1bf..c0fb2936e82 100644 --- a/tools/bigwig_outlier_bed/test-data/bedoutlo_sample +++ b/tools/bigwig_outlier_bed/test-data/bedoutlo_sample @@ -1,69 +1,2 @@ -Merlin 80 90 bigwig_sample_lo -1 -Merlin 430 440 bigwig_sample_lo -1 -Merlin 1230 1240 bigwig_sample_lo -1 -Merlin 2670 2680 bigwig_sample_lo -1 -Merlin 3740 3750 bigwig_sample_lo -1 -Merlin 4700 4710 bigwig_sample_lo -1 -Merlin 5870 5890 bigwig_sample_lo -1 -Merlin 6290 6300 bigwig_sample_lo -1 -Merlin 8860 8870 bigwig_sample_lo -1 -Merlin 10520 10530 bigwig_sample_lo -1 -Merlin 11190 11200 bigwig_sample_lo -1 -Merlin 11380 11390 bigwig_sample_lo -1 -Merlin 11810 11820 bigwig_sample_lo -1 -Merlin 12660 12670 bigwig_sample_lo -1 -Merlin 14160 14170 bigwig_sample_lo -1 -Merlin 14750 14760 bigwig_sample_lo -1 -Merlin 16270 16280 bigwig_sample_lo -1 -Merlin 17240 17250 bigwig_sample_lo -1 -Merlin 18290 18300 bigwig_sample_lo -1 -Merlin 19080 19090 bigwig_sample_lo -1 -Merlin 19220 19230 bigwig_sample_lo -1 -Merlin 20240 20250 bigwig_sample_lo -1 -Merlin 21650 21660 bigwig_sample_lo -1 -Merlin 21810 21820 bigwig_sample_lo -1 -Merlin 23630 23640 bigwig_sample_lo -1 -Merlin 25030 25040 bigwig_sample_lo -1 -Merlin 26260 26270 bigwig_sample_lo -1 -Merlin 26560 26570 bigwig_sample_lo -1 -Merlin 26610 26620 bigwig_sample_lo -1 -Merlin 27670 27680 bigwig_sample_lo -1 -Merlin 27970 27980 bigwig_sample_lo -1 -Merlin 29400 29410 bigwig_sample_lo -1 -Merlin 29910 29920 bigwig_sample_lo -1 -Merlin 33460 33470 bigwig_sample_lo -1 -Merlin 33910 33920 bigwig_sample_lo -1 -Merlin 34470 34490 bigwig_sample_lo -1 -Merlin 35320 35330 bigwig_sample_lo -1 -Merlin 35620 35630 bigwig_sample_lo -1 -Merlin 35880 35890 bigwig_sample_lo -1 -Merlin 36810 36820 bigwig_sample_lo -1 -Merlin 37230 37240 bigwig_sample_lo -1 -Merlin 37560 37570 bigwig_sample_lo -1 -Merlin 37750 37760 bigwig_sample_lo -1 -Merlin 38330 38340 bigwig_sample_lo -1 -Merlin 39600 39610 bigwig_sample_lo -1 -Merlin 41900 41910 bigwig_sample_lo -1 -Merlin 42050 42060 bigwig_sample_lo -1 -Merlin 44440 44450 bigwig_sample_lo -1 -Merlin 46610 46620 bigwig_sample_lo -1 -Merlin 49290 49300 bigwig_sample_lo -1 -Merlin 50880 50890 bigwig_sample_lo -1 -Merlin 52230 52240 bigwig_sample_lo -1 -Merlin 52460 52470 bigwig_sample_lo -1 -Merlin 52740 52750 bigwig_sample_lo -1 -Merlin 52770 52780 bigwig_sample_lo -1 -Merlin 53150 53160 bigwig_sample_lo -1 -Merlin 54830 54840 bigwig_sample_lo -1 -Merlin 56020 56030 bigwig_sample_lo -1 -Merlin 57220 57230 bigwig_sample_lo -1 -Merlin 61250 61260 bigwig_sample_lo -1 -Merlin 63190 63200 bigwig_sample_lo -1 -Merlin 63290 63300 bigwig_sample_lo -1 -Merlin 64660 64670 bigwig_sample_lo -1 -Merlin 65050 65060 bigwig_sample_lo -1 -Merlin 66660 66670 bigwig_sample_lo -1 -Merlin 66900 66910 bigwig_sample_lo -1 -Merlin 67150 67160 bigwig_sample_lo -1 -Merlin 68790 68800 bigwig_sample_lo -1 -Merlin 69660 69670 bigwig_sample_lo -1 +Merlin 0 9 bigwig_sample_0 0 +Merlin 70049 180929 bigwig_sample_0 0 diff --git a/tools/bigwig_outlier_bed/test-data/table2_sample b/tools/bigwig_outlier_bed/test-data/table2_sample index 9bd8ec9de46..b0eb8b009f7 100644 --- a/tools/bigwig_outlier_bed/test-data/table2_sample +++ b/tools/bigwig_outlier_bed/test-data/table2_sample @@ -1,3 +1,3 @@ bigwig contig n mean std min max qtop qbot -bigwig_sample Merlin 70040 16414.614934 9523.634628 13.000000 32767.000000 32387.000000 323.000000 -1.bigwig chr21 4995 33.203203 21.071159 0.000000 100.000000 80.000000 0.000000 +bigwig_sample Merlin 180929 6354.313736 9951.749936 0.000000 32767.000000 24359.00 0.00 +1.bigwig chr21 48129895 0.003446 0.400601 0.000000 100.000000 0.00 0.00 diff --git a/tools/bigwig_outlier_bed/test-data/table3_sample b/tools/bigwig_outlier_bed/test-data/table3_sample new file mode 100644 index 00000000000..6584ceaa011 --- /dev/null +++ b/tools/bigwig_outlier_bed/test-data/table3_sample @@ -0,0 +1,2 @@ +bigwig contig n mean std min max qtop qbot +bigwig_sample Merlin 180929 6354.313736 9951.749936 0.000000 32767.000000 24359.00 0.00 diff --git a/tools/bigwig_outlier_bed/test-data/table_qlo_notset_sample b/tools/bigwig_outlier_bed/test-data/table_qlo_notset_sample new file mode 100644 index 00000000000..7201af44db0 --- /dev/null +++ b/tools/bigwig_outlier_bed/test-data/table_qlo_notset_sample @@ -0,0 +1,2 @@ +bigwig contig n mean std min max qtop qbot +bigwig_sample Merlin 180929 6354.313736 9951.749936 0.000000 32767.000000 31906.72 noqlo diff --git a/tools/bigwig_outlier_bed/test-data/table_sample b/tools/bigwig_outlier_bed/test-data/table_sample index 54864364e09..fda14140e50 100644 --- a/tools/bigwig_outlier_bed/test-data/table_sample +++ b/tools/bigwig_outlier_bed/test-data/table_sample @@ -1,2 +1,2 @@ bigwig contig n mean std min max qtop qbot -bigwig_sample Merlin 70040 16414.614934 9523.634628 13.000000 32767.000000 32387.000000 323.000000 +bigwig_sample Merlin 180929 6354.313736 9951.749936 0.000000 32767.000000 31906.72 0.00