Mercurial > repos > iuc > bigwig_outlier_bed

annotate bigwig_outlier_bed.py @ 0:ebcd48f183b3 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigwig_outlier_bed commit 091caba3c5b066b293745ccee5cd31132fec3b4b
author iuc
date Fri, 05 Jul 2024 06:00:15 +0000
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ebcd48f183b3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigwig_outlier_bed commit 091caba3c5b066b293745ccee5cd31132fec3b4b
iuc
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1 """
ebcd48f183b3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigwig_outlier_bed commit 091caba3c5b066b293745ccee5cd31132fec3b4b
iuc
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2 Ross Lazarus June 2024 for VGP
ebcd48f183b3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigwig_outlier_bed commit 091caba3c5b066b293745ccee5cd31132fec3b4b
iuc
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3 Bigwigs are great, but hard to reliably "see" small low coverage or small very high coverage regions.
ebcd48f183b3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigwig_outlier_bed commit 091caba3c5b066b293745ccee5cd31132fec3b4b
iuc
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4 Colouring in JB2 tracks will need a new plugin, so this code will find bigwig regions above and below a chosen percentile point.
ebcd48f183b3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigwig_outlier_bed commit 091caba3c5b066b293745ccee5cd31132fec3b4b
iuc
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5 0.99 and 0.01 work well in testing with a minimum span of 10 bp.
ebcd48f183b3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigwig_outlier_bed commit 091caba3c5b066b293745ccee5cd31132fec3b4b
iuc
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6 Multiple bigwigs **with the same reference** can be combined - bed segments will be named appropriately
ebcd48f183b3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigwig_outlier_bed commit 091caba3c5b066b293745ccee5cd31132fec3b4b
iuc
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7 Combining multiple references works but is silly because only display will rely on one reference so others will not be shown...
ebcd48f183b3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigwig_outlier_bed commit 091caba3c5b066b293745ccee5cd31132fec3b4b
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8 Tricksy numpy method from http://gregoryzynda.com/python/numpy/contiguous/interval/2019/11/29/contiguous-regions.html
ebcd48f183b3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigwig_outlier_bed commit 091caba3c5b066b293745ccee5cd31132fec3b4b
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9 takes about 95 seconds for a 17MB test wiggle
ebcd48f183b3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigwig_outlier_bed commit 091caba3c5b066b293745ccee5cd31132fec3b4b
iuc
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10 JBrowse2 bed normally displays ignore the score, so could provide separate low/high bed file outputs as an option.
ebcd48f183b3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigwig_outlier_bed commit 091caba3c5b066b293745ccee5cd31132fec3b4b
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11 Update june 30 2024: wrote a 'no-build' plugin for beds to display red/blue if >0/<0 so those are used for scores
ebcd48f183b3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigwig_outlier_bed commit 091caba3c5b066b293745ccee5cd31132fec3b4b
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12 Bed interval naming must be short for JB2 but needs input bigwig name and (lo or hi).
ebcd48f183b3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigwig_outlier_bed commit 091caba3c5b066b293745ccee5cd31132fec3b4b
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13 """
ebcd48f183b3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigwig_outlier_bed commit 091caba3c5b066b293745ccee5cd31132fec3b4b
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14
ebcd48f183b3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigwig_outlier_bed commit 091caba3c5b066b293745ccee5cd31132fec3b4b
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15 import argparse
ebcd48f183b3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigwig_outlier_bed commit 091caba3c5b066b293745ccee5cd31132fec3b4b
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16 import copy
ebcd48f183b3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigwig_outlier_bed commit 091caba3c5b066b293745ccee5cd31132fec3b4b
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17 import os
ebcd48f183b3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigwig_outlier_bed commit 091caba3c5b066b293745ccee5cd31132fec3b4b
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18 import sys
ebcd48f183b3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigwig_outlier_bed commit 091caba3c5b066b293745ccee5cd31132fec3b4b
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19 from pathlib import Path
ebcd48f183b3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigwig_outlier_bed commit 091caba3c5b066b293745ccee5cd31132fec3b4b
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20
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21 import numpy as np
ebcd48f183b3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigwig_outlier_bed commit 091caba3c5b066b293745ccee5cd31132fec3b4b
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22 import pybigtools
ebcd48f183b3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigwig_outlier_bed commit 091caba3c5b066b293745ccee5cd31132fec3b4b
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23
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24
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25 class findOut:
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26
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27 def __init__(self, args):
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28 self.bwnames = args.bigwig
ebcd48f183b3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigwig_outlier_bed commit 091caba3c5b066b293745ccee5cd31132fec3b4b
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29 self.bwlabels = args.bigwiglabels
ebcd48f183b3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigwig_outlier_bed commit 091caba3c5b066b293745ccee5cd31132fec3b4b
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30 self.bedwin = args.minwin
ebcd48f183b3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigwig_outlier_bed commit 091caba3c5b066b293745ccee5cd31132fec3b4b
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31 self.qlo = args.qlo
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32 self.qhi = args.qhi
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33 self.outbeds = args.outbeds
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34 self.bedouthi = args.bedouthi
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35 self.bedoutlo = args.bedoutlo
ebcd48f183b3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigwig_outlier_bed commit 091caba3c5b066b293745ccee5cd31132fec3b4b
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36 self.bedouthilo = args.bedouthilo
ebcd48f183b3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigwig_outlier_bed commit 091caba3c5b066b293745ccee5cd31132fec3b4b
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37 self.tableoutfile = args.tableoutfile
ebcd48f183b3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigwig_outlier_bed commit 091caba3c5b066b293745ccee5cd31132fec3b4b
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38 self.bedwin = args.minwin
ebcd48f183b3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigwig_outlier_bed commit 091caba3c5b066b293745ccee5cd31132fec3b4b
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39 self.qhi = args.qhi
ebcd48f183b3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigwig_outlier_bed commit 091caba3c5b066b293745ccee5cd31132fec3b4b
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40 self.qlo = args.qlo
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41 nbw = len(args.bigwig)
ebcd48f183b3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigwig_outlier_bed commit 091caba3c5b066b293745ccee5cd31132fec3b4b
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42 nlab = len(args.bigwiglabels)
ebcd48f183b3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigwig_outlier_bed commit 091caba3c5b066b293745ccee5cd31132fec3b4b
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43 if nlab < nbw:
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44 self.bwlabels += ["Nolabel"] * (nbw - nlab)
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45 self.makeBed()
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46
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47 def processVals(self, bw, isTop):
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48 """
ebcd48f183b3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigwig_outlier_bed commit 091caba3c5b066b293745ccee5cd31132fec3b4b
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49 idea from http://gregoryzynda.com/python/numpy/contiguous/interval/2019/11/29/contiguous-regions.html
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50 Fast segmentation into regions by taking np.diff on the boolean array of over (under) cutpoint indicators in bwex.
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51 This only gives non-zero values at the segment boundaries where there's a change, so those zeros are all removed in bwexdnz
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52 leaving an array of segment start/end positions. That's twisted around into an array of start/end coordinates.
ebcd48f183b3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigwig_outlier_bed commit 091caba3c5b066b293745ccee5cd31132fec3b4b
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53 Magical. Fast. Could do the same for means or medians over windows for sparse bigwigs like repeat regions.
ebcd48f183b3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigwig_outlier_bed commit 091caba3c5b066b293745ccee5cd31132fec3b4b
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54 """
ebcd48f183b3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigwig_outlier_bed commit 091caba3c5b066b293745ccee5cd31132fec3b4b
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55 if isTop:
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56 bwex = np.r_[False, bw >= self.bwtop, False] # extend with 0s
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57 else:
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58 bwex = np.r_[False, bw <= self.bwbot, False]
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59 bwexd = np.diff(bwex)
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60 bwexdnz = bwexd.nonzero()[0]
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61 bwregions = np.reshape(bwexdnz, (-1, 2))
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62 return bwregions
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63
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64 def writeBed(self, bed, bedfname):
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65 """
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66 potentially multiple
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67 """
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68 bed.sort()
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69 beds = ["%s\t%d\t%d\t%s\t%d" % x for x in bed]
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70 with open(bedfname, "w") as bedf:
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71 bedf.write("\n".join(beds))
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72 bedf.write("\n")
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73
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74 def makeTableRow(self, bw, bwlabel, chr):
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75 """
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76 called for every contig, but messy inline
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77 """
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78 bwmean = np.mean(bw)
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79 bwstd = np.std(bw)
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80 bwmax = np.max(bw)
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81 nrow = np.size(bw)
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82 bwmin = np.min(bw)
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83 row = "%s\t%s\t%d\t%f\t%f\t%f\t%f" % (
ebcd48f183b3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigwig_outlier_bed commit 091caba3c5b066b293745ccee5cd31132fec3b4b
iuc
parents:
diff changeset
84 bwlabel,
ebcd48f183b3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigwig_outlier_bed commit 091caba3c5b066b293745ccee5cd31132fec3b4b
iuc
parents:
diff changeset
85 chr,
ebcd48f183b3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigwig_outlier_bed commit 091caba3c5b066b293745ccee5cd31132fec3b4b
iuc
parents:
diff changeset
86 nrow,
ebcd48f183b3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigwig_outlier_bed commit 091caba3c5b066b293745ccee5cd31132fec3b4b
iuc
parents:
diff changeset
87 bwmean,
ebcd48f183b3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigwig_outlier_bed commit 091caba3c5b066b293745ccee5cd31132fec3b4b
iuc
parents:
diff changeset
88 bwstd,
ebcd48f183b3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigwig_outlier_bed commit 091caba3c5b066b293745ccee5cd31132fec3b4b
iuc
parents:
diff changeset
89 bwmin,
ebcd48f183b3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigwig_outlier_bed commit 091caba3c5b066b293745ccee5cd31132fec3b4b
iuc
parents:
diff changeset
90 bwmax,
ebcd48f183b3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigwig_outlier_bed commit 091caba3c5b066b293745ccee5cd31132fec3b4b
iuc
parents:
diff changeset
91 )
ebcd48f183b3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigwig_outlier_bed commit 091caba3c5b066b293745ccee5cd31132fec3b4b
iuc
parents:
diff changeset
92 if self.qhi is not None:
ebcd48f183b3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigwig_outlier_bed commit 091caba3c5b066b293745ccee5cd31132fec3b4b
iuc
parents:
diff changeset
93 row += "\t%f" % self.bwtop
ebcd48f183b3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigwig_outlier_bed commit 091caba3c5b066b293745ccee5cd31132fec3b4b
iuc
parents:
diff changeset
94 else:
ebcd48f183b3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigwig_outlier_bed commit 091caba3c5b066b293745ccee5cd31132fec3b4b
iuc
parents:
diff changeset
95 row += "\t"
ebcd48f183b3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigwig_outlier_bed commit 091caba3c5b066b293745ccee5cd31132fec3b4b
iuc
parents:
diff changeset
96 if self.qlo is not None:
ebcd48f183b3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigwig_outlier_bed commit 091caba3c5b066b293745ccee5cd31132fec3b4b
iuc
parents:
diff changeset
97 row += "\t%f" % self.bwbot
ebcd48f183b3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigwig_outlier_bed commit 091caba3c5b066b293745ccee5cd31132fec3b4b
iuc
parents:
diff changeset
98 else:
ebcd48f183b3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigwig_outlier_bed commit 091caba3c5b066b293745ccee5cd31132fec3b4b
iuc
parents:
diff changeset
99 row += "\t"
ebcd48f183b3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigwig_outlier_bed commit 091caba3c5b066b293745ccee5cd31132fec3b4b
iuc
parents:
diff changeset
100 return row
ebcd48f183b3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigwig_outlier_bed commit 091caba3c5b066b293745ccee5cd31132fec3b4b
iuc
parents:
diff changeset
101
ebcd48f183b3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigwig_outlier_bed commit 091caba3c5b066b293745ccee5cd31132fec3b4b
iuc
parents:
diff changeset
102 def makeBed(self):
ebcd48f183b3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigwig_outlier_bed commit 091caba3c5b066b293745ccee5cd31132fec3b4b
iuc
parents:
diff changeset
103 bedhi = []
ebcd48f183b3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigwig_outlier_bed commit 091caba3c5b066b293745ccee5cd31132fec3b4b
iuc
parents:
diff changeset
104 bedlo = []
ebcd48f183b3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigwig_outlier_bed commit 091caba3c5b066b293745ccee5cd31132fec3b4b
iuc
parents:
diff changeset
105 bwlabels = self.bwlabels
ebcd48f183b3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigwig_outlier_bed commit 091caba3c5b066b293745ccee5cd31132fec3b4b
iuc
parents:
diff changeset
106 bwnames = self.bwnames
ebcd48f183b3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigwig_outlier_bed commit 091caba3c5b066b293745ccee5cd31132fec3b4b
iuc
parents:
diff changeset
107 if self.tableoutfile:
ebcd48f183b3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigwig_outlier_bed commit 091caba3c5b066b293745ccee5cd31132fec3b4b
iuc
parents:
diff changeset
108 restab = ["bigwig\tcontig\tn\tmean\tstd\tmin\tmax\tqtop\tqbot"]
ebcd48f183b3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigwig_outlier_bed commit 091caba3c5b066b293745ccee5cd31132fec3b4b
iuc
parents:
diff changeset
109 for i, bwname in enumerate(bwnames):
ebcd48f183b3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigwig_outlier_bed commit 091caba3c5b066b293745ccee5cd31132fec3b4b
iuc
parents:
diff changeset
110 bwlabel = bwlabels[i].replace(" ", "")
ebcd48f183b3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigwig_outlier_bed commit 091caba3c5b066b293745ccee5cd31132fec3b4b
iuc
parents:
diff changeset
111 fakepath = "in%d.bw" % i
ebcd48f183b3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigwig_outlier_bed commit 091caba3c5b066b293745ccee5cd31132fec3b4b
iuc
parents:
diff changeset
112 if os.path.isfile(fakepath):
ebcd48f183b3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigwig_outlier_bed commit 091caba3c5b066b293745ccee5cd31132fec3b4b
iuc
parents:
diff changeset
113 os.remove(fakepath)
ebcd48f183b3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigwig_outlier_bed commit 091caba3c5b066b293745ccee5cd31132fec3b4b
iuc
parents:
diff changeset
114 p = Path(fakepath)
ebcd48f183b3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigwig_outlier_bed commit 091caba3c5b066b293745ccee5cd31132fec3b4b
iuc
parents:
diff changeset
115 p.symlink_to(bwname) # required by pybigtools (!)
ebcd48f183b3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigwig_outlier_bed commit 091caba3c5b066b293745ccee5cd31132fec3b4b
iuc
parents:
diff changeset
116 bwf = pybigtools.open(fakepath)
ebcd48f183b3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigwig_outlier_bed commit 091caba3c5b066b293745ccee5cd31132fec3b4b
iuc
parents:
diff changeset
117 chrlist = bwf.chroms()
ebcd48f183b3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigwig_outlier_bed commit 091caba3c5b066b293745ccee5cd31132fec3b4b
iuc
parents:
diff changeset
118 chrs = list(chrlist.keys())
ebcd48f183b3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigwig_outlier_bed commit 091caba3c5b066b293745ccee5cd31132fec3b4b
iuc
parents:
diff changeset
119 chrs.sort()
ebcd48f183b3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigwig_outlier_bed commit 091caba3c5b066b293745ccee5cd31132fec3b4b
iuc
parents:
diff changeset
120 for chr in chrs:
ebcd48f183b3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigwig_outlier_bed commit 091caba3c5b066b293745ccee5cd31132fec3b4b
iuc
parents:
diff changeset
121 bw = bwf.values(chr)
ebcd48f183b3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigwig_outlier_bed commit 091caba3c5b066b293745ccee5cd31132fec3b4b
iuc
parents:
diff changeset
122 bw = bw[~np.isnan(bw)] # some have NaN if parts of a contig not covered
ebcd48f183b3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigwig_outlier_bed commit 091caba3c5b066b293745ccee5cd31132fec3b4b
iuc
parents:
diff changeset
123 if self.qhi is not None:
ebcd48f183b3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigwig_outlier_bed commit 091caba3c5b066b293745ccee5cd31132fec3b4b
iuc
parents:
diff changeset
124 self.bwtop = np.quantile(bw, self.qhi)
ebcd48f183b3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigwig_outlier_bed commit 091caba3c5b066b293745ccee5cd31132fec3b4b
iuc
parents:
diff changeset
125 bwhi = self.processVals(bw, isTop=True)
ebcd48f183b3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigwig_outlier_bed commit 091caba3c5b066b293745ccee5cd31132fec3b4b
iuc
parents:
diff changeset
126 for j, seg in enumerate(bwhi):
ebcd48f183b3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigwig_outlier_bed commit 091caba3c5b066b293745ccee5cd31132fec3b4b
iuc
parents:
diff changeset
127 if seg[1] - seg[0] >= self.bedwin:
ebcd48f183b3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigwig_outlier_bed commit 091caba3c5b066b293745ccee5cd31132fec3b4b
iuc
parents:
diff changeset
128 bedhi.append((chr, seg[0], seg[1], "%s_hi" % (bwlabel), 1))
ebcd48f183b3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigwig_outlier_bed commit 091caba3c5b066b293745ccee5cd31132fec3b4b
iuc
parents:
diff changeset
129 if self.qlo is not None:
ebcd48f183b3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigwig_outlier_bed commit 091caba3c5b066b293745ccee5cd31132fec3b4b
iuc
parents:
diff changeset
130 self.bwbot = np.quantile(bw, self.qlo)
ebcd48f183b3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigwig_outlier_bed commit 091caba3c5b066b293745ccee5cd31132fec3b4b
iuc
parents:
diff changeset
131 bwlo = self.processVals(bw, isTop=False)
ebcd48f183b3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigwig_outlier_bed commit 091caba3c5b066b293745ccee5cd31132fec3b4b
iuc
parents:
diff changeset
132 for j, seg in enumerate(bwlo):
ebcd48f183b3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigwig_outlier_bed commit 091caba3c5b066b293745ccee5cd31132fec3b4b
iuc
parents:
diff changeset
133 if seg[1] - seg[0] >= self.bedwin:
ebcd48f183b3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigwig_outlier_bed commit 091caba3c5b066b293745ccee5cd31132fec3b4b
iuc
parents:
diff changeset
134 bedlo.append((chr, seg[0], seg[1], "%s_lo" % (bwlabel), -1))
ebcd48f183b3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigwig_outlier_bed commit 091caba3c5b066b293745ccee5cd31132fec3b4b
iuc
parents:
diff changeset
135 if self.tableoutfile:
ebcd48f183b3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigwig_outlier_bed commit 091caba3c5b066b293745ccee5cd31132fec3b4b
iuc
parents:
diff changeset
136 row = self.makeTableRow(bw, bwlabel, chr)
ebcd48f183b3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigwig_outlier_bed commit 091caba3c5b066b293745ccee5cd31132fec3b4b
iuc
parents:
diff changeset
137 restab.append(copy.copy(row))
ebcd48f183b3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigwig_outlier_bed commit 091caba3c5b066b293745ccee5cd31132fec3b4b
iuc
parents:
diff changeset
138 if self.tableoutfile:
ebcd48f183b3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigwig_outlier_bed commit 091caba3c5b066b293745ccee5cd31132fec3b4b
iuc
parents:
diff changeset
139 stable = "\n".join(restab)
ebcd48f183b3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigwig_outlier_bed commit 091caba3c5b066b293745ccee5cd31132fec3b4b
iuc
parents:
diff changeset
140 with open(self.tableoutfile, "w") as t:
ebcd48f183b3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigwig_outlier_bed commit 091caba3c5b066b293745ccee5cd31132fec3b4b
iuc
parents:
diff changeset
141 t.write(stable)
ebcd48f183b3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigwig_outlier_bed commit 091caba3c5b066b293745ccee5cd31132fec3b4b
iuc
parents:
diff changeset
142 t.write("\n")
ebcd48f183b3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigwig_outlier_bed commit 091caba3c5b066b293745ccee5cd31132fec3b4b
iuc
parents:
diff changeset
143 some = False
ebcd48f183b3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigwig_outlier_bed commit 091caba3c5b066b293745ccee5cd31132fec3b4b
iuc
parents:
diff changeset
144 if self.qlo:
ebcd48f183b3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigwig_outlier_bed commit 091caba3c5b066b293745ccee5cd31132fec3b4b
iuc
parents:
diff changeset
145 if self.outbeds in ["outall", "outlo", "outlohi"]:
ebcd48f183b3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigwig_outlier_bed commit 091caba3c5b066b293745ccee5cd31132fec3b4b
iuc
parents:
diff changeset
146 self.writeBed(bedlo, self.bedoutlo)
ebcd48f183b3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigwig_outlier_bed commit 091caba3c5b066b293745ccee5cd31132fec3b4b
iuc
parents:
diff changeset
147 some = True
ebcd48f183b3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigwig_outlier_bed commit 091caba3c5b066b293745ccee5cd31132fec3b4b
iuc
parents:
diff changeset
148 if self.qhi:
ebcd48f183b3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigwig_outlier_bed commit 091caba3c5b066b293745ccee5cd31132fec3b4b
iuc
parents:
diff changeset
149 if self.outbeds in ["outall", "outlohi", "outhi"]:
ebcd48f183b3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigwig_outlier_bed commit 091caba3c5b066b293745ccee5cd31132fec3b4b
iuc
parents:
diff changeset
150 self.writeBed(bedhi, self.bedouthi)
ebcd48f183b3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigwig_outlier_bed commit 091caba3c5b066b293745ccee5cd31132fec3b4b
iuc
parents:
diff changeset
151 some = True
ebcd48f183b3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigwig_outlier_bed commit 091caba3c5b066b293745ccee5cd31132fec3b4b
iuc
parents:
diff changeset
152 if self.outbeds in ["outall", "outhilo"]:
ebcd48f183b3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigwig_outlier_bed commit 091caba3c5b066b293745ccee5cd31132fec3b4b
iuc
parents:
diff changeset
153 allbed = bedlo + bedhi
ebcd48f183b3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigwig_outlier_bed commit 091caba3c5b066b293745ccee5cd31132fec3b4b
iuc
parents:
diff changeset
154 self.writeBed(allbed, self.bedouthilo)
ebcd48f183b3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigwig_outlier_bed commit 091caba3c5b066b293745ccee5cd31132fec3b4b
iuc
parents:
diff changeset
155 some = True
ebcd48f183b3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigwig_outlier_bed commit 091caba3c5b066b293745ccee5cd31132fec3b4b
iuc
parents:
diff changeset
156 if not some:
ebcd48f183b3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigwig_outlier_bed commit 091caba3c5b066b293745ccee5cd31132fec3b4b
iuc
parents:
diff changeset
157 sys.stderr.write(
ebcd48f183b3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigwig_outlier_bed commit 091caba3c5b066b293745ccee5cd31132fec3b4b
iuc
parents:
diff changeset
158 "Invalid configuration - no output could be created. Was qlo missing and only low output requested for example?"
ebcd48f183b3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigwig_outlier_bed commit 091caba3c5b066b293745ccee5cd31132fec3b4b
iuc
parents:
diff changeset
159 )
ebcd48f183b3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigwig_outlier_bed commit 091caba3c5b066b293745ccee5cd31132fec3b4b
iuc
parents:
diff changeset
160 sys.exit(2)
ebcd48f183b3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigwig_outlier_bed commit 091caba3c5b066b293745ccee5cd31132fec3b4b
iuc
parents:
diff changeset
161
ebcd48f183b3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigwig_outlier_bed commit 091caba3c5b066b293745ccee5cd31132fec3b4b
iuc
parents:
diff changeset
162
ebcd48f183b3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigwig_outlier_bed commit 091caba3c5b066b293745ccee5cd31132fec3b4b
iuc
parents:
diff changeset
163 if __name__ == "__main__":
ebcd48f183b3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigwig_outlier_bed commit 091caba3c5b066b293745ccee5cd31132fec3b4b
iuc
parents:
diff changeset
164 parser = argparse.ArgumentParser()
ebcd48f183b3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigwig_outlier_bed commit 091caba3c5b066b293745ccee5cd31132fec3b4b
iuc
parents:
diff changeset
165 a = parser.add_argument
ebcd48f183b3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigwig_outlier_bed commit 091caba3c5b066b293745ccee5cd31132fec3b4b
iuc
parents:
diff changeset
166 a("-m", "--minwin", default=10, type=int)
ebcd48f183b3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigwig_outlier_bed commit 091caba3c5b066b293745ccee5cd31132fec3b4b
iuc
parents:
diff changeset
167 a("-l", "--qlo", default=None, type=float)
ebcd48f183b3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigwig_outlier_bed commit 091caba3c5b066b293745ccee5cd31132fec3b4b
iuc
parents:
diff changeset
168 a("-i", "--qhi", default=None, type=float)
ebcd48f183b3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigwig_outlier_bed commit 091caba3c5b066b293745ccee5cd31132fec3b4b
iuc
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169 a("--bedouthi", default=None)
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170 a("--bedoutlo", default=None)
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171 a("--bedouthilo", default=None)
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172 a("-w", "--bigwig", nargs="+")
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173 a("-n", "--bigwiglabels", nargs="+")
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174 a("-o", "--outbeds", default="outhilo", help="optional high and low combined bed")
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175 a("-t", "--tableoutfile", default=None)
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176 args = parser.parse_args()
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177 findOut(args)