Mercurial > repos > iuc > bigwig_outlier_bed

annotate bigwig_outlier_bed.py @ 4:2488bcddaf14 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigwig_outlier_bed commit d27456ca56231eb9a4eb360c99f44af6c18a0afc
author iuc
date Mon, 30 Sep 2024 01:42:34 +0000
parents 00b3da7776a0
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ebcd48f183b3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigwig_outlier_bed commit 091caba3c5b066b293745ccee5cd31132fec3b4b
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1 """
ebcd48f183b3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigwig_outlier_bed commit 091caba3c5b066b293745ccee5cd31132fec3b4b
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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
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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
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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
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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
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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
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16 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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17 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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18 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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19
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20 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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21 import pybigtools
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22
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23
2
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24 class asciihist:
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25
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26 def __init__(
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27 self,
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28 data,
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29 bins=10,
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30 minmax=None,
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31 str_tag="",
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32 scale_output=80,
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33 generate_only=True,
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34 ):
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35 """
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36 https://gist.github.com/bgbg/608d9ef4fd75032731651257fe67fc81
61946b8bd43b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigwig_outlier_bed commit 3cce4c76a60b9353298fdcf759e893b8fcdfaa77
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37 Create an ASCII histogram from an interable of numbers.
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38 Author: Boris Gorelik boris@gorelik.net. based on http://econpy.googlecode.com/svn/trunk/pytrix/pytrix.py
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39 License: MIT
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40 """
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41 self.data = data
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42 self.minmax = minmax
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43 self.str_tag = str_tag
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44 self.bins = bins
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45 self.generate_only = generate_only
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46 self.scale_output = scale_output
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47 self.itarray = np.asanyarray(self.data)
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48 if self.minmax == "auto":
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49 self.minmax = np.percentile(data, [5, 95])
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50 if self.minmax[0] == self.minmax[1]:
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51 # for very ugly distributions
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52 self.minmax = None
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53 if self.minmax is not None:
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54 # discard values that are outside minmax range
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55 mn = self.minmax[0]
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56 mx = self.minmax[1]
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57 self.itarray = self.itarray[self.itarray >= mn]
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58 self.itarray = self.itarray[self.itarray <= mx]
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59
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60 def draw(self):
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61 values, counts = np.unique(self.data, return_counts=True)
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62 if len(values) <= 20:
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63 self.bins = len(values)
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64 ret = []
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65 if self.itarray.size:
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66 total = len(self.itarray)
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67 counts, cutoffs = np.histogram(self.itarray, bins=self.bins)
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68 cutoffs = cutoffs[1:]
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69 if self.str_tag:
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70 self.str_tag = "%s " % self.str_tag
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71 else:
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72 self.str_tag = ""
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73 if self.scale_output is not None:
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74 scaled_counts = counts.astype(float) / counts.sum() * self.scale_output
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75 else:
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76 scaled_counts = counts
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77 footerbar = "{:s}{:s} |{:s} |".format(
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78 self.str_tag,
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79 "-" * 12,
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80 "-" * 12,
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81 )
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82 if self.minmax is not None:
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83 ret.append(
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84 "Trimmed to range (%s - %s)"
61946b8bd43b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigwig_outlier_bed commit 3cce4c76a60b9353298fdcf759e893b8fcdfaa77
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parents: 1
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85 % (str(self.minmax[0]), str(self.minmax[1]))
61946b8bd43b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigwig_outlier_bed commit 3cce4c76a60b9353298fdcf759e893b8fcdfaa77
iuc
parents: 1
diff changeset
86 )
61946b8bd43b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigwig_outlier_bed commit 3cce4c76a60b9353298fdcf759e893b8fcdfaa77
iuc
parents: 1
diff changeset
87 for cutoff, original_count, scaled_count in zip(
61946b8bd43b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigwig_outlier_bed commit 3cce4c76a60b9353298fdcf759e893b8fcdfaa77
iuc
parents: 1
diff changeset
88 cutoffs, counts, scaled_counts
61946b8bd43b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigwig_outlier_bed commit 3cce4c76a60b9353298fdcf759e893b8fcdfaa77
iuc
parents: 1
diff changeset
89 ):
61946b8bd43b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigwig_outlier_bed commit 3cce4c76a60b9353298fdcf759e893b8fcdfaa77
iuc
parents: 1
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90 ret.append(
61946b8bd43b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigwig_outlier_bed commit 3cce4c76a60b9353298fdcf759e893b8fcdfaa77
iuc
parents: 1
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91 "{:s}{:>12.2f} |{:>12,d} | {:s}".format(
61946b8bd43b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigwig_outlier_bed commit 3cce4c76a60b9353298fdcf759e893b8fcdfaa77
iuc
parents: 1
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92 self.str_tag, cutoff, original_count, "*" * int(scaled_count)
61946b8bd43b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigwig_outlier_bed commit 3cce4c76a60b9353298fdcf759e893b8fcdfaa77
iuc
parents: 1
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93 )
61946b8bd43b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigwig_outlier_bed commit 3cce4c76a60b9353298fdcf759e893b8fcdfaa77
iuc
parents: 1
diff changeset
94 )
61946b8bd43b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigwig_outlier_bed commit 3cce4c76a60b9353298fdcf759e893b8fcdfaa77
iuc
parents: 1
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95 ret.append(footerbar)
61946b8bd43b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigwig_outlier_bed commit 3cce4c76a60b9353298fdcf759e893b8fcdfaa77
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parents: 1
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96 ret.append("{:s}{:>12s} |{:>12,d} |".format(self.str_tag, "N=", total))
61946b8bd43b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigwig_outlier_bed commit 3cce4c76a60b9353298fdcf759e893b8fcdfaa77
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97 ret.append(footerbar)
61946b8bd43b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigwig_outlier_bed commit 3cce4c76a60b9353298fdcf759e893b8fcdfaa77
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98 ret.append("")
61946b8bd43b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigwig_outlier_bed commit 3cce4c76a60b9353298fdcf759e893b8fcdfaa77
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99 else:
61946b8bd43b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigwig_outlier_bed commit 3cce4c76a60b9353298fdcf759e893b8fcdfaa77
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100 ret = []
61946b8bd43b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigwig_outlier_bed commit 3cce4c76a60b9353298fdcf759e893b8fcdfaa77
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101 if not self.generate_only:
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102 for line in ret:
61946b8bd43b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigwig_outlier_bed commit 3cce4c76a60b9353298fdcf759e893b8fcdfaa77
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103 print(line)
61946b8bd43b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigwig_outlier_bed commit 3cce4c76a60b9353298fdcf759e893b8fcdfaa77
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104 ret = "\n".join(ret)
61946b8bd43b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigwig_outlier_bed commit 3cce4c76a60b9353298fdcf759e893b8fcdfaa77
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105 return ret
61946b8bd43b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigwig_outlier_bed commit 3cce4c76a60b9353298fdcf759e893b8fcdfaa77
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106
61946b8bd43b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigwig_outlier_bed commit 3cce4c76a60b9353298fdcf759e893b8fcdfaa77
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107
0
ebcd48f183b3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigwig_outlier_bed commit 091caba3c5b066b293745ccee5cd31132fec3b4b
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108 class findOut:
ebcd48f183b3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigwig_outlier_bed commit 091caba3c5b066b293745ccee5cd31132fec3b4b
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109
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110 def __init__(self, args):
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111 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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112 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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113 self.bedwin = args.minwin
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114 self.outbeds = args.outbeds
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115 self.bedouthi = args.bedouthi
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116 self.bedoutlo = args.bedoutlo
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117 self.bedouthilo = args.bedouthilo
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118 self.tableoutfile = args.tableoutfile
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119 self.bedwin = args.minwin
4
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120 self.bedoutzero = args.bedoutzero
1
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121 self.qlo = None
2
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122 self.qhi = None
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123 if args.outbeds != "outtab":
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124 self.qhi = args.qhi
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125 if args.qlo:
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126 try:
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127 f = float(args.qlo)
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128 self.qlo = f
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129 except Exception:
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130 print("qlo not provided")
0
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131 nbw = len(args.bigwig)
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132 nlab = len(args.bigwiglabels)
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133 if nlab < nbw:
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134 self.bwlabels += ["Nolabel"] * (nbw - nlab)
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135 self.makeBed()
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136
4
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137 def processVals(self, bw, isTop, isZero):
0
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138 """
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139 idea 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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140 Fast segmentation into regions by taking np.diff on the boolean array of over (under) cutpoint indicators in bwex.
ebcd48f183b3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigwig_outlier_bed commit 091caba3c5b066b293745ccee5cd31132fec3b4b
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141 This only gives non-zero values at the segment boundaries where there's a change, so those zeros are all removed in bwexdnz
ebcd48f183b3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigwig_outlier_bed commit 091caba3c5b066b293745ccee5cd31132fec3b4b
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142 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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143 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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144 """
ebcd48f183b3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigwig_outlier_bed commit 091caba3c5b066b293745ccee5cd31132fec3b4b
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145 if isTop:
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146 bwex = np.r_[False, bw >= self.bwtop, False] # extend with 0s
4
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147 elif isZero:
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148 bwex = np.r_[False, bw == 0, False] # extend with 0s
0
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149 else:
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150 bwex = np.r_[False, bw <= self.bwbot, False]
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151 bwexd = np.diff(bwex)
3
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152 bwexdnz = bwexd.nonzero()[0] # start and end transition of each segment - nice!
0
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153 bwregions = np.reshape(bwexdnz, (-1, 2))
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154 return bwregions
ebcd48f183b3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigwig_outlier_bed commit 091caba3c5b066b293745ccee5cd31132fec3b4b
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155
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156 def writeBed(self, bed, bedfname):
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157 """
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diff changeset
158 potentially multiple
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159 """
ebcd48f183b3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigwig_outlier_bed commit 091caba3c5b066b293745ccee5cd31132fec3b4b
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diff changeset
160 bed.sort()
ebcd48f183b3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigwig_outlier_bed commit 091caba3c5b066b293745ccee5cd31132fec3b4b
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161 with open(bedfname, "w") as bedf:
3
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162 for b in bed:
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163 bedf.write("%s\t%d\t%d\t%s\t%d\n" % b)
0
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164
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165 def makeTableRow(self, bw, bwlabel, chr):
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166 """
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parents:
diff changeset
167 called for every contig, but messy inline
ebcd48f183b3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigwig_outlier_bed commit 091caba3c5b066b293745ccee5cd31132fec3b4b
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168 """
ebcd48f183b3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigwig_outlier_bed commit 091caba3c5b066b293745ccee5cd31132fec3b4b
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169 bwmean = np.mean(bw)
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parents:
diff changeset
170 bwstd = np.std(bw)
ebcd48f183b3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigwig_outlier_bed commit 091caba3c5b066b293745ccee5cd31132fec3b4b
iuc
parents:
diff changeset
171 bwmax = np.max(bw)
ebcd48f183b3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigwig_outlier_bed commit 091caba3c5b066b293745ccee5cd31132fec3b4b
iuc
parents:
diff changeset
172 nrow = np.size(bw)
ebcd48f183b3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigwig_outlier_bed commit 091caba3c5b066b293745ccee5cd31132fec3b4b
iuc
parents:
diff changeset
173 bwmin = np.min(bw)
ebcd48f183b3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigwig_outlier_bed commit 091caba3c5b066b293745ccee5cd31132fec3b4b
iuc
parents:
diff changeset
174 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
175 bwlabel,
ebcd48f183b3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigwig_outlier_bed commit 091caba3c5b066b293745ccee5cd31132fec3b4b
iuc
parents:
diff changeset
176 chr,
ebcd48f183b3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigwig_outlier_bed commit 091caba3c5b066b293745ccee5cd31132fec3b4b
iuc
parents:
diff changeset
177 nrow,
ebcd48f183b3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigwig_outlier_bed commit 091caba3c5b066b293745ccee5cd31132fec3b4b
iuc
parents:
diff changeset
178 bwmean,
ebcd48f183b3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigwig_outlier_bed commit 091caba3c5b066b293745ccee5cd31132fec3b4b
iuc
parents:
diff changeset
179 bwstd,
ebcd48f183b3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigwig_outlier_bed commit 091caba3c5b066b293745ccee5cd31132fec3b4b
iuc
parents:
diff changeset
180 bwmin,
ebcd48f183b3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigwig_outlier_bed commit 091caba3c5b066b293745ccee5cd31132fec3b4b
iuc
parents:
diff changeset
181 bwmax,
ebcd48f183b3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigwig_outlier_bed commit 091caba3c5b066b293745ccee5cd31132fec3b4b
iuc
parents:
diff changeset
182 )
ebcd48f183b3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigwig_outlier_bed commit 091caba3c5b066b293745ccee5cd31132fec3b4b
iuc
parents:
diff changeset
183 if self.qhi is not None:
1
8377a6abb4da planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigwig_outlier_bed commit 92ffe42a6ad6e81f3f157bbc9b942c000d450416
iuc
parents: 0
diff changeset
184 row += "\t%.2f" % self.bwtop
0
ebcd48f183b3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigwig_outlier_bed commit 091caba3c5b066b293745ccee5cd31132fec3b4b
iuc
parents:
diff changeset
185 else:
1
8377a6abb4da planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigwig_outlier_bed commit 92ffe42a6ad6e81f3f157bbc9b942c000d450416
iuc
parents: 0
diff changeset
186 row += "\tnoqhi"
0
ebcd48f183b3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigwig_outlier_bed commit 091caba3c5b066b293745ccee5cd31132fec3b4b
iuc
parents:
diff changeset
187 if self.qlo is not None:
1
8377a6abb4da planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigwig_outlier_bed commit 92ffe42a6ad6e81f3f157bbc9b942c000d450416
iuc
parents: 0
diff changeset
188 row += "\t%.2f" % self.bwbot
0
ebcd48f183b3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigwig_outlier_bed commit 091caba3c5b066b293745ccee5cd31132fec3b4b
iuc
parents:
diff changeset
189 else:
1
8377a6abb4da planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigwig_outlier_bed commit 92ffe42a6ad6e81f3f157bbc9b942c000d450416
iuc
parents: 0
diff changeset
190 row += "\tnoqlo"
0
ebcd48f183b3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigwig_outlier_bed commit 091caba3c5b066b293745ccee5cd31132fec3b4b
iuc
parents:
diff changeset
191 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
192
ebcd48f183b3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigwig_outlier_bed commit 091caba3c5b066b293745ccee5cd31132fec3b4b
iuc
parents:
diff changeset
193 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
194 bedhi = []
ebcd48f183b3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigwig_outlier_bed commit 091caba3c5b066b293745ccee5cd31132fec3b4b
iuc
parents:
diff changeset
195 bedlo = []
4
2488bcddaf14 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigwig_outlier_bed commit d27456ca56231eb9a4eb360c99f44af6c18a0afc
iuc
parents: 3
diff changeset
196 bedzero = []
2
61946b8bd43b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigwig_outlier_bed commit 3cce4c76a60b9353298fdcf759e893b8fcdfaa77
iuc
parents: 1
diff changeset
197 restab = []
0
ebcd48f183b3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigwig_outlier_bed commit 091caba3c5b066b293745ccee5cd31132fec3b4b
iuc
parents:
diff changeset
198 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
199 bwnames = self.bwnames
2
61946b8bd43b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigwig_outlier_bed commit 3cce4c76a60b9353298fdcf759e893b8fcdfaa77
iuc
parents: 1
diff changeset
200 reshead = "bigwig\tcontig\tn\tmean\tstd\tmin\tmax\tqtop\tqbot"
0
ebcd48f183b3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigwig_outlier_bed commit 091caba3c5b066b293745ccee5cd31132fec3b4b
iuc
parents:
diff changeset
201 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
202 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
203 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
204 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
205 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
206 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
207 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
208 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
209 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
210 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
211 for chr in chrs:
2
61946b8bd43b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigwig_outlier_bed commit 3cce4c76a60b9353298fdcf759e893b8fcdfaa77
iuc
parents: 1
diff changeset
212 first_few = None
0
ebcd48f183b3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigwig_outlier_bed commit 091caba3c5b066b293745ccee5cd31132fec3b4b
iuc
parents:
diff changeset
213 bw = bwf.values(chr)
2
61946b8bd43b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigwig_outlier_bed commit 3cce4c76a60b9353298fdcf759e893b8fcdfaa77
iuc
parents: 1
diff changeset
214 values, counts = np.unique(bw, return_counts=True)
61946b8bd43b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigwig_outlier_bed commit 3cce4c76a60b9353298fdcf759e893b8fcdfaa77
iuc
parents: 1
diff changeset
215 nvalues = len(values)
61946b8bd43b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigwig_outlier_bed commit 3cce4c76a60b9353298fdcf759e893b8fcdfaa77
iuc
parents: 1
diff changeset
216 if nvalues <= 20:
61946b8bd43b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigwig_outlier_bed commit 3cce4c76a60b9353298fdcf759e893b8fcdfaa77
iuc
parents: 1
diff changeset
217 histo = "\n".join(
61946b8bd43b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigwig_outlier_bed commit 3cce4c76a60b9353298fdcf759e893b8fcdfaa77
iuc
parents: 1
diff changeset
218 [
61946b8bd43b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigwig_outlier_bed commit 3cce4c76a60b9353298fdcf759e893b8fcdfaa77
iuc
parents: 1
diff changeset
219 "%s: %f occurs %d times" % (chr, values[x], counts[x])
61946b8bd43b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigwig_outlier_bed commit 3cce4c76a60b9353298fdcf759e893b8fcdfaa77
iuc
parents: 1
diff changeset
220 for x in range(len(values))
61946b8bd43b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigwig_outlier_bed commit 3cce4c76a60b9353298fdcf759e893b8fcdfaa77
iuc
parents: 1
diff changeset
221 ]
61946b8bd43b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigwig_outlier_bed commit 3cce4c76a60b9353298fdcf759e893b8fcdfaa77
iuc
parents: 1
diff changeset
222 )
61946b8bd43b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigwig_outlier_bed commit 3cce4c76a60b9353298fdcf759e893b8fcdfaa77
iuc
parents: 1
diff changeset
223 else:
61946b8bd43b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigwig_outlier_bed commit 3cce4c76a60b9353298fdcf759e893b8fcdfaa77
iuc
parents: 1
diff changeset
224 last10 = range(nvalues - 10, nvalues)
61946b8bd43b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigwig_outlier_bed commit 3cce4c76a60b9353298fdcf759e893b8fcdfaa77
iuc
parents: 1
diff changeset
225 first_few = ["%.2f\t%d" % (values[x], counts[x]) for x in range(10)]
61946b8bd43b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigwig_outlier_bed commit 3cce4c76a60b9353298fdcf759e893b8fcdfaa77
iuc
parents: 1
diff changeset
226 first_few += ["%.2f\t%d" % (values[x], counts[x]) for x in last10]
61946b8bd43b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigwig_outlier_bed commit 3cce4c76a60b9353298fdcf759e893b8fcdfaa77
iuc
parents: 1
diff changeset
227 first_few.insert(0, "First/Last 10 value counts\nValue\tCount")
61946b8bd43b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigwig_outlier_bed commit 3cce4c76a60b9353298fdcf759e893b8fcdfaa77
iuc
parents: 1
diff changeset
228 ha = asciihist(data=bw, bins=20, str_tag="%s_%s" % (bwlabel, chr))
61946b8bd43b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigwig_outlier_bed commit 3cce4c76a60b9353298fdcf759e893b8fcdfaa77
iuc
parents: 1
diff changeset
229 histo = ha.draw()
61946b8bd43b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigwig_outlier_bed commit 3cce4c76a60b9353298fdcf759e893b8fcdfaa77
iuc
parents: 1
diff changeset
230 histo = (
61946b8bd43b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigwig_outlier_bed commit 3cce4c76a60b9353298fdcf759e893b8fcdfaa77
iuc
parents: 1
diff changeset
231 "\n".join(first_few)
61946b8bd43b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigwig_outlier_bed commit 3cce4c76a60b9353298fdcf759e893b8fcdfaa77
iuc
parents: 1
diff changeset
232 + "\nHistogram of %s bigwig values\n" % bwlabel
61946b8bd43b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigwig_outlier_bed commit 3cce4c76a60b9353298fdcf759e893b8fcdfaa77
iuc
parents: 1
diff changeset
233 + histo
61946b8bd43b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigwig_outlier_bed commit 3cce4c76a60b9353298fdcf759e893b8fcdfaa77
iuc
parents: 1
diff changeset
234 )
0
ebcd48f183b3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigwig_outlier_bed commit 091caba3c5b066b293745ccee5cd31132fec3b4b
iuc
parents:
diff changeset
235 bw = bw[~np.isnan(bw)] # some have NaN if parts of a contig not covered
4
2488bcddaf14 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigwig_outlier_bed commit d27456ca56231eb9a4eb360c99f44af6c18a0afc
iuc
parents: 3
diff changeset
236 if self.bedoutzero is not None:
2488bcddaf14 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigwig_outlier_bed commit d27456ca56231eb9a4eb360c99f44af6c18a0afc
iuc
parents: 3
diff changeset
237 bwzero = self.processVals(bw, isTop=False, isZero=True)
2488bcddaf14 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigwig_outlier_bed commit d27456ca56231eb9a4eb360c99f44af6c18a0afc
iuc
parents: 3
diff changeset
238 for j, seg in enumerate(bwzero):
2488bcddaf14 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigwig_outlier_bed commit d27456ca56231eb9a4eb360c99f44af6c18a0afc
iuc
parents: 3
diff changeset
239 seglen = seg[1] - seg[0]
2488bcddaf14 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigwig_outlier_bed commit d27456ca56231eb9a4eb360c99f44af6c18a0afc
iuc
parents: 3
diff changeset
240 if seglen >= self.bedwin:
2488bcddaf14 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigwig_outlier_bed commit d27456ca56231eb9a4eb360c99f44af6c18a0afc
iuc
parents: 3
diff changeset
241 score = seglen
2488bcddaf14 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigwig_outlier_bed commit d27456ca56231eb9a4eb360c99f44af6c18a0afc
iuc
parents: 3
diff changeset
242 bedzero.append(
2488bcddaf14 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigwig_outlier_bed commit d27456ca56231eb9a4eb360c99f44af6c18a0afc
iuc
parents: 3
diff changeset
243 (
2488bcddaf14 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigwig_outlier_bed commit d27456ca56231eb9a4eb360c99f44af6c18a0afc
iuc
parents: 3
diff changeset
244 chr,
2488bcddaf14 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigwig_outlier_bed commit d27456ca56231eb9a4eb360c99f44af6c18a0afc
iuc
parents: 3
diff changeset
245 seg[0],
2488bcddaf14 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigwig_outlier_bed commit d27456ca56231eb9a4eb360c99f44af6c18a0afc
iuc
parents: 3
diff changeset
246 seg[1],
2488bcddaf14 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigwig_outlier_bed commit d27456ca56231eb9a4eb360c99f44af6c18a0afc
iuc
parents: 3
diff changeset
247 "%s_%d" % (bwlabel, score),
2488bcddaf14 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigwig_outlier_bed commit d27456ca56231eb9a4eb360c99f44af6c18a0afc
iuc
parents: 3
diff changeset
248 score,
2488bcddaf14 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigwig_outlier_bed commit d27456ca56231eb9a4eb360c99f44af6c18a0afc
iuc
parents: 3
diff changeset
249 )
2488bcddaf14 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigwig_outlier_bed commit d27456ca56231eb9a4eb360c99f44af6c18a0afc
iuc
parents: 3
diff changeset
250 )
0
ebcd48f183b3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigwig_outlier_bed commit 091caba3c5b066b293745ccee5cd31132fec3b4b
iuc
parents:
diff changeset
251 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
252 self.bwtop = np.quantile(bw, self.qhi)
4
2488bcddaf14 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigwig_outlier_bed commit d27456ca56231eb9a4eb360c99f44af6c18a0afc
iuc
parents: 3
diff changeset
253 bwhi = self.processVals(bw, isTop=True, isZero=False)
0
ebcd48f183b3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigwig_outlier_bed commit 091caba3c5b066b293745ccee5cd31132fec3b4b
iuc
parents:
diff changeset
254 for j, seg in enumerate(bwhi):
2
61946b8bd43b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigwig_outlier_bed commit 3cce4c76a60b9353298fdcf759e893b8fcdfaa77
iuc
parents: 1
diff changeset
255 seglen = seg[1] - seg[0]
61946b8bd43b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigwig_outlier_bed commit 3cce4c76a60b9353298fdcf759e893b8fcdfaa77
iuc
parents: 1
diff changeset
256 if seglen >= self.bedwin:
61946b8bd43b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigwig_outlier_bed commit 3cce4c76a60b9353298fdcf759e893b8fcdfaa77
iuc
parents: 1
diff changeset
257 score = np.sum(bw[seg[0]:seg[1]]) / float(seglen)
1
8377a6abb4da planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigwig_outlier_bed commit 92ffe42a6ad6e81f3f157bbc9b942c000d450416
iuc
parents: 0
diff changeset
258 bedhi.append(
8377a6abb4da planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigwig_outlier_bed commit 92ffe42a6ad6e81f3f157bbc9b942c000d450416
iuc
parents: 0
diff changeset
259 (
8377a6abb4da planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigwig_outlier_bed commit 92ffe42a6ad6e81f3f157bbc9b942c000d450416
iuc
parents: 0
diff changeset
260 chr,
8377a6abb4da planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigwig_outlier_bed commit 92ffe42a6ad6e81f3f157bbc9b942c000d450416
iuc
parents: 0
diff changeset
261 seg[0],
8377a6abb4da planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigwig_outlier_bed commit 92ffe42a6ad6e81f3f157bbc9b942c000d450416
iuc
parents: 0
diff changeset
262 seg[1],
8377a6abb4da planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigwig_outlier_bed commit 92ffe42a6ad6e81f3f157bbc9b942c000d450416
iuc
parents: 0
diff changeset
263 "%s_%d" % (bwlabel, score),
8377a6abb4da planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigwig_outlier_bed commit 92ffe42a6ad6e81f3f157bbc9b942c000d450416
iuc
parents: 0
diff changeset
264 score,
8377a6abb4da planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigwig_outlier_bed commit 92ffe42a6ad6e81f3f157bbc9b942c000d450416
iuc
parents: 0
diff changeset
265 )
8377a6abb4da planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigwig_outlier_bed commit 92ffe42a6ad6e81f3f157bbc9b942c000d450416
iuc
parents: 0
diff changeset
266 )
0
ebcd48f183b3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigwig_outlier_bed commit 091caba3c5b066b293745ccee5cd31132fec3b4b
iuc
parents:
diff changeset
267 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
268 self.bwbot = np.quantile(bw, self.qlo)
4
2488bcddaf14 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigwig_outlier_bed commit d27456ca56231eb9a4eb360c99f44af6c18a0afc
iuc
parents: 3
diff changeset
269 bwlo = self.processVals(bw, isTop=False, isZero=False)
0
ebcd48f183b3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigwig_outlier_bed commit 091caba3c5b066b293745ccee5cd31132fec3b4b
iuc
parents:
diff changeset
270 for j, seg in enumerate(bwlo):
3
00b3da7776a0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigwig_outlier_bed commit 06c54e8066ecbc6292167e7c5bdfb8af945a41ba
iuc
parents: 2
diff changeset
271 seglen = seg[1] - seg[0]
0
ebcd48f183b3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigwig_outlier_bed commit 091caba3c5b066b293745ccee5cd31132fec3b4b
iuc
parents:
diff changeset
272 if seg[1] - seg[0] >= self.bedwin:
3
00b3da7776a0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigwig_outlier_bed commit 06c54e8066ecbc6292167e7c5bdfb8af945a41ba
iuc
parents: 2
diff changeset
273 score = (
00b3da7776a0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigwig_outlier_bed commit 06c54e8066ecbc6292167e7c5bdfb8af945a41ba
iuc
parents: 2
diff changeset
274 -1 * np.sum(bw[seg[0]:seg[1]]) / float(seglen)
00b3da7776a0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigwig_outlier_bed commit 06c54e8066ecbc6292167e7c5bdfb8af945a41ba
iuc
parents: 2
diff changeset
275 )
1
8377a6abb4da planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigwig_outlier_bed commit 92ffe42a6ad6e81f3f157bbc9b942c000d450416
iuc
parents: 0
diff changeset
276 bedlo.append(
8377a6abb4da planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigwig_outlier_bed commit 92ffe42a6ad6e81f3f157bbc9b942c000d450416
iuc
parents: 0
diff changeset
277 (
8377a6abb4da planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigwig_outlier_bed commit 92ffe42a6ad6e81f3f157bbc9b942c000d450416
iuc
parents: 0
diff changeset
278 chr,
8377a6abb4da planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigwig_outlier_bed commit 92ffe42a6ad6e81f3f157bbc9b942c000d450416
iuc
parents: 0
diff changeset
279 seg[0],
8377a6abb4da planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigwig_outlier_bed commit 92ffe42a6ad6e81f3f157bbc9b942c000d450416
iuc
parents: 0
diff changeset
280 seg[1],
8377a6abb4da planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigwig_outlier_bed commit 92ffe42a6ad6e81f3f157bbc9b942c000d450416
iuc
parents: 0
diff changeset
281 "%s_%d" % (bwlabel, score),
8377a6abb4da planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigwig_outlier_bed commit 92ffe42a6ad6e81f3f157bbc9b942c000d450416
iuc
parents: 0
diff changeset
282 score,
8377a6abb4da planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigwig_outlier_bed commit 92ffe42a6ad6e81f3f157bbc9b942c000d450416
iuc
parents: 0
diff changeset
283 )
8377a6abb4da planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigwig_outlier_bed commit 92ffe42a6ad6e81f3f157bbc9b942c000d450416
iuc
parents: 0
diff changeset
284 )
0
ebcd48f183b3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigwig_outlier_bed commit 091caba3c5b066b293745ccee5cd31132fec3b4b
iuc
parents:
diff changeset
285 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
286 row = self.makeTableRow(bw, bwlabel, chr)
2
61946b8bd43b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigwig_outlier_bed commit 3cce4c76a60b9353298fdcf759e893b8fcdfaa77
iuc
parents: 1
diff changeset
287 resheadl = reshead.split("\t")
61946b8bd43b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigwig_outlier_bed commit 3cce4c76a60b9353298fdcf759e893b8fcdfaa77
iuc
parents: 1
diff changeset
288 rowl = row.split()
61946b8bd43b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigwig_outlier_bed commit 3cce4c76a60b9353298fdcf759e893b8fcdfaa77
iuc
parents: 1
diff changeset
289 desc = ["%s\t%s" % (resheadl[x], rowl[x]) for x in range(len(rowl))]
61946b8bd43b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigwig_outlier_bed commit 3cce4c76a60b9353298fdcf759e893b8fcdfaa77
iuc
parents: 1
diff changeset
290 desc.insert(0, "Descriptive measures")
61946b8bd43b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigwig_outlier_bed commit 3cce4c76a60b9353298fdcf759e893b8fcdfaa77
iuc
parents: 1
diff changeset
291 descn = "\n".join(desc)
61946b8bd43b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigwig_outlier_bed commit 3cce4c76a60b9353298fdcf759e893b8fcdfaa77
iuc
parents: 1
diff changeset
292 restab.append(descn)
61946b8bd43b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigwig_outlier_bed commit 3cce4c76a60b9353298fdcf759e893b8fcdfaa77
iuc
parents: 1
diff changeset
293 restab.append(histo)
61946b8bd43b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigwig_outlier_bed commit 3cce4c76a60b9353298fdcf759e893b8fcdfaa77
iuc
parents: 1
diff changeset
294 if os.path.isfile(fakepath):
61946b8bd43b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigwig_outlier_bed commit 3cce4c76a60b9353298fdcf759e893b8fcdfaa77
iuc
parents: 1
diff changeset
295 os.remove(fakepath)
0
ebcd48f183b3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigwig_outlier_bed commit 091caba3c5b066b293745ccee5cd31132fec3b4b
iuc
parents:
diff changeset
296 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
297 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
298 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
299 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
300 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
301 some = False
4
2488bcddaf14 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigwig_outlier_bed commit d27456ca56231eb9a4eb360c99f44af6c18a0afc
iuc
parents: 3
diff changeset
302 if self.outbeds in ["outzero"]:
2488bcddaf14 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigwig_outlier_bed commit d27456ca56231eb9a4eb360c99f44af6c18a0afc
iuc
parents: 3
diff changeset
303 self.writeBed(bedzero, self.bedoutzero)
2488bcddaf14 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigwig_outlier_bed commit d27456ca56231eb9a4eb360c99f44af6c18a0afc
iuc
parents: 3
diff changeset
304 some = True
0
ebcd48f183b3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigwig_outlier_bed commit 091caba3c5b066b293745ccee5cd31132fec3b4b
iuc
parents:
diff changeset
305 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
306 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
307 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
308 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
309 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
310 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
311 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
312 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
313 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
314 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
315 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
316 some = True
2
61946b8bd43b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigwig_outlier_bed commit 3cce4c76a60b9353298fdcf759e893b8fcdfaa77
iuc
parents: 1
diff changeset
317 if not ((self.outbeds == "outtab") or some):
0
ebcd48f183b3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigwig_outlier_bed commit 091caba3c5b066b293745ccee5cd31132fec3b4b
iuc
parents:
diff changeset
318 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
319 "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
320 )
ebcd48f183b3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigwig_outlier_bed commit 091caba3c5b066b293745ccee5cd31132fec3b4b
iuc
parents:
diff changeset
321 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
322
ebcd48f183b3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigwig_outlier_bed commit 091caba3c5b066b293745ccee5cd31132fec3b4b
iuc
parents:
diff changeset
323
ebcd48f183b3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigwig_outlier_bed commit 091caba3c5b066b293745ccee5cd31132fec3b4b
iuc
parents:
diff changeset
324 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
325 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
326 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
327 a("-m", "--minwin", default=10, type=int)
1
8377a6abb4da planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigwig_outlier_bed commit 92ffe42a6ad6e81f3f157bbc9b942c000d450416
iuc
parents: 0
diff changeset
328 a("-l", "--qlo", default=None)
0
ebcd48f183b3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigwig_outlier_bed commit 091caba3c5b066b293745ccee5cd31132fec3b4b
iuc
parents:
diff changeset
329 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
parents:
diff changeset
330 a("--bedouthi", default=None)
ebcd48f183b3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigwig_outlier_bed commit 091caba3c5b066b293745ccee5cd31132fec3b4b
iuc
parents:
diff changeset
331 a("--bedoutlo", default=None)
ebcd48f183b3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigwig_outlier_bed commit 091caba3c5b066b293745ccee5cd31132fec3b4b
iuc
parents:
diff changeset
332 a("--bedouthilo", default=None)
4
2488bcddaf14 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigwig_outlier_bed commit d27456ca56231eb9a4eb360c99f44af6c18a0afc
iuc
parents: 3
diff changeset
333 a("--bedoutzero", default=None)
0
ebcd48f183b3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigwig_outlier_bed commit 091caba3c5b066b293745ccee5cd31132fec3b4b
iuc
parents:
diff changeset
334 a("-w", "--bigwig", nargs="+")
ebcd48f183b3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigwig_outlier_bed commit 091caba3c5b066b293745ccee5cd31132fec3b4b
iuc
parents:
diff changeset
335 a("-n", "--bigwiglabels", nargs="+")
ebcd48f183b3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigwig_outlier_bed commit 091caba3c5b066b293745ccee5cd31132fec3b4b
iuc
parents:
diff changeset
336 a("-o", "--outbeds", default="outhilo", help="optional high and low combined bed")
ebcd48f183b3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigwig_outlier_bed commit 091caba3c5b066b293745ccee5cd31132fec3b4b
iuc
parents:
diff changeset
337 a("-t", "--tableoutfile", default=None)
ebcd48f183b3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigwig_outlier_bed commit 091caba3c5b066b293745ccee5cd31132fec3b4b
iuc
parents:
diff changeset
338 args = parser.parse_args()
ebcd48f183b3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigwig_outlier_bed commit 091caba3c5b066b293745ccee5cd31132fec3b4b
iuc
parents:
diff changeset
339 findOut(args)