Mercurial > repos > fubar > bigwig_outlier_bed

annotate bigwig_outlier_bed_slow1.py @ 3:d4c50cb2042d draft

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planemo upload for repository https://github.com/jackh726/bigtools commit ce6b9f638ebcebcad5a5b10219f252962f30e5cc-dirty
author fubar
date Mon, 01 Jul 2024 03:08:11 +0000
parents c71db540eb38
children
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c71db540eb38 planemo upload for repository https://github.com/jackh726/bigtools commit ce6b9f638ebcebcad5a5b10219f252962f30e5cc-dirty
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diff changeset
1 import os
c71db540eb38 planemo upload for repository https://github.com/jackh726/bigtools commit ce6b9f638ebcebcad5a5b10219f252962f30e5cc-dirty
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2 import pyBigWig
c71db540eb38 planemo upload for repository https://github.com/jackh726/bigtools commit ce6b9f638ebcebcad5a5b10219f252962f30e5cc-dirty
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3
c71db540eb38 planemo upload for repository https://github.com/jackh726/bigtools commit ce6b9f638ebcebcad5a5b10219f252962f30e5cc-dirty
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4
c71db540eb38 planemo upload for repository https://github.com/jackh726/bigtools commit ce6b9f638ebcebcad5a5b10219f252962f30e5cc-dirty
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5 class findOut():
c71db540eb38 planemo upload for repository https://github.com/jackh726/bigtools commit ce6b9f638ebcebcad5a5b10219f252962f30e5cc-dirty
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6
c71db540eb38 planemo upload for repository https://github.com/jackh726/bigtools commit ce6b9f638ebcebcad5a5b10219f252962f30e5cc-dirty
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7 def __init__(self, bwname="test.bw", bedname="test.bed", sd_lo=3, sd_hi=3, bedwin=10):
c71db540eb38 planemo upload for repository https://github.com/jackh726/bigtools commit ce6b9f638ebcebcad5a5b10219f252962f30e5cc-dirty
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8 self.bedwin = bedwin
c71db540eb38 planemo upload for repository https://github.com/jackh726/bigtools commit ce6b9f638ebcebcad5a5b10219f252962f30e5cc-dirty
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9 self.bwf = pyBigWig.open(bwname, "r")
c71db540eb38 planemo upload for repository https://github.com/jackh726/bigtools commit ce6b9f638ebcebcad5a5b10219f252962f30e5cc-dirty
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10 self.chrlist = self.bwf.chroms()
c71db540eb38 planemo upload for repository https://github.com/jackh726/bigtools commit ce6b9f638ebcebcad5a5b10219f252962f30e5cc-dirty
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11 self.bedf = open(bedname, "w")
c71db540eb38 planemo upload for repository https://github.com/jackh726/bigtools commit ce6b9f638ebcebcad5a5b10219f252962f30e5cc-dirty
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12 self.sd_lo = sd_lo
c71db540eb38 planemo upload for repository https://github.com/jackh726/bigtools commit ce6b9f638ebcebcad5a5b10219f252962f30e5cc-dirty
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13 self.sd_hi = sd_hi
c71db540eb38 planemo upload for repository https://github.com/jackh726/bigtools commit ce6b9f638ebcebcad5a5b10219f252962f30e5cc-dirty
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14 self.makeBed(self.chrlist)
c71db540eb38 planemo upload for repository https://github.com/jackh726/bigtools commit ce6b9f638ebcebcad5a5b10219f252962f30e5cc-dirty
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15
c71db540eb38 planemo upload for repository https://github.com/jackh726/bigtools commit ce6b9f638ebcebcad5a5b10219f252962f30e5cc-dirty
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16 def makeBed(self, chrlist):
c71db540eb38 planemo upload for repository https://github.com/jackh726/bigtools commit ce6b9f638ebcebcad5a5b10219f252962f30e5cc-dirty
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17 bed = []
c71db540eb38 planemo upload for repository https://github.com/jackh726/bigtools commit ce6b9f638ebcebcad5a5b10219f252962f30e5cc-dirty
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18 for chr in chrlist:
c71db540eb38 planemo upload for repository https://github.com/jackh726/bigtools commit ce6b9f638ebcebcad5a5b10219f252962f30e5cc-dirty
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19 print(chr)
c71db540eb38 planemo upload for repository https://github.com/jackh726/bigtools commit ce6b9f638ebcebcad5a5b10219f252962f30e5cc-dirty
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20 gm = self.bwf.stats(chr, 0, type="mean")[0]
c71db540eb38 planemo upload for repository https://github.com/jackh726/bigtools commit ce6b9f638ebcebcad5a5b10219f252962f30e5cc-dirty
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21 gstd = self.bwf.stats(chr, 0, type="std")[0]
c71db540eb38 planemo upload for repository https://github.com/jackh726/bigtools commit ce6b9f638ebcebcad5a5b10219f252962f30e5cc-dirty
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22 cutlow = gm - (self.sd_lo * gstd)
c71db540eb38 planemo upload for repository https://github.com/jackh726/bigtools commit ce6b9f638ebcebcad5a5b10219f252962f30e5cc-dirty
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23 cuthi = gm + (self.sd_hi * gstd)
c71db540eb38 planemo upload for repository https://github.com/jackh726/bigtools commit ce6b9f638ebcebcad5a5b10219f252962f30e5cc-dirty
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24 chr_len = self.chrlist[chr]
c71db540eb38 planemo upload for repository https://github.com/jackh726/bigtools commit ce6b9f638ebcebcad5a5b10219f252962f30e5cc-dirty
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25 nb = chr_len // self.bedwin
c71db540eb38 planemo upload for repository https://github.com/jackh726/bigtools commit ce6b9f638ebcebcad5a5b10219f252962f30e5cc-dirty
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26 means = self.bwf.stats(chr, 0, chr_len, type="mean", nBins=nb)
c71db540eb38 planemo upload for repository https://github.com/jackh726/bigtools commit ce6b9f638ebcebcad5a5b10219f252962f30e5cc-dirty
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27 inlo = False
c71db540eb38 planemo upload for repository https://github.com/jackh726/bigtools commit ce6b9f638ebcebcad5a5b10219f252962f30e5cc-dirty
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28 inhi = False
c71db540eb38 planemo upload for repository https://github.com/jackh726/bigtools commit ce6b9f638ebcebcad5a5b10219f252962f30e5cc-dirty
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29 reg_start = None
c71db540eb38 planemo upload for repository https://github.com/jackh726/bigtools commit ce6b9f638ebcebcad5a5b10219f252962f30e5cc-dirty
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30 reg_end = None
c71db540eb38 planemo upload for repository https://github.com/jackh726/bigtools commit ce6b9f638ebcebcad5a5b10219f252962f30e5cc-dirty
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31 reg_means = []
c71db540eb38 planemo upload for repository https://github.com/jackh726/bigtools commit ce6b9f638ebcebcad5a5b10219f252962f30e5cc-dirty
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32 print('got %d means, gm=%f, lo=%f, hi=%f' % (len(means), gm, cutlow, cuthi))
c71db540eb38 planemo upload for repository https://github.com/jackh726/bigtools commit ce6b9f638ebcebcad5a5b10219f252962f30e5cc-dirty
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33 for i, m in enumerate(means):
c71db540eb38 planemo upload for repository https://github.com/jackh726/bigtools commit ce6b9f638ebcebcad5a5b10219f252962f30e5cc-dirty
fubar
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34 bend = min(chr_len, (i + 1) * self.bedwin)
c71db540eb38 planemo upload for repository https://github.com/jackh726/bigtools commit ce6b9f638ebcebcad5a5b10219f252962f30e5cc-dirty
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35 featname = "%s_%d" % (chr,i)
c71db540eb38 planemo upload for repository https://github.com/jackh726/bigtools commit ce6b9f638ebcebcad5a5b10219f252962f30e5cc-dirty
fubar
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36 if m and (m < cutlow or m > cuthi):
c71db540eb38 planemo upload for repository https://github.com/jackh726/bigtools commit ce6b9f638ebcebcad5a5b10219f252962f30e5cc-dirty
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37 if inlo:
c71db540eb38 planemo upload for repository https://github.com/jackh726/bigtools commit ce6b9f638ebcebcad5a5b10219f252962f30e5cc-dirty
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38 if m < cutlow: # extend
c71db540eb38 planemo upload for repository https://github.com/jackh726/bigtools commit ce6b9f638ebcebcad5a5b10219f252962f30e5cc-dirty
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39 reg_end = bend
c71db540eb38 planemo upload for repository https://github.com/jackh726/bigtools commit ce6b9f638ebcebcad5a5b10219f252962f30e5cc-dirty
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40 reg_means.append(m)
c71db540eb38 planemo upload for repository https://github.com/jackh726/bigtools commit ce6b9f638ebcebcad5a5b10219f252962f30e5cc-dirty
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41 else: # high so close
c71db540eb38 planemo upload for repository https://github.com/jackh726/bigtools commit ce6b9f638ebcebcad5a5b10219f252962f30e5cc-dirty
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42 rm = sum(reg_means) / len(reg_means)
c71db540eb38 planemo upload for repository https://github.com/jackh726/bigtools commit ce6b9f638ebcebcad5a5b10219f252962f30e5cc-dirty
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43 bed.append(
c71db540eb38 planemo upload for repository https://github.com/jackh726/bigtools commit ce6b9f638ebcebcad5a5b10219f252962f30e5cc-dirty
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44 "%s\t%d\t%d\t%s\t%.3f\n"
c71db540eb38 planemo upload for repository https://github.com/jackh726/bigtools commit ce6b9f638ebcebcad5a5b10219f252962f30e5cc-dirty
fubar
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45 % (chr, reg_start, reg_end, featname, rm)
c71db540eb38 planemo upload for repository https://github.com/jackh726/bigtools commit ce6b9f638ebcebcad5a5b10219f252962f30e5cc-dirty
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46 )
c71db540eb38 planemo upload for repository https://github.com/jackh726/bigtools commit ce6b9f638ebcebcad5a5b10219f252962f30e5cc-dirty
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47 inlo = False
c71db540eb38 planemo upload for repository https://github.com/jackh726/bigtools commit ce6b9f638ebcebcad5a5b10219f252962f30e5cc-dirty
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48 reg_means = []
c71db540eb38 planemo upload for repository https://github.com/jackh726/bigtools commit ce6b9f638ebcebcad5a5b10219f252962f30e5cc-dirty
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49 elif inhi:
c71db540eb38 planemo upload for repository https://github.com/jackh726/bigtools commit ce6b9f638ebcebcad5a5b10219f252962f30e5cc-dirty
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50 if m > cuthi: # extend
c71db540eb38 planemo upload for repository https://github.com/jackh726/bigtools commit ce6b9f638ebcebcad5a5b10219f252962f30e5cc-dirty
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51 reg_end = bend
c71db540eb38 planemo upload for repository https://github.com/jackh726/bigtools commit ce6b9f638ebcebcad5a5b10219f252962f30e5cc-dirty
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52 reg_means.append(m)
c71db540eb38 planemo upload for repository https://github.com/jackh726/bigtools commit ce6b9f638ebcebcad5a5b10219f252962f30e5cc-dirty
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53 else:
c71db540eb38 planemo upload for repository https://github.com/jackh726/bigtools commit ce6b9f638ebcebcad5a5b10219f252962f30e5cc-dirty
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54 rm = sum(reg_means) / len(reg_means)
c71db540eb38 planemo upload for repository https://github.com/jackh726/bigtools commit ce6b9f638ebcebcad5a5b10219f252962f30e5cc-dirty
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55 bed.append(
c71db540eb38 planemo upload for repository https://github.com/jackh726/bigtools commit ce6b9f638ebcebcad5a5b10219f252962f30e5cc-dirty
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56 "%s\t%d\t%d\t%s\t%.3f\n"
c71db540eb38 planemo upload for repository https://github.com/jackh726/bigtools commit ce6b9f638ebcebcad5a5b10219f252962f30e5cc-dirty
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57 % (chr, reg_start, reg_end, featname, rm)
c71db540eb38 planemo upload for repository https://github.com/jackh726/bigtools commit ce6b9f638ebcebcad5a5b10219f252962f30e5cc-dirty
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58 )
c71db540eb38 planemo upload for repository https://github.com/jackh726/bigtools commit ce6b9f638ebcebcad5a5b10219f252962f30e5cc-dirty
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59 inhi = False
c71db540eb38 planemo upload for repository https://github.com/jackh726/bigtools commit ce6b9f638ebcebcad5a5b10219f252962f30e5cc-dirty
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60 reg_means = []
c71db540eb38 planemo upload for repository https://github.com/jackh726/bigtools commit ce6b9f638ebcebcad5a5b10219f252962f30e5cc-dirty
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61 elif m < cutlow: # start new low region
c71db540eb38 planemo upload for repository https://github.com/jackh726/bigtools commit ce6b9f638ebcebcad5a5b10219f252962f30e5cc-dirty
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62 inlo = True
c71db540eb38 planemo upload for repository https://github.com/jackh726/bigtools commit ce6b9f638ebcebcad5a5b10219f252962f30e5cc-dirty
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63 reg_start = i * self.bedwin
c71db540eb38 planemo upload for repository https://github.com/jackh726/bigtools commit ce6b9f638ebcebcad5a5b10219f252962f30e5cc-dirty
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64 reg_end = bend
c71db540eb38 planemo upload for repository https://github.com/jackh726/bigtools commit ce6b9f638ebcebcad5a5b10219f252962f30e5cc-dirty
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65 reg_means = [m]
c71db540eb38 planemo upload for repository https://github.com/jackh726/bigtools commit ce6b9f638ebcebcad5a5b10219f252962f30e5cc-dirty
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66 elif m > cuthi:
c71db540eb38 planemo upload for repository https://github.com/jackh726/bigtools commit ce6b9f638ebcebcad5a5b10219f252962f30e5cc-dirty
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67 inhi = True
c71db540eb38 planemo upload for repository https://github.com/jackh726/bigtools commit ce6b9f638ebcebcad5a5b10219f252962f30e5cc-dirty
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68 reg_start = i * self.bedwin
c71db540eb38 planemo upload for repository https://github.com/jackh726/bigtools commit ce6b9f638ebcebcad5a5b10219f252962f30e5cc-dirty
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69 reg_end = bend
c71db540eb38 planemo upload for repository https://github.com/jackh726/bigtools commit ce6b9f638ebcebcad5a5b10219f252962f30e5cc-dirty
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70 reg_means = [m]
c71db540eb38 planemo upload for repository https://github.com/jackh726/bigtools commit ce6b9f638ebcebcad5a5b10219f252962f30e5cc-dirty
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71 else: # not out of range - write current extended bed region
c71db540eb38 planemo upload for repository https://github.com/jackh726/bigtools commit ce6b9f638ebcebcad5a5b10219f252962f30e5cc-dirty
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72 if inhi or inlo:
c71db540eb38 planemo upload for repository https://github.com/jackh726/bigtools commit ce6b9f638ebcebcad5a5b10219f252962f30e5cc-dirty
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73 inhi = False
c71db540eb38 planemo upload for repository https://github.com/jackh726/bigtools commit ce6b9f638ebcebcad5a5b10219f252962f30e5cc-dirty
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74 inlo = False
c71db540eb38 planemo upload for repository https://github.com/jackh726/bigtools commit ce6b9f638ebcebcad5a5b10219f252962f30e5cc-dirty
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75 rm = sum(reg_means) / len(reg_means)
c71db540eb38 planemo upload for repository https://github.com/jackh726/bigtools commit ce6b9f638ebcebcad5a5b10219f252962f30e5cc-dirty
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76 bed.append(
c71db540eb38 planemo upload for repository https://github.com/jackh726/bigtools commit ce6b9f638ebcebcad5a5b10219f252962f30e5cc-dirty
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77 "%s\t%d\t%d\t%s\t%.3f\n"
c71db540eb38 planemo upload for repository https://github.com/jackh726/bigtools commit ce6b9f638ebcebcad5a5b10219f252962f30e5cc-dirty
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78 % (chr, reg_start, reg_end, featname, rm)
c71db540eb38 planemo upload for repository https://github.com/jackh726/bigtools commit ce6b9f638ebcebcad5a5b10219f252962f30e5cc-dirty
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79 )
c71db540eb38 planemo upload for repository https://github.com/jackh726/bigtools commit ce6b9f638ebcebcad5a5b10219f252962f30e5cc-dirty
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80 reg_means = []
c71db540eb38 planemo upload for repository https://github.com/jackh726/bigtools commit ce6b9f638ebcebcad5a5b10219f252962f30e5cc-dirty
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81 reg_start = None
c71db540eb38 planemo upload for repository https://github.com/jackh726/bigtools commit ce6b9f638ebcebcad5a5b10219f252962f30e5cc-dirty
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82 reg_end = None
c71db540eb38 planemo upload for repository https://github.com/jackh726/bigtools commit ce6b9f638ebcebcad5a5b10219f252962f30e5cc-dirty
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83 self.bedf.write(''.join(bed))
c71db540eb38 planemo upload for repository https://github.com/jackh726/bigtools commit ce6b9f638ebcebcad5a5b10219f252962f30e5cc-dirty
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84 self.bedf.close()
c71db540eb38 planemo upload for repository https://github.com/jackh726/bigtools commit ce6b9f638ebcebcad5a5b10219f252962f30e5cc-dirty
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85
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86
c71db540eb38 planemo upload for repository https://github.com/jackh726/bigtools commit ce6b9f638ebcebcad5a5b10219f252962f30e5cc-dirty
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87 if __name__ == "__main__":
c71db540eb38 planemo upload for repository https://github.com/jackh726/bigtools commit ce6b9f638ebcebcad5a5b10219f252962f30e5cc-dirty
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88 fo = findOut(bwname="test.bw", bedname="test.bed", sd_lo=2, sd_hi=2, bedwin=100)