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1 _bedtools_path = ""
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2 _R_path = ""
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3
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4 tempfile_prefix = "pybedtools."
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5 tempfile_suffix = ".tmp"
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6
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7 # Checking for BEDTools will happen when creating the first BedTool; other
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8 # checks happen at first use (BAM object creation; tabix-ing a BedTool)
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9 _bedtools_installed = False
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10 _R_installed = False
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11 _v_2_15_plus = False
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12 _v_2_27_plus = False
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13 bedtools_version = []
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14
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15 KEEP_TEMPFILES = False
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16 _DEBUG = True
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17
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18 # Check calls against these names to only allow calls to known BEDTools
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19 # programs (basic security)
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20 #
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21 _prog_names = {
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22 # Genome arithmetic
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23 "intersectBed": "intersect",
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24 "windowBed": "window",
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25 "closestBed": "closest",
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26 "coverageBed": "coverage",
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27 "mapBed": "map",
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28 "genomeCoverageBed": "genomecov",
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29 "mergeBed": "merge",
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30 "clusterBed": "cluster",
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31 "complementBed": "complement",
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32 "subtractBed": "subtract",
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33 "slopBed": "slop",
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34 "shiftBed": "shift",
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35 "flankBed": "flank",
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36 "sortBed": "sort",
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37 "randomBed": "random",
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38 "shuffleBed": "shuffle",
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39 "annotateBed": "annotate",
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40 "spacing": "spacing",
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41 # multi-way
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42 "multiIntersectBed": "multiinter",
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43 "unionBedGraphs": "unionbedg",
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44 # PE
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45 "pairToBed": "pairtobed",
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46 "pairToPair": "pairtopair",
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47 # format conversion
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48 "bamToBed": "bamtobed",
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49 "bedToBam": "bedtobam",
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50 "bedpeToBam": "bedpetobam",
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51 "bed12ToBed6": "bed12tobed6",
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52 "bamToFastq": "bamtofastq",
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53 # fasta
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54 "fastaFromBed": "getfasta",
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55 "maskFastaFromBed": "maskfasta",
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56 "nucBed": "nuc",
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57 # bam-centric
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58 "multiBamCov": "multicov",
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59 "tagBam": "tag",
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60 # stats
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61 "jaccard": "jaccard",
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62 "reldist": "reldist",
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63 # misc
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64 "getOverlap": "overlap",
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65 "bedToIgv": "igv",
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66 "linksBed": "links",
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67 "windowMaker": "makewindows",
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68 "groupBy": "groupby",
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69 "expandCols": "expand",
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70 "sample": "sample",
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71 "fisher": "fisher",
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72 "split": "split",
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73 }
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74
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75 _old_names = list(_prog_names.keys())
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76 _new_names = list(_prog_names.values())
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77
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78 _column_names = {
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79 "bed": [
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80 "chrom",
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81 "start",
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82 "end",
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83 "name",
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84 "score",
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85 "strand",
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86 "thickStart",
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87 "thickEnd",
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88 "itemRgb",
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89 "blockCount",
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90 "blockSizes",
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91 "blockStarts",
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92 ],
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93 "gff": [
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94 "seqname",
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95 "source",
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96 "feature",
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97 "start",
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98 "end",
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99 "score",
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100 "strand",
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101 "frame",
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102 "attributes",
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103 ],
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104 }
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