Mercurial > repos > rliterman > csp2

comparison CSP2/CSP2_env/env-d9b9114564458d9d-741b3de822f2aaca6c6caa4325c4afce/lib/python3.8/site-packages/pybedtools/settings.py @ 68:5028fdace37b

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planemo upload commit 2e9511a184a1ca667c7be0c6321a36dc4e3d116d
author jpayne
date Tue, 18 Mar 2025 16:23:26 -0400
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67:0e9998148a16 68:5028fdace37b
1 _bedtools_path = ""
2 _R_path = ""
3
4 tempfile_prefix = "pybedtools."
5 tempfile_suffix = ".tmp"
6
7 # Checking for BEDTools will happen when creating the first BedTool; other
8 # checks happen at first use (BAM object creation; tabix-ing a BedTool)
9 _bedtools_installed = False
10 _R_installed = False
11 _v_2_15_plus = False
12 _v_2_27_plus = False
13 bedtools_version = []
14
15 KEEP_TEMPFILES = False
16 _DEBUG = True
17
18 # Check calls against these names to only allow calls to known BEDTools
19 # programs (basic security)
20 #
21 _prog_names = {
22 # Genome arithmetic
23 "intersectBed": "intersect",
24 "windowBed": "window",
25 "closestBed": "closest",
26 "coverageBed": "coverage",
27 "mapBed": "map",
28 "genomeCoverageBed": "genomecov",
29 "mergeBed": "merge",
30 "clusterBed": "cluster",
31 "complementBed": "complement",
32 "subtractBed": "subtract",
33 "slopBed": "slop",
34 "shiftBed": "shift",
35 "flankBed": "flank",
36 "sortBed": "sort",
37 "randomBed": "random",
38 "shuffleBed": "shuffle",
39 "annotateBed": "annotate",
40 "spacing": "spacing",
41 # multi-way
42 "multiIntersectBed": "multiinter",
43 "unionBedGraphs": "unionbedg",
44 # PE
45 "pairToBed": "pairtobed",
46 "pairToPair": "pairtopair",
47 # format conversion
48 "bamToBed": "bamtobed",
49 "bedToBam": "bedtobam",
50 "bedpeToBam": "bedpetobam",
51 "bed12ToBed6": "bed12tobed6",
52 "bamToFastq": "bamtofastq",
53 # fasta
54 "fastaFromBed": "getfasta",
55 "maskFastaFromBed": "maskfasta",
56 "nucBed": "nuc",
57 # bam-centric
58 "multiBamCov": "multicov",
59 "tagBam": "tag",
60 # stats
61 "jaccard": "jaccard",
62 "reldist": "reldist",
63 # misc
64 "getOverlap": "overlap",
65 "bedToIgv": "igv",
66 "linksBed": "links",
67 "windowMaker": "makewindows",
68 "groupBy": "groupby",
69 "expandCols": "expand",
70 "sample": "sample",
71 "fisher": "fisher",
72 "split": "split",
73 }
74
75 _old_names = list(_prog_names.keys())
76 _new_names = list(_prog_names.values())
77
78 _column_names = {
79 "bed": [
80 "chrom",
81 "start",
82 "end",
83 "name",
84 "score",
85 "strand",
86 "thickStart",
87 "thickEnd",
88 "itemRgb",
89 "blockCount",
90 "blockSizes",
91 "blockStarts",
92 ],
93 "gff": [
94 "seqname",
95 "source",
96 "feature",
97 "start",
98 "end",
99 "score",
100 "strand",
101 "frame",
102 "attributes",
103 ],
104 }