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