jpayne@68: _bedtools_path = ""
jpayne@68: _R_path = ""
jpayne@68: 
jpayne@68: tempfile_prefix = "pybedtools."
jpayne@68: tempfile_suffix = ".tmp"
jpayne@68: 
jpayne@68: # Checking for BEDTools will happen when creating the first BedTool; other
jpayne@68: # checks happen at first use (BAM object creation; tabix-ing a BedTool)
jpayne@68: _bedtools_installed = False
jpayne@68: _R_installed = False
jpayne@68: _v_2_15_plus = False
jpayne@68: _v_2_27_plus = False
jpayne@68: bedtools_version = []
jpayne@68: 
jpayne@68: KEEP_TEMPFILES = False
jpayne@68: _DEBUG = True
jpayne@68: 
jpayne@68: # Check calls against these names to only allow calls to known BEDTools
jpayne@68: # programs (basic security)
jpayne@68: #
jpayne@68: _prog_names = {
jpayne@68:     # Genome arithmetic
jpayne@68:     "intersectBed": "intersect",
jpayne@68:     "windowBed": "window",
jpayne@68:     "closestBed": "closest",
jpayne@68:     "coverageBed": "coverage",
jpayne@68:     "mapBed": "map",
jpayne@68:     "genomeCoverageBed": "genomecov",
jpayne@68:     "mergeBed": "merge",
jpayne@68:     "clusterBed": "cluster",
jpayne@68:     "complementBed": "complement",
jpayne@68:     "subtractBed": "subtract",
jpayne@68:     "slopBed": "slop",
jpayne@68:     "shiftBed": "shift",
jpayne@68:     "flankBed": "flank",
jpayne@68:     "sortBed": "sort",
jpayne@68:     "randomBed": "random",
jpayne@68:     "shuffleBed": "shuffle",
jpayne@68:     "annotateBed": "annotate",
jpayne@68:     "spacing": "spacing",
jpayne@68:     # multi-way
jpayne@68:     "multiIntersectBed": "multiinter",
jpayne@68:     "unionBedGraphs": "unionbedg",
jpayne@68:     # PE
jpayne@68:     "pairToBed": "pairtobed",
jpayne@68:     "pairToPair": "pairtopair",
jpayne@68:     # format conversion
jpayne@68:     "bamToBed": "bamtobed",
jpayne@68:     "bedToBam": "bedtobam",
jpayne@68:     "bedpeToBam": "bedpetobam",
jpayne@68:     "bed12ToBed6": "bed12tobed6",
jpayne@68:     "bamToFastq": "bamtofastq",
jpayne@68:     # fasta
jpayne@68:     "fastaFromBed": "getfasta",
jpayne@68:     "maskFastaFromBed": "maskfasta",
jpayne@68:     "nucBed": "nuc",
jpayne@68:     # bam-centric
jpayne@68:     "multiBamCov": "multicov",
jpayne@68:     "tagBam": "tag",
jpayne@68:     # stats
jpayne@68:     "jaccard": "jaccard",
jpayne@68:     "reldist": "reldist",
jpayne@68:     # misc
jpayne@68:     "getOverlap": "overlap",
jpayne@68:     "bedToIgv": "igv",
jpayne@68:     "linksBed": "links",
jpayne@68:     "windowMaker": "makewindows",
jpayne@68:     "groupBy": "groupby",
jpayne@68:     "expandCols": "expand",
jpayne@68:     "sample": "sample",
jpayne@68:     "fisher": "fisher",
jpayne@68:     "split": "split",
jpayne@68: }
jpayne@68: 
jpayne@68: _old_names = list(_prog_names.keys())
jpayne@68: _new_names = list(_prog_names.values())
jpayne@68: 
jpayne@68: _column_names = {
jpayne@68:     "bed": [
jpayne@68:         "chrom",
jpayne@68:         "start",
jpayne@68:         "end",
jpayne@68:         "name",
jpayne@68:         "score",
jpayne@68:         "strand",
jpayne@68:         "thickStart",
jpayne@68:         "thickEnd",
jpayne@68:         "itemRgb",
jpayne@68:         "blockCount",
jpayne@68:         "blockSizes",
jpayne@68:         "blockStarts",
jpayne@68:     ],
jpayne@68:     "gff": [
jpayne@68:         "seqname",
jpayne@68:         "source",
jpayne@68:         "feature",
jpayne@68:         "start",
jpayne@68:         "end",
jpayne@68:         "score",
jpayne@68:         "strand",
jpayne@68:         "frame",
jpayne@68:         "attributes",
jpayne@68:     ],
jpayne@68: }