bbcflib::bFlatMajor::bedtools Namespace Reference

Functions
def	bedtools
def	annotateBed
def	bamToBed
def	bamToFastq
def	bed12ToBed6
def	bedpeToBam
def	bedToBam
def	bedToIgv
def	closestBed
def	clusterBed
def	complementBed
def	coverageBed
def	expandCols
def	fastaFromBed
def	flankBed
def	genomeCoverageBed
def	getOverlap
def	groupBy
def	intersectBed
def	linksBed
def	mapBed
def	maskFastaFromBed
def	mergeBed
def	multiBamCov
def	multiIntersectBed
def	nucBed
def	pairToBed
def	pairToPair
def	randomBed
def	shuffleBed
def	slopBed
def	sortBed
def	subtractBed
def	tagBam
def	unionBedGraphs
def	windowBed
def	windowMaker

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Detailed Description

========
BedTools
========
Binding of the entire collection of `BedTools <http://code.google.com/p/bedtools/>`_.

The generic binding is::

    def bedtools(tool, args=None)

with parameters *tool*, the name of the tool, and
*args*, a string ("-i file"), a list (["-i","file"]) or a dictionary ({"i": "file"}) of command-line options passed to *tool*.

Each individual tool has its own call, like::

    annotateBed(ex,bedfile,files,wait=True,via='local',**kw)

with obligatory arguments *bedfile* and *files* (see the BedTools `documentation <http://code.google.com/p/bedtools/wiki/Usage>`_), and any additional optional arguments via `**kw`.
If *wait* is True, then the function will wait for completion and return the output filename, otherwise it runs a nonblocking job (with the parameter *via*) and returns a tuple (bein.Future, filename).