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.. include:: includeme.rst
Create a :class:`BedTool`
-------------------------
First, follow the :ref:`installation` instructions if you haven't already
done so to install both BEDTools_ and :mod:`pybedtools`.
Then import the :mod:`pybedtools` module and make a new :class:`BedTool`. A
:class:`BedTool` object encapsulates all of the available BEDTools programs and
makes them easier to use within Python. Most of the time when working with
:mod:`pybedtools` you'll be using :class:`BedTool` objects. In general, a
single :class:`BedTool` object points to an interval file (BED, GFF, GTF, VCF,
SAM, or BAM format).
::
>>> import pybedtools
>>> # use a BED file that ships with pybedtools...
>>> a = pybedtools.example_bedtool('a.bed')
>>> # ...or use your own by passing a filename
>>> a = pybedtools.BedTool('peaks.bed')
This documentation uses example files that ship with :mod:`pybedtools`. To
access these files from their installation location, we use the
:func:`example_bedtool` function. This is convenient because if you copy-paste
the examples, they will work. When using the :func:`example_bedtool` function,
the resulting :class:`BedTool` object will point to the corresponding file in
the `test/data` directory of your :mod:`pybedtools` installation. If you would
rather learn using your own files, just pass the filename to a new
:class:`BedTool`, like the above example.
You can use any file that BEDTools_ supports -- this includes BED, VCF,
GFF, and gzipped versions of any of these. See :ref:`Creating a BedTool`
for more on the different ways of creating a :class:`BedTool`, including
from iterators and directly from a string.
Now, let's see how to do a common task performed on BED files: intersections.
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