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.. include:: includeme.rst
.. _intersections:
Intersections
=============
One common use of BEDTools_ and :mod:`pybedtools` is to perform
intersections.
First, let's create some example :class:`BedTool` instances:
.. doctest::
>>> a = pybedtools.example_bedtool('a.bed')
>>> b = pybedtools.example_bedtool('b.bed')
Then do the intersection with the :meth:`BedTool.intersect` method:
.. doctest::
>>> a_and_b = a.intersect(b)
`a_and_b` is a new :class:`BedTool` instance. It now points to a temp file
on disk, which is stored in the attribute `a_and_b.fn`; this temp file contains
the intersection of `a` and `b`.
We can either print the new :class:`BedTool` (which will show ALL features
-- use with caution if you have huge files!) or use the
:meth:`BedTool.head` method to show up to the first N lines (10 by
default). Here's what `a`, `b`, and `a_and_b` look like:
.. doctest::
:options: +NORMALIZE_WHITESPACE
>>> a.head()
chr1 1 100 feature1 0 +
chr1 100 200 feature2 0 +
chr1 150 500 feature3 0 -
chr1 900 950 feature4 0 +
>>> b.head()
chr1 155 200 feature5 0 -
chr1 800 901 feature6 0 +
>>> a_and_b.head()
chr1 155 200 feature2 0 +
chr1 155 200 feature3 0 -
chr1 900 901 feature4 0 +
The :meth:`BedTool.intersect` method simply wraps the BEDTools_ program
`intersectBed`. This means that we can pass :meth:`BedTool.intersect` any
arguments that `intersectBed` accepts. For example, if we want to use the
`intersectBed` switch `-u` (which, according to the BEDTools documentation,
acts as a True/False switch to indicate that we want to see the features in `a`
that overlapped something in `b`), then we can use the keyword argument
`u=True`, like this:
.. doctest::
:options: +NORMALIZE_WHITESPACE
>>> # Intersection using the -u switch
>>> a_with_b = a.intersect(b, u=True)
>>> a_with_b.head()
chr1 100 200 feature2 0 +
chr1 150 500 feature3 0 -
chr1 900 950 feature4 0 +
This time, `a_with_b` is another :class:`BedTool` object that points to a
different temp file whose name is stored in `a_with_b.fn`. You can read
more about the use of temp files in :ref:`temp principle`. More on
arguments that you can pass to :class:`BedTool` objects in a moment, but
first, some info about saving files.
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