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.. include:: includeme.rst
.. _saveresults:
Saving the results
==================
If you want to save the results as a meaningful filename for later use, use
the :meth:`BedTool.saveas` method. This does a copy operation on the file
pointed to by the :class:`BedTool`. This method also lets you optionally specify a
trackline for directly uploading to the UCSC Genome Browser, instead of
opening up the files afterward and manually adding a trackline:
.. doctest::
:hide:
>>> a = pybedtools.example_bedtool('a.bed')
>>> b = pybedtools.example_bedtool('b.bed')
>>> a_with_b = a.intersect(b)
.. doctest::
:options: +NORMALIZE_WHITESPACE
>>> c = a_with_b.saveas('intersection-of-a-and-b.bed', trackline='track name="a and b"')
>>> print(c.fn)
intersection-of-a-and-b.bed
>>> # opening the underlying file shows the track line
>>> print(open(c.fn).read())
track name="a and b"
chr1 155 200 feature2 0 +
chr1 155 200 feature3 0 -
chr1 900 901 feature4 0 +
<BLANKLINE>
>>> # printing file-based BedTool objects will not print the track line
>>> print(c)
chr1 155 200 feature2 0 +
chr1 155 200 feature3 0 -
chr1 900 901 feature4 0 +
<BLANKLINE>
Note that the :meth:`BedTool.saveas` method returns a new :class:`BedTool`
object which points to the newly created file on disk. This allows you to
insert a :meth:`BedTool.saveas` call in the middle of a chain of commands
(described in another section below).
Alternatively, if you do not want to add a track line, you can use the
:meth:`BedTool.moveto` method which can be much faster, especially on larger
files. This does rename operation rather than a copy operation, which means
that trying to call :class:`BedTool` methods on the original will no longer
work because the underlying file no longer exists:
.. doctest::
>>> d = a_with_b.moveto('another_location.bed')
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