1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
|
.. include:: includeme.rst
Low-level operations
--------------------
We can use the :meth:`BedTool.as_intervalfile` method to return an
:class:`IntervalFile` instance. This class provides low-level support to
the BEDTools C++ API.
The method :meth:`IntervalFile.all_hits` takes a single :class:`Interval`
as the query and returns a list of all features in the
:class:`IntervalFile` that intersect:
.. doctest::
:options: +NORMALIZE_WHITESPACE
>>> a = pybedtools.example_bedtool('a.bed')
>>> ivf = a.as_intervalfile()
>>> query = a[2]
>>> ivf.all_hits(query)
[Interval(chr1:100-200), Interval(chr1:150-500)]
Similarly, we can just return if there were *any* hits, a much faster
operation:
.. doctest::
:options: +NORMALIZE_WHITESPACE
>>> ivf.any_hits(query)
1
Or count how many hits:
.. doctest::
:options: +NORMALIZE_WHITESPACE
>>> ivf.count_hits(query)
2
See the docstrings for :meth:`IntervalFile.all_hits`,
:meth:`IntervalFile.any_hits`, and :meth:`IntervalFile.count_hits` for
more, including stranded hits and restricting hits to a specific overlap.
.. note::
These methods are now available as :class:`BedTool` methods,
:meth:`BedTool.all_hits`, :meth:`BedTool.any_hits`, and
:meth:`BedTool.count_hits`
|
