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
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
|
.. _BEDTools: http://github.com/arq5x/bedtools
.. _3examples:
Three brief examples
--------------------
Here are three examples to show typical usage of :mod:`pybedtools`. More
info can be found in the docstrings of :mod:`pybedtools` methods and in the
:ref:`tutorial`.
You can also check out :ref:`shell_comparison` for a simple
example of how :mod:`pybedtools` can improve readability of your code with no
loss of speed compared to bash scripting.
.. note::
Please take the time to read and understand the conventions
:mod:`pybedtools` uses to handle files with different coordinate systems
(e.g., 0-based BED files vs 1-based GFF files) which are described
:ref:`here <zero_based_coords>`.
In summary,
* **Integer** values representing start/stop are *always in 0-based
coordinates*, regardless of file format. This means that all
:class:`Interval` objects can be treated identically, and greatly
simplifies underlying code.
* **String** values representing start/stop will use coordinates appropriate
for the format (1-based for GFF; 0-based for BED).
Example 1: Save a BED file of intersections, with track line
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
This example saves a new BED file of intersections between your files `mydata/snps.bed` and
`mydata/exons.bed`, adding a track line to the output::
>>> import pybedtools
>>> a = pybedtools.BedTool('mydata/snps.bed')
>>> a.intersect('mydata/exons.bed').saveas('snps-in-exons.bed', trackline="track name='SNPs in exons' color=128,0,0")
Example 2: Intersections for a 3-way Venn diagram
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
This example gets values for a 3-way Venn diagram of overlaps. This
demonstrates operator overloading of :class:`BedTool` objects. It assumes that
you have the files `a.bed`, `b.bed`, and `c.bed` in your current working
directory. If you'd like to use example files that come with
:mod:`pybedtools`, then replace strings like `'a.bed'` with
`pybedtools.example_filename('a.bed')`, which will retrieve the absolute path
to the example data file.::
>>> import pybedtools
>>> # set up 3 different bedtools
>>> a = pybedtools.BedTool('a.bed')
>>> b = pybedtools.BedTool('b.bed')
>>> c = pybedtools.BedTool('c.bed')
>>> (a-b-c).count() # unique to a
>>> (a+b-c).count() # in a and b, not c
>>> (a+b+c).count() # common to all
>>> # ... and so on, for all the combinations.
For more, see the :mod:`pybedtools.scripts.venn_mpl` and
:mod:`pybedtools.scripts.venn_gchart` scripts, which wrap this functionality in
command-line scripts to create Venn diagrams using either matplotlib or Google
Charts API respectively. Also see the :mod:`pybedtools.contrib.venn_maker`
module for a flexible interface to the VennDiagram `R` package.
.. _third example:
Example 3: Count reads in introns and exons, in parallel
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
This example shows how to count the number of reads in introns and exons in
parallel. It is somewhat more involved, but illustrates several additional
features of :mod:`pybedtools` such as:
* BAM file support (for more, see :ref:`bam`)
* indexing into Interval objects (for more, see :ref:`intervals`)
* filtering (for more, see :ref:`filtering`)
* streaming (for more, see :ref:`BedTools as iterators`)
* ability to use parallel processing
.. literalinclude:: example_3
For more on using :mod:`pybedtools`, continue on to the :ref:`tutorial` . . .
|
