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
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
294
295
296
297
298
299
300
301
302
303
304
305
306
307
308
309
310
311
312
313
314
315
316
317
318
319
320
321
322
323
324
325
326
327
328
329
330
331
332
333
334
335
336
337
338
339
340
341
342
343
344
345
346
347
348
349
350
351
352
353
354
355
356
357
358
359
360
|
.. _autodoc:
.. _pybedtools reference:
.. currentmodule:: pybedtools
:mod:`pybedtools` Reference
===========================
The following tables summarize the methods and functions; click on a method or
function name to see the complete documentation.
.. contents::
:class:`BedTool` creation
-------------------------
The main :class:`BedTool` documentation, with a list of all methods in
alphabetical order at the bottom. For more details, please see :ref:`creating
a BedTool`.
.. autosummary::
:toctree: autodocs
pybedtools.bedtool.BedTool
`BEDTools` wrappers
-------------------
These methods wrap `BEDTools` programs for easy use with Python; you can then
use the other :mod:`pybedtools` functionality for further manipulation and
analysis.
The documentation of each of these methods starts with
:mod:`pybedtools`-specific documentation, possibly followed by an example.
Finally, the `BEDTools` help is copied verbatim from whatever version was
installed when generating these docs.
In general the `BEDTool` wrapper methods adhere to the :ref:`Design principles`:
* :ref:`temp principle`
* :ref:`similarity principle`
* :ref:`version principle`
* :ref:`default args principle`
.. autosummary::
:toctree: autodocs
pybedtools.bedtool.BedTool.intersect
pybedtools.bedtool.BedTool.window
pybedtools.bedtool.BedTool.closest
pybedtools.bedtool.BedTool.coverage
pybedtools.bedtool.BedTool.map
pybedtools.bedtool.BedTool.genome_coverage
pybedtools.bedtool.BedTool.merge
pybedtools.bedtool.BedTool.cluster
pybedtools.bedtool.BedTool.complement
pybedtools.bedtool.BedTool.subtract
pybedtools.bedtool.BedTool.slop
pybedtools.bedtool.BedTool.flank
pybedtools.bedtool.BedTool.sort
pybedtools.bedtool.BedTool.random
pybedtools.bedtool.BedTool.shuffle
pybedtools.bedtool.BedTool.annotate
pybedtools.bedtool.BedTool.multi_intersect
pybedtools.bedtool.BedTool.union_bedgraphs
pybedtools.bedtool.BedTool.pair_to_bed
pybedtools.bedtool.BedTool.pair_to_pair
pybedtools.bedtool.BedTool.bam_to_bed
pybedtools.bedtool.BedTool.to_bam
pybedtools.bedtool.BedTool.bedpe_to_bam
pybedtools.bedtool.BedTool.bed6
pybedtools.bedtool.BedTool.bam_to_fastq
pybedtools.bedtool.BedTool.sequence
pybedtools.bedtool.BedTool.mask_fasta
pybedtools.bedtool.BedTool.nucleotide_content
pybedtools.bedtool.BedTool.multi_bam_coverage
pybedtools.bedtool.BedTool.tag_bam
pybedtools.bedtool.BedTool.jaccard
pybedtools.bedtool.BedTool.reldist
pybedtools.bedtool.BedTool.overlap
pybedtools.bedtool.BedTool.links
pybedtools.bedtool.BedTool.igv
pybedtools.bedtool.BedTool.window_maker
pybedtools.bedtool.BedTool.groupby
pybedtools.bedtool.BedTool.expand
Other :class:`BedTool` methods
------------------------------
These methods are some of the ways in which :mod:`pybedtools` extend the
BEDTools suite.
Feature-by-feature operations
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Methods that operate on a feature-by-feature basis to modify or filter features
on the fly.
.. autosummary::
:toctree: autodocs
pybedtools.bedtool.BedTool.each
pybedtools.bedtool.BedTool.filter
pybedtools.bedtool.BedTool.split
pybedtools.bedtool.BedTool.truncate_to_chrom
pybedtools.bedtool.BedTool.remove_invalid
The :mod:`pybedtools.featurefuncs` module contains some commonly-used functions
that can be passed to :meth:`BedTool.each`:
.. currentmodule:: pybedtools
.. autosummary::
:toctree:
pybedtools.featurefuncs.three_prime
pybedtools.featurefuncs.five_prime
pybedtools.featurefuncs.TSS
pybedtools.featurefuncs.extend_fields
pybedtools.featurefuncs.center
pybedtools.featurefuncs.midpoint
pybedtools.featurefuncs.normalized_to_length
pybedtools.featurefuncs.rename
pybedtools.featurefuncs.greater_than
pybedtools.featurefuncs.less_than
pybedtools.featurefuncs.normalized_to_length
pybedtools.featurefuncs.rename
pybedtools.featurefuncs.bedgraph_scale
pybedtools.featurefuncs.add_color
pybedtools.featurefuncs.gff2bed
pybedtools.featurefuncs.bed2gff
Searching for features
~~~~~~~~~~~~~~~~~~~~~~
These methods take a single interval as input and return the intervals of the
BedTool that overlap.
This can be useful when searching across many BED files for a particular
coordinate range -- for example, they can be used identify all binding sites,
stored in many different BED files, that fall within a gene's coordinates.
.. autosummary::
:toctree: autodocs
pybedtools.bedtool.BedTool.all_hits
pybedtools.bedtool.BedTool.any_hits
pybedtools.bedtool.BedTool.count_hits
pybedtools.bedtool.BedTool.tabix_intervals
pybedtools.bedtool.BedTool.tabix
pybedtools.bedtool.BedTool.bgzip
:class:`BedTool` introspection
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
These methods provide information on the :class:`BedTool` object.
If using :meth:`BedTool.head`, don't forget that you can index into
:class:`BedTool` objects, too.
.. autosummary::
:toctree: autodocs
pybedtools.bedtool.BedTool.head
pybedtools.bedtool.BedTool.count
pybedtools.bedtool.BedTool.field_count
pybedtools.bedtool.BedTool.file_type
Randomization helpers
~~~~~~~~~~~~~~~~~~~~~
Helper methods useful for assessing empirical instersection
distributions between interval files.
.. autosummary::
:toctree: autodocs
pybedtools.bedtool.BedTool.parallel_apply
pybedtools.bedtool.BedTool.randomstats
pybedtools.bedtool.BedTool.randomintersection
pybedtools.bedtool.BedTool.randomintersection_bp
pybedtools.bedtool.BedTool.random_subset
pybedtools.bedtool.BedTool.random_jaccard
pybedtools.bedtool.BedTool.random_op
Managing :class:`BedTool` objects on disk
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
These methods are used to specify where to save results from :class:`BedTool`
operations.
.. autosummary::
:toctree: autodocs
pybedtools.bedtool.BedTool.saveas
pybedtools.bedtool.BedTool.moveto
Misc operations
~~~~~~~~~~~~~~~
Methods that can't quite be categorized into the above sections.
.. autosummary::
:toctree: autodocs
pybedtools.bedtool.BedTool.cat
pybedtools.bedtool.BedTool.at
pybedtools.bedtool.BedTool.absolute_distance
pybedtools.bedtool.BedTool.cut
pybedtools.bedtool.BedTool.total_coverage
pybedtools.bedtool.BedTool.with_attrs
pybedtools.bedtool.BedTool.as_intervalfile
pybedtools.bedtool.BedTool.introns
pybedtools.bedtool.BedTool.set_chromsizes
pybedtools.bedtool.BedTool.print_sequence
pybedtools.bedtool.BedTool.save_seqs
pybedtools.bedtool.BedTool.seq
pybedtools.bedtool.BedTool.liftover
pybedtools.bedtool.BedTool.colormap_normalize
pybedtools.bedtool.BedTool.relative_distance
Module-level functions
----------------------
Working with example files
~~~~~~~~~~~~~~~~~~~~~~~~~~
:mod:`pybedtools` comes with many example files. Here are some useful
functions for accessing them.
.. autosummary::
:toctree: autodocs
pybedtools.bedtool.example_bedtool
pybedtools.filenames.list_example_files
pybedtools.filenames.example_filename
Creating :class:`Interval` objects from scratch
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
:class:`Interval` objects are the core object in :mod:`pybedtools` to represent
a genomic interval, written in Cython for speed.
.. autosummary::
:toctree: autodocs
pybedtools.cbedtools.Interval
pybedtools.cbedtools.create_interval_from_list
:mod:`pybedtools` setup and config
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Use these functions right after importing in order to use custom paths or to
clean up the temp directory.
.. autosummary::
:toctree: autodocs
pybedtools.helpers.set_bedtools_path
pybedtools.helpers.get_tempdir
pybedtools.helpers.set_tempdir
pybedtools.helpers.cleanup
pybedtools.debug_mode
Working with "chromsizes" or assembly coordinate files
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Many `BEDTools` programs need "genome files" or "chromsizes" files so as to
remain within the coordinates of the assembly you're working on. These
functions help manage these files.
.. autosummary::
:toctree: autodocs
pybedtools.helpers.get_chromsizes_from_ucsc
pybedtools.helpers.chromsizes
pybedtools.helpers.chromsizes_to_file
Performing operations in parallel (multiprocessing)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
.. autosummary::
:toctree: autodocs
pybedtools.parallel.parallel_apply
:mod:`pybedtools.contrib`
-------------------------
The :mod:`pybedtools.contrib` module contains higher-level code that leverages
:class:`BedTool` objects for common analyses.
Plotting
~~~~~~~~
Plotting results from BEDTools/pybedtools operations is very useful for
exploring and understanding the tools as well as for teaching purposes.
.. autosummary::
:toctree: autodocs
pybedtools.contrib.plotting.Track
pybedtools.contrib.plotting.TrackCollection
pybedtools.contrib.plotting.binary_heatmap
pybedtools.contrib.plotting.binary_summary
pybedtools.contrib.plotting.BedToolsDemo
pybedtools.contrib.plotting.ConfiguredBedToolsDemo
Working with bigWig files
~~~~~~~~~~~~~~~~~~~~~~~~~
At this time, :mod:`pybedtools` does not support reading bigWig files, only
creating them via UCSC utilities.
.. autosummary::
:toctree: autodocs
pybedtools.contrib.bigwig.bam_to_bigwig
pybedtools.contrib.bigwig.bedgraph_to_bigwig
pybedtools.contrib.bigwig.wig_to_bigwig
Working with bigBed files
~~~~~~~~~~~~~~~~~~~~~~~~~
.. autosummary::
:toctree: autodocs
pybedtools.contrib.bigbed.bigbed
pybedtools.contrib.bigbed.bigbed_to_bed
:class:`IntersectionMatrix`
~~~~~~~~~~~~~~~~~~~~~~~~~~~
The :class:`IntersectionMatrix` class makes it easy to intersect a large number
of interval files with each other.
.. autosummary::
:toctree: autodocs
pybedtools.contrib.IntersectionMatrix
:mod:`contrib.venn_maker`
~~~~~~~~~~~~~~~~~~~~~~~~~
The :mod:`venn_maker` module helps you make Venn diagrams using the R package
`VennDiagram <http://www.biomedcentral.com/1471-2105/12/35>`_.
Note that Venn diagrams are not good for when you have nested intersections.
See the docs for :func:`pybedtools.contrib.venn_maker.cleaned_intersect` and
its source for more details.
.. autosummary::
:toctree: autodocs
pybedtools.contrib.venn_maker
pybedtools.contrib.venn_maker.venn_maker
pybedtools.contrib.venn_maker.cleaned_intersect
:mod:`contrib.long_range_interaction`
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
.. autosummary::
:toctree: autodocs
pybedtools.contrib.long_range_interaction.tag_bedpe
pybedtools.contrib.long_range_interaction.cis_trans_interactions
|
