Scripts¶
pybedtools
comes with several scripts that illustrate common use-cases.
In Python 2.7, you can use:
python -m pybedtools
to get a list of scripts and their description.
Venn diagram scripts¶
There are two scripts for making Venn diagrams, depending on how you’d like the
diagrams to look. Both simply take 3 BED files as input. venn_gchart.py
uses the Google Chart API, while venn_mpl.py
uses matplotlib if you have it
installed.
Upon installing pybedtools
, these scripts should be available on your
path. Calling them with the -h
option will print the help, and using the
--test
option will run a test, creating a new file out.png
in the current
working directory.
Intron/exon classification¶
The script intron_exon_reads.py
accepts a GFF file (with introns and exons
annotated) and a BAM file. When complete, it prints out the number of exonic,
intronic, and both intronic and exonic (i.e., from overlapping genes or
isoforms). This script is also a good example of how to do use Python’s
multiprocessing
for parallel computation.
Annotate.py¶
The annotate.py
script extends closestBed
by classifying features (intron,
exon) that are a distance of 0 away from the query features.