Introduction to Biopython
This is a basic introduction to Biopython, intended for a classroom based workshop. It assumes you have been introduced to both working at the command line, and basic Python - for example as covered in Martin Jones' free eBook Python for Biologists.
The Biopython website http://www.biopython.org has more information including the Biopython Tutorial & Cookbook (html, PDF available), which is worth going through once you have mastered the basics of Python. That Tutorial & Cookbook is also available as Jupyter Notebooks, as is another short introductory tutorial.
I've broken up the workshop into sections:
- Reading sequence files.
- Writing sequence files.
- Working with sequence features.
- Reading and writing alignment files.
This material focuses on Biopython's SeqIO and AlignIO modules (these links include an overview and tables of supported file formats), each of which also has a whole chapter in the Biopython Tutorial & Cookbook (PDF) which would be worth reading after this workshop to learn more.
Text blocks starting with
$ show something you would type and run at the
command line prompt, where the
$ itself represents the prompt. For example:
$ python -V Python 2.7.5
Depending how your system is configured, rather than just
$ you may see your
user name and the current working directory. Here you would only type
(python space minus capital V) to find out the default version of Python installed.
>>> represent the interactive Python prompt, and something
you would type inside Python. For example:
$ python Python 2.7.3 (default, Nov 7 2012, 23:34:47) [GCC 4.4.6 20120305 (Red Hat 4.4.6-4)] on linux2 Type "help", "copyright", "credits" or "license" for more information. >>> 7 * 6 42 >>> quit()
Here you would only need to type
7 * 6 (and enter) into Python, the
is already there. To quit the interactive Python prompt use
quit() (and enter).
This example would usually be shortened to just:
>>> 7 * 6 42
These text blocks are also used for entire short Python scripts, which you can
copy and save as a plain text file with the extension
.py to run them.
Each workshop section was written in a separate directory, and in addition
to the main text (named
README.rst which is plain text file with markup
to make it look pretty on GitHub), the folders contain sample solution
Python scripts (named as in the text).
Prerequisites & Sample Data
If you are reading this on GitHub.com, you can view, copy/paste or download individual examples from your web browser.
To make a local copy of the entire workshop, you can use the
command line tool:
$ git clone https://github.com/peterjc/biopython_workshop.git
Alternatively, depending on your firewall settings, use:
$ git clone email@example.com:peterjc/biopython_workshop.git
To learn more about
git and software version control, I recommend attending a
Software Carpentry Workshop
or similar course.
This should make a new sub-directory,
biopython_workshop/ which we will now
$ cd biopython_workshop
Most of the examples use real biological data files. You should download them now using the provided shell script:
$ bash fetch_sample_data.sh
We assume you have Python and Biopython 1.63 or later installed and working. Biopython 1.63 supports Python 2.6, 2.7 and 3.3 (and should work on more recent versions). The examples here assume you are using Python 2.6 or 2.7, but in general should work with Python 3 with minimal changes. Check this works:
$ python -c "import Bio; print(Bio.__version__)" 1.63
This material was first used as part of a two-day course "Introduction to Python for Biologists" (Kathryn Crouch, Peter Cock and Tim Booth), part of a two-week course Keystone Skills in Bioinformatics, held in February 2014 at Centre for Ecology & Hydrology (CEH), Wallingford, UK. In a morning session lasting about 2.5 hours (plus coffee break), we covered all of reading sequence files and writing sequence files - and I quickly talked through alignment files.
I presented much of it again later in February 2014 at the University of Dundee as part of the third year undergraduate course BS32010 Applied Bioinformatics run by Dr David Martin and Dr David Booth. In the two hour slot we covered all of reading sequence files and most of writing sequence files.
I repeated this in March 2015 for the same third year undergraduate course, BS32010 Applied Bioinformatics at the University of Dundee. In a three hour slot we covered reading sequence files most of writing sequence files (up to editing sequences, but not filtering by identifier), and the start of multiple-sequence alignments.
Copyright and Licence
Copyright 2014-2015 by Peter Cock, The James Hutton Institute, Dundee, UK. All rights reserved.
This work is licensed under a Creative Commons Attribution-ShareAlike 4.0 International License (CC-BY-SA 4.0).
Note this documentation links to and uses external and separately licenced sample data files.