biopython_workshop

by peterjc

A basic introduction to Biopython, intended for a classroom based workshop

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=========================

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 
_.

=================

Workshop Sections

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.

========

Notation

Text blocks starting with

$
show something you would type and run at the command line prompt, where the
$
itself represents the prompt. For example:

.. sourcecode:: console

$ 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 -V
(python space minus capital V) to find out the default version of Python installed.

Lines starting

>>>
represent the interactive Python prompt, and something you would type inside Python. For example:

.. sourcecode:: pycon

$ 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:

.. sourcecode:: pycon

>>> 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.

================

Sample Solutions

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

git
command line tool:

.. sourcecode:: console

$ git clone https://github.com/peterjc/biopython_workshop.git

Alternatively, depending on your firewall settings, use:

.. sourcecode:: console

$ git clone [email protected]: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 change into:

.. sourcecode:: console

$ cd biopython_workshop

Most of the examples use real biological data files. You should download them now using the

provided shell script 
_:

.. sourcecode:: console

$ 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:

.. sourcecode:: console

$ python -c "import Bio; print(Bio.__version__)"
1.63

=======

History

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 <readingsequencefiles/README.rst>` 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).

.. image:: http://i.creativecommons.org/l/by-sa/4.0/88x31.png

Note this documentation links to and uses external and separately licenced sample data files.

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