Introduction to Biopython

This is a basic introduction to Biopython.It assumes you have been introduced to both working at the command line, and some basic Python.

The content was created as part of the Workshop session for SciPy India 2015. The slides can be accessed here

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.

Workshop Sections

This material focuses on Biopython's SeqIO and AlignIO modules (these links include an overview and tables of supported file formats) and Seq Objects, 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:

$ 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:

$ 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.

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:

$ git clone https://github.com/souravsingh/learning_biopython.git

Alternatively, depending on your firewall settings, use:

$ git clone git@github.com:souravsingh/learning_biopython.git

To learn more about git and software version control, I recommend attending using Try Git or similar courses.

This should make a new sub-directory, learning_biopython/ which we will now change into:

$ cd learning_biopython

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