Wednesday, December 14, 2011

Basic Python for Bioinformatics

I've been silent online for the last few months, due to other commitments associated with my day job. But I haven't forgotten all of you in the ether.

Just before I got busy, I wrote a book about basic programming with Python using lots of biological examples. It's been proofed once or twice, but is not quite a beta version, so let's call it the gamma release. I want to push it out now, even it could certainly use some more polish, because it's not clear when I'll get the time to do that.

The target audience is the novice programmer who is interested in biology. However, it differs from most similar material because there are lots of biological and sequence analysis examples, collected from various sources including posts on this site.

Here is a screenshot of the toc for the middle section of the book.

The book is in html format (link to Dropbox zip). It was built using the Sphinx software. One can generate a pdf version of the book as well, but it suffers from the major limitation that cut-and-paste of the code loses the indentation. The version linked to here has code examples that can be pasted directly into a text file and executed, and often will work in the interpreter as well.

I hope you like it. I would be very grateful for comments, criticisms, corrections, and even complaints. Post 'em as comments here, or find my work email through the aboutme. Enjoy!


Arafat Rahman শুভ said...

Thanks for this book. I'm also a student of Microbiology from Bangladesh, doing my MSc but interested in Bioinformatics. I know a little bit of python and it is very interesting! Recently heard name of R. Was looking for a simple, free book in BI. Thanks again

Murat Sincan said...

Thanks for doing all this work.

Sasuga said...

Give me 1 month. I will learn Python and try your book. Then I'll come back with some feedback.

Thanks a lot.

Sasuga said...

Hi telliot99,

I am a newbie in Python and I am using your tutorials to get into bioinformatics with Python. I have question about the DNA section where you write and why do you need the "data.strip()" and the "title.strip().split()" if the output is the same without them?
Thank you for this material. It is awesome!!!

telliott99 said...

@Sasuga: the "strip" is just insurance. If we have a newline and then a space and another newline, we'll get an extra value in the list from splitting on newline. I've been burned many times by this in various ways. Feel free to leave it out.

ALpoptosis said...

Thank you for generously providing this wonderful resource! I am a aspiring bioinformatics student. I wanted to venture into phython and stumbled upon to your blog! I will come back with comments after reading them. Thank you very much