Beginning Python for Bioinformatics

Via Bioinformatics Zen:

As mentioned on the last post I am moving the current repository, an html page, to an actual Git repository on github.com. The link to the repository is

http://github.com/nuin/beginning-python-for-bioinformatics/tree/master

and it can be accessed by anyone. There are only a handful of scripts there but I am slowly adding more comments to the scripts and moving them to github. The web interface at github is pretty nice and the code can be viewed on the website with a nice code highlighting, for example. Also there is an RSS feed to receive updates, commits, etc.

How to create a local copy

Git is very easy to use and it is very simple to create a local copy of the repository on your local machine. Git is available on most systems as a command-line utility (there is a gui but I haven’t used yet) and to have an updated copy of the Beginning Python for Bioinformatics, two commands are needed.

- first you have to clone the repository

$ git clone git://github.com/nuin/beginning-python-for-bioinformatics.git

that will create a beginning-python-for-bioinformatics directory wherever you run git (this only needs to be done once)

and to keep the clone updated

$ git pull

from inside the clone directory.

Any questions please let me know.

I had problems installing Google’s AppEngine in Vista. I had Python 2.5.1 installed in my machine but every time I tried to install the msi package it failed, claiming that Python was not present, even though C:\Python25 was in the path. AppEngine issues site did not help much either, the “solution” listed there was to make sure Python was in the path.

So, I decided to start over. I removed Python (and ActiveState Python, which I installed before to see if AppEngine would work) and re-installed it, or tried to. Strangely, Python’s msi package was installing it in the C drive root, not under Python25. For half an hour I tested all possible combinations, versions and tricks to have it installed in the proper directory/folder. Then I remembered msiexec, a command line tool that runs msi packages. Running msiexec with no parameters shows a window with options, but basically /i is the the only required. /i tells msiexec the input package, while ‘code>/qb make the installation quiet and with a basic interface. msiexec worked flawlessly and then Python was in its right place.

msiexec /i python-2.5.2.msi TARGETDIR="C:\Python25" /qb

Then the same “trick” was used with AppEngine, but without a TARGETDIR. Bingo, it installed perfectly (I am assuming that).

Now, I just have to wait for my AppEngine account.

import sys
for i in file:
    print i

Just for fun, let’s see if there is any advantage (apart from generating a smaller code) in using either of the approaches to create an unique list. A list of 741 gene IDs and another one with 1322 (that contained all the 741 IDs from the first) were used. Instead of hard coding the lists in the script, normal I/O was used and the files were read automatically. Using a for loop the scripts were run 10 times and the final time averaged.

Here are the results

Using dictionaries 0.08540
Using sets 0.15890

Almost twice as fast for the dictionaries. Why? One thing, and one thing only: Python version. My system’s box default Python is 2.3.4, which has one of the first implementations of set. I have a “personal” Python version 2.5 so the test was redone with the newer Python

Using dictionaries 0.04520
Using sets 0.03770

Ok. That shows a little bit of advantage for sets what is expected. But it shows us that different versions of Python have a huge difference between them. This is a rather crude and simple test, with a small list of entries, but there is a huge gain from version 2.3 to versio 2.5, either in dicts or sets.

For a more comprehensive test and more functions with a similar objective check this page.

This is a blog devoted to basic Python, but I could not refrain myself of suggesting the new Python Magazine, that has its first issue free online.

Enjoy.

A new feature has been add to the blog: ratings. As I don’t receive many comments on the posts but there is a steady stream of viewers of the website, I decided to add the possibility of rating a post. So, if you feel the post was useful for you, well or badly written, just click the rate you feel the post deserves. It is an Ajax-like feature so there is no reloads or any other intrusion on your normal browsing.

A suggestion: whenever you are coding or leaning a new language it is always opportune to have at hand some code to compare, check and learn. One of the good tools to do code search is Krugle, where you can extensively search code based on language, project name, among other variables.

One example: I searched for IUPAC entries on Krugle and found a lot of results, in different computer languages and could see the projects that they were linked to. It is a way to check if your approach is the ideal or if there is a way to improve your code.

Due to the lack of updates in the past weeks (yup, a lot of work), I decided to add some features to the website, for the time being. The first one is the code repository, that can be accessed on the menu bar above.

I will try to include all the relevant code presented in the posts with extra comments.

I will probably be back with a regular post at the end of May.

See you then.

For now on I will be using this layout for the blog. It gives me more power on displaying code, what was really annoying with Movable Type.

If you are using the RSS feed, please update. Cheers.