Comments on: Short bioinformatics hacks, ch. 2: chunk it.

By: vaibhav asthana

vaibhav asthana — Thu, 11 Jun 2009 22:46:12 +0000

must have a look, and plz pass ur review and comments on this site on bioinformatics http://bionet.awardspace.info/index.html

By: gioby

gioby — Mon, 08 Jun 2009 12:25:24 +0000

Well, I would also add some good documentation and at least one doctest to your scripts.
Moreover, speaking of bioinformatics tips, I would put at least an example to a makefile

By: gioby

gioby — Mon, 08 Jun 2009 12:11:38 +0000

I suggest you to install biopython with easy_install, rather than with the package manager from your distribution.
The egg on pypi is usually more up-to-date, moreover easy_install can work in any operating system.
Usually easy_install is included in the package python-setuptools in debian.

$: sudo apt-get install python-setuptools
$: sudo easy_install biopython

By: Iddo

Iddo — Tue, 02 Jun 2009 01:36:54 +0000

Hi Peter: enumerate will start n at 0, I need it at 1. I could do:

for i, seq_record in enumerate(SeqIO.parse(infile, seq_format)):
n = i+1 #continue to use n as before
.
.
.

But to me, that is less clear than what I am doing right now.

close output handles: good point

explicit divide: you mean I am not working in Python 1.5 anymore? Good point.

SeqRecord: D’oh!

I’ll fix this soon, based on your suggestions. Thanks!

By: Peter Cock

Peter Cock — Mon, 01 Jun 2009 21:12:08 +0000

Hi Iddo,

Nice post!

I hope you don’t mind if I nit pic, and point out a few minor things you could improve:

(1) Use enumerate(…) to keep track of the record number index (n), rather than incrementing it in the loop. This is just a style thing.

(2) Close your output handles with a couple of fout.close() statements. This should be happening for you behind the scenes when the script finishes, but it is good practice.

(3) Use an explicit integer divide (n//chunk_size rather than n/chunk_size). Good practice looking ahead to Python 3.

(4) You don’t actually need to import the SeqRecord class in this example.

Peter