[Biopython-dev] Hmmer API

[Michiel Jan Laurens de Hoon]

Iddo Friedberg wrote:
> Glen actually gave me the code, but I cannot really give him the 
> response it merits, not within th time frame he would like. From a 
> cursory look it is "yes, we can accept it, give us contingency tests as 
> well". But if soeone can actually run it a couple of times, and see what 
> it's like, that would be great.

I'm not a hmmer user either, so it's hard to assess the code in great detail. 
What I like about the code is that it has extensive documentation (in the source 
code) and makes use of and is well integrated with the existing Biopython 
software. Since Hmmer is a rather standard bioinformatics tool, I think 
Biopython should support it. So I vote to accept this into Biopython. Once users 
start using Bio.Hmmer, maybe some issues with the code will show up, but then 
these users will be more familiar with Hmmer than we are, and can give more 
useful advice.

About the documentation, it is quite extensive in the source code (which is fine 
too), but it would be nice to have some documentation outside of the source 
code. For example, this is something I wrote a while ago for Bio.LogisticRegression:

http://www.biopython.org/docs/cookbook/LogisticRegression.html

With such a documentation, the code will be more accessible. Without such 
documentation, people have to look through the CVS tree to search for the Hmmer 
package, or may not even notice it.

--Michiel.

-- 
Michiel de Hoon, Assistant Professor
University of Tokyo, Institute of Medical Science
Human Genome Center
4-6-1 Shirokane-dai, Minato-ku
Tokyo 108-8639
Japan
http://bonsai.ims.u-tokyo.ac.jp/~mdehoon