[Biopython-dev] Hmmer integration modules/package

[Glen van Ginkel]

Hi Guys

As a project for my MRes in bioinformatics I have had to write a Python 
package that would expand Biopythons capabilities in interacting with useful 
programs. Here I submit code to interact with the Hmmer suite of programs. 

Basically, you instantiate the Hmmer object (Like a Hmmer commandline builder 
object), build a commandline, execute it and grab the results. Really simple 
for the user. This only works in UNIX since Hmmer is not available on Windows 
platforms and it obviously assumes you have Hmmer already installed on your 
PC. 
I have also tried to integrate the Bio.Align.Generic alignment object sothat 
the Hmmer object is able to handle alignment objects by writing the records 
of the alignment object to a temporary fasta file. 

Since I have to write this up as a report I would greatly appreciate any 
criticism of any kind and perhaps some suggestions as to how I might improve 
the code. Also, If you can think of any other ways to implement the Hmmer 
stuff please let me know. 

At the moment I am working on a test suite for the project. If you would like 
the code I have written to exercise some of the methods please let me know 
and I'll send it over. 
I also have a bit of documentation I would like to add to the Application 
package because I feel if failed to help me concerning certain aspects. How 
would I go about this?

I look forward to hearing your suggestions. 

Glen van Ginkel

Attatched is the code as well as an example of a test suite using the files 
from Eddy2003 and an experiment file experiment.fas
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