[Biopython-dev] Hmmer integration modules/package
Glen van Ginkel
gvg500 at york.ac.uk
Thu Apr 7 03:13:39 EDT 2005
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
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
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