[Biopython-dev] Fasta Module [was: To the core developers...]

Peter biopython-dev at maubp.freeserve.co.uk
Sat Dec 11 08:14:44 EST 2004

James wrote:

> OK, well that's a a step in the right direction, but now comes 
> the hard part:  getting more people involved in looking after 
> parts of the project.
> I suppose a good place to start is finding out how many of the 
> original authors of modules are still maintaining them.  A quick 
> and dirty search reveals the list below.  So my question is, from
> the list who is still out there, and who is still interested in
> maintaining their code? This way we can find the orphaned
> modules.

You may have noticed from the recent stream of emails from the bug
tracking system, that I've suggested some improvements to the
Bio.Fasta module's FastaDictionary support.

This file (Bio/Fasta/__init__.py) does not have a copyright
statement at the top.  Looking back in the CVS logs, Jeffrey Chang 
used to do most of the maintenance.  However, in 2004, Brad Chapman 
seems to have done a major overhaul to use the Mindy.

I'm guessing either of these two lucky people are the de facto owners
of Bio.Fasta and would be best qualified to comment on my suggestions.

Basically I want to make the FastaDictionary act more like a Python
Dictionary, and not throw weird errors when an invalid key is used.

Fasta.Dictionary should throw KeyError for invalid keys

Fasta.Dictionary should support has_key

Fasta.Dictionary should support "in" (the __contains__ method)

[I'm not ready to volunteer myself as the module owner, as I still 
have no idea what Martel and Mindy do, which would probably be a 

PhD Student
MOAC Doctoral Training Centre
University Of Warwick, UK

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