[Biopython-dev] [BioPython] Distance Matrix Parsers

[Marc Colosimo]

[cross-posting to biopython-dev]

Chris,

Oops, didn't notice this was on the general biopython mailing list. I  
think many of the developers also subscribe to this list, but just in  
case I'm cross posting this.

Iddo pointed out the Bio.SubsMat, which I didn't know what  that  
module did. One problem with names like that, but the API Docs are  
helpful only when you look at them <http://biopython.org/DIST/docs/ 
api/public/trees.html> (Kuddos for those who add documentation).

Given Bio.SubsMat and the BioPerl Module, I would strongly consider  
combining the Bio.SubsMat and the PhylipDist into a new Bio.Matrix  
module. From a Phylo module, a function/class can always call the  
Bio.Matrix classes.

Marc

On Jun 9, 2006, at 5:13 PM, Chris Lasher wrote:

>> I likewise didn't know about the Bio::Matrix::PhylipDist module.
>> Personally, I would opt for a Matrix Object (since this is Python a
>> OO language) and store it internally as a nested list. That way you
>> have the best of both worlds. The next question is the object
>> hierarchy. Here I would opt for a top level Matrix class (or module)
>> and then subclass that under Phylo. So, something like this:
>>
>> Bio.Matrix
>> Bio.Phylo.Matrix
>
> So is this more appropriate than Bio.Matrix.Phylo? A phylogenetic
> matrix is a type of matrix, so that hierarchy is immediately
> appealing, however, a phylogenetic matrix is not of much use in and of
> itself, so I can see the argument that it should be placed in a
> phylogeny package (which we have yet to write but as mentioned
> earlier, could be very useful).
>
>> and maybe things like the following (which isn't used/followed much
>> here in BioPython)
>>
>> Bio.Phylo.IO
>> Bio.Phylo.Parsers.PhylipDist
>> Bio.Phylo.Parsers.Newick
>> Bio.Phylo.Parsers.Nexus
>>
>> And/or have
>> Bio.Phylo.Matrix.IO that uses the PhylipDist parser.
>
> This is very very good, in my opinion. Thanks for doing the
> heavy-lifting of the brainwork on this! =-)
>
>> The next big question is what should Bio.Phylo.IO return? For
>> inspiration, we might want to look at Mesquite <http://
>> mesquiteproject.org/mesquite/mesquite.html>.
>
> I must give a better look at this site before commenting, but once
> again, thanks for bringing this to my awareness! What a helpful past
> couple of emails. I will be out for the weekend but will think more
> about this.
>
> As a sidenote, should this discussion be moved to biopython-dev or is
> it fine here?
>
> Thanks again Marc,
> Chris
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