[BioPython] Distance Matrix Parsers

[Chris Lasher]

Hi Marc,

Thanks for the reply. I had not seen the Bio::Phylo package before.
Thanks for pointing that out. That seems to have be a really useful
library, though it's not exactly what I was thinking about when I
originally posted. I was thinking more along the lines of the
Bio::Matrix modules
(http://bio.perl.org/wiki/Special:Search?search=matrix&go=Go).

I don't think writing parsers for these formats will be that
difficult. I am unsure, however, about what type of data structure the
matrix should be. The simplest solution is a nested list. Perhaps this
is the proper solution, as the user can then convert this over to a
NumPy multi-dimensional array, say, or some matrix object. I dunno.
Thoughts, comments, suggestions?

Chris

On 6/9/06, Marc Colosimo <mcolosimo at mitre.org> wrote:
> Hi Chris,
>
> I don't think there is a parser for those. I have in the past thought
> about writing them up. I was looking over the structure of BioPython
> to see where it would best fit [I'll save my rant on this for another
> time, maybe later today]. In the mean time, the folks at BioPerl have
> Bio-Phylo CPAN module <http://search.cpan.org/~rvosa/Bio-Phylo/>,
> which looks nice, but it does NOT have what you are looking for.
> However, I am planning on following that.
>
> Marc
>
> On Jun 8, 2006, at 5:32 PM, Chris Lasher wrote:
>
> > Hi all,
> >   Are there any modules in BioPython to parse distance matrices? My
> > poking around the BioPython modules and Google searching does not turn
> > up any signs indicating there are distance matrix parsers, currently.
> > Two particularly useful parsers would be a parser for the output of
> > DNADIST/PROTDIST/RESTDIST from PHYLIP
> > (http://evolution.genetics.washington.edu/phylip.html), and a parser
> > for the MEGA (http://www.megasoftware.net/mega.html) distance matrix
> > format. If not, would there be any interest in creating parsers for
> > these matrices, other than my own? I think parsers for distance
> > matrices could be very useful to the community.
> >
> > Chris
> > _______________________________________________
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>
>