SubsMat.MatrixInfo update

[biologyguy]

I've updated Bio.SubsMat.MatrixInfo.py with a new substitution matrix (PHAT) and written a little function to output the matrices in a more useable format. I've been using the new version for months, and figured I should polish it up and submit it to be included in the official package. Anyone interested in taking a look?
-Steve

[peterjc]

That sounds potential quite useful - you're talking about this paper?

Ng et al (2000) PHAT: a transmembrane-specific substitution matrix.
http://dx.doi.org/10.1093/bioinformatics/16.9.760

It looks like the URL in their abstract is dead, http://www.blocks.fhcrc.org/~pauline - but at least their PHAT 55/73 matrix was given in Figure 3. I've only skimmed the paper but it sounds like they also made some variants.

On the technical side, I would suggest you prepare the new PHAT matrix (this is probably the more straightforward part), and the output bit (these is where I expect more feedback/suggestions on the proposed interface) as separate commits (or even separate pull requests?). Hopefully someone working more closely with substitution matrices can comment:
http://lists.open-bio.org/pipermail/biopython-dev/2014-February/011067.html

[biologyguy]

Hi Peter,
The Ng et al., paper is indeed the one that I extracted the values from, and I've actually included the SLIM161 matrix as well (from dx.doi.org/10.1093/bioinformatics/17.suppl_1.S182). I haven't looked into implementing the algorithms to generate these matrices de novo, so I don't have easy access to variants (I suppose I could try to track down the authors).
-Steve

[peterjc]

The finished static matrices should be useful on their own.

[biologyguy]

Okay Peter,
I've added a new pull request. This is essentially my first time using Git, so hopefully I've done everything correctly.
There are two commits in the pull request, as you suggested (I wasn't sure about sending in two different pull requests, hopefully this is okay). The first is just the matrices, and the second is the new function.
-Steve

[peterjc]

Closed in favour of #283

[pledor]

Hi,
I'm interested!
Where can I download it?

[peterjc]

You can find the updated code on pull request #283, linked to here and in the preceding comment.

[pledor]

Thanks a lot!