[Biopython-dev] Parsing PAML supplementary output

[Brandon Invergo]

> I would consider that to be a meta file containing a PHYLIP
> alignment and a tree, but in itself it isn't a PHYLIP alignment.
> 
> That looks like exactly the kind of issue NEXUS was designed
> to solve: how to embed alignments, trees and other stuff into
> a single plain text file for input into a phylogenetic tool.
> 
> Doesn't PHYLIP have an XML format these days? Trying
> to parse something like that text (without a formal standard)
> seems like a painful exercise and long term maintenance
> headache.

I'm not suggesting that Biopython parse and store the information
because I agree that it would be an unmaintainable nightmare. To bring
myself out of the clouds a bit and back to the basics of my original
intent: if I work on better integrating the PAML module so that the user
can pass a MultipleSeqAlignment object, I will need a way to write that
alignment to a file with potentially more information than the default
PhylipWriter allows. So, just as simple as that, Bio.Phylo.PAML would
need its own alignment writer....something I'm not going to worry about
right now.

With this mentality, then yes, anything containing such option flags and
info is no longer a PHYLIP alignment but is rather an input file to some
program. As such, the existing PhylipIO module should *not* be modified
to handle this metadata. Please ignore all my other half-baked ideas.

So, current, phylip-related tasks:
- implement SequentialPhylipWriter and SequentialPhylipIterator classes
in PhylipIO


That's it, I think. I'll revisit this alignment-writing stuff at some
other point. One task at a time...

-brandon