[Biopython-dev] GSoC Weekly Update: PhyloXML for Biopython

[Eric Talevich]

On Thu, Jun 18, 2009 at 4:52 PM, Peter <biopython at maubp.freeserve.co.uk>wrote:

> On Thu, Jun 18, 2009 at 9:22 PM, Eric Talevich<eric.talevich at gmail.com>
> wrote:
> >
> > The new SeqRecord chapter is very informative -- I was originally just
> > looking at the wiki and epydoc pages.
>
> I can't take all the credit - a good chunk of it was reused from the
> "Advanced"
> chapter. Do let me know if you spot any typos. Did you think it makes sense
> to have this before the SeqIO chapter (as it is now), or afterwards? Right
> now the SeqRecord chapter uses SeqIO in order to load some complex
> records to show how they are represented - so you could put them in either
> order.
>

I didn't notice any typos other than Python being consistently lowercase,
which I assume is how the author likes it. The ordering is good -- the SeqIO
chapter makes more advanced use of sequences of SeqRecord objects, so it's
good to be familiar with the basic objects first. In general, I like the
organization of covering fundamental types first, then moving on to larger
collections, rather than covering the majority of a big collection in one
shot and leaving the tricky parts unaddressed.

A quick discussion of SeqFeature objects at the end of the SeqRecord chapter
instead of in the "Advanced" chapter would be nice, since apparently it's
easy to disregard that last section as an appendix of less important
material (I guess I did originally). In that final section it seems like
SeqFeature is not meant to be handled by mere mortals, mainly because of the
fuzzy positions -- maybe integrating it a little more comfortably into other
modules like PDB would help with that.

I pushed some work to github, involving the PhyloXML<->SeqRecord
translation:
http://github.com/etal/biopython/tree/phyloxml/Bio/PhyloXML

-Eric