[Biopython-dev] SeqRecord in Tutorial (was GSoC and PhyloXML)

[Peter]

On Thu, Jun 18, 2009 at 10:49 PM, Eric Talevich<eric.talevich at gmail.com> wrote:
>
> I didn't notice any typos other than Python being consistently lowercase,
> which I assume is how the author likes it.

I was aiming for consistency, with no strong preference - at the time
there were more uses of "python" than "Python" so I picked that. We
can change it easily enough - does anyone care either way?

> 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.

There is a case for leaving messy corner cases to the end, as long as
the main chapters cover the core.

> 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).

Yes, the SeqFeature stuff did originally risk being ignored when it was
just part of the "Advanced" chapter near the end. I think it made sense
to move it to the new SeqRecord chapter (and there is still room for
improvement - I'm thinking of going over one of the features in the
example GenBank file in more detail).

> In that final section it seems like SeqFeature is not meant to be
> handled by mere mortals, mainly because of the fuzzy positions

The fuzzy locations are by their nature really horrible to code with.
Doing something with SeqFeature objects and locations has been
discussed on the mailing list in the last month or so (in connection
with GFF files). I hope to have a good chat about this with Brad in
person at the BOSC hackathon.

> -- maybe integrating it a little more comfortably into other
> modules like PDB would help with that.

I don't see how SeqFeature objects and their FeatureLocations
related to PDB. Could you elaborate?

Peter