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

[Eric Talevich]

On Thu, Jun 18, 2009 at 6:05 PM, Peter <biopython at maubp.freeserve.co.uk>wrote:

> 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?
>

Python.org capitalizes it. Shrug.

> 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.
>

Agreed. In the SeqRecord chapter, I was looking for a paragraph or so on
what sort of information goes into a SeqFeature to see whether it would be a
suitable stand-in for PhyloXML's DomainArchitecture. From the initial
description I wasn't sure if annotations or letter_annotations would be more
appropriate, and the other mentionings are basically "here be dragons"...
which is true, but a quick example would be helpful. The GenBank parsing
section would be a good place for that.

> -- 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?
>

If secondary structure or miscellaneous information is listed in the PDB
header, then parse_pdb_header could produce SeqFeatures from that. Right now
it doesn't build any Biopython objects at all.

-Eric