[Biopython-dev] Biopython 1.60 plans and beyond

[Peter Cock]

On Sat, Feb 18, 2012 at 7:20 PM, Eric Talevich <eric.talevich at gmail.com> wrote:
>
> 3. SeqIO read-only support for PDB files
> (https://redmine.open-bio.org/issues/3295). I've been using this code on my
> own. It fails to parse at least one PDB file I care about (3BEG); I haven't
> tried it on a larger set of PDB files. In any case this shouldn't be too
> hard to fix, and I'd like to see it in a stable Biopython release.


If right now it has known failures, I don't want to squeeze this into
Biopython 1.59 next week.

Does your code manage to produce the same FASTA sequence as
the PDB themselves offer for download? That would be my expectation
as an end user. It should be easy enough to test if you've already
done a full local PDB download.

I'm still uneasy about this making SeqIO depend on NumPy (even as
a soft dependency at runtime), given the fact that the rest of SeqIO
should work fine under Jython and PpPy. Support for the NumPy
API under PyPy is coming along, but isn't likely for Jython for now
(although PyPy's efforts may help there).

Peter