[Biopython-dev] Quality scores (and per-letter-annotation) in a SeqRecord?

[Peter]

On Wed, Feb 25, 2009 at 10:02 AM, Giovanni Marco Dall'Olio
<dalloliogm at gmail.com> wrote:
>
> Of course you can stick with bugzilla, ...
>

I've put an updated patch on Bug 2507 which implements the
per-letter-annotations as a restricted dictionary (as the
letter_annotations property for now), and adds a __getitem__ method to
the SeqRecord object which is aware of it.  This changes both
SeqRecord.py and SeqFeature.py (required for switching the
co-ordinates on SeqFeature objects as part of a SeqRecord slice), and
is against the current CVS code.

http://bugzilla.open-bio.org/show_bug.cgi?id=2507

If any of you aren't familiar with using the command line tools diff
and patch, here's what you would do to try this code.  Get a copy of
the latest Biopython code from CVS, change to the Bio directory,
download the attachment and save it in that directory as
attachment.patch (for example) then and run "patch < attachment.patch"
to update the code.

Peter