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

Giovanni Marco Dall'Olio dalloliogm at gmail.com
Fri Feb 27 11:50:03 UTC 2009

On Wed, Feb 25, 2009 at 11:00 PM, Peter <biopython at maubp.freeserve.co.uk> wrote:
> 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.

I have applied your patch to my unofficial github branch.
Here it is:
- http://github.com/dalloliogm/biopython/commit/51383b0e91b46f66ca20b36707c3a21a3dcbf0fb

People not wishing to use git can download the code anyway, by
clicking on 'download' in this page:
- http://github.com/dalloliogm/biopython/tree/qualityscores-experimental
The right button to click is the 'download' near the 'watch' button. I
know there is a second 'Downloads' page which creates confusion, but
it doesn't have nothing to do with it.

On the branches graph there is a bit of confusion now (my fault), but
you can see that I have applied your patch over a recent version of
biopython (there are some commits that I didn't include yet).

p.s. on your patch
(http://bugzilla.open-bio.org/attachment.cgi?id=1249), on the third
change, you modify this in SeqRecord.__init__:

<         self.seq = seq
>         self._seq = seq

can it be an error? Why self.seq has been moved to self._seq?

> 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


My blog on bioinformatics (now in English): http://bioinfoblog.it

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