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

[Leighton Pritchard]

On 24/02/2009 12:46, "Peter" <biopython at maubp.freeserve.co.uk> wrote:

> On Tue, Feb 24, 2009 at 10:24 AM, Jose Blanca <jblanca at btc.upv.es> wrote:
>> 
>> An alternternative implementation using weakref to link the RestrictedDict
>> with the SeqRecord.
>> 
>> ...
>> 
> 
> Your code seems a little more complicated, but should work too.  It
> would mean that if the parent SeqRecord's seq property was altered,
> the per-letter-annotation dictionary would know the new length.  This
> is better - but if someone did change the parent SeqRecord's seq, then
> perhaps we should also automatically clear the per-letter-annotation?
> We could do this by using a full property for the seq attribute, which
> would also us to clear any existing per-letter-annotation by replacing
> it with a new restricted dictionary using the new length.

I can think of two particular incompatible situations here:

1) I change the parent SeqRecord sequence, by slicing it to a region I'm
interested in.  I want to keep the per-symbol-annotation, but adjusted to
the new sequence.

2) I change the parent SeqRecord sequence by adding some more symbols to it.
I've just destroyed the association between the per-symbol-annotation and my
sequence without even realising it.  I'd prefer a warning that this is going
to happen before it destroys my earlier work, so I can make the change in a
duplicate SeqRecord object.

I think it's worth considering which behaviours we would find desirable, and
how to handle others.  We'll all have different use cases, I imagine...

L.


-- 
Dr Leighton Pritchard MRSC
D131, Plant Pathology Programme, SCRI
Errol Road, Invergowrie, Perth and Kinross, Scotland, DD2 5DA
e:lpritc at scri.ac.uk       w:http://www.scri.ac.uk/staff/leightonpritchard
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