[Biopython-dev] [Bug 2883] Errors after unpickling of 1.49 seqrecords

bugzilla-daemon at portal.open-bio.org bugzilla-daemon at portal.open-bio.org
Thu Jul 23 09:20:20 UTC 2009


------- Comment #6 from biopython-bugzilla at maubp.freeserve.co.uk  2009-07-23 05:20 EST -------
(In reply to comment #5)
> > Would you like to discuss your storage strategy on the mailing list?
> Sure, which one? Discussion, developement..... But are you sure it is
> necessary?

I was thinking the main discussion list - but if this was just for your
own testing, maybe we don't need to.

> > I'm curious what you are doing that made you choose to use pickle like
> > this (instead of saving to a standard sequence file format, or BioSQL).
> I'm using pickled object only for testing purposes. So implement a BioSQL
> system for that is too much... (also if it is available for sql lite)
> Maybe saving data in other format (for sure not fasta)... for example
> GenBank it could be another good solution but i will add a possible 
> "layer of failure" related to parsing problems.... (And i think, unpickling
> of dictionary will not introduce this possible "layer of failure").
> Were you thinking about GenBank format? Do you suggest something different?

If your SeqRecord objects are all simply loaded from sequence files in the
first place (and not modified), I would just keep the original file and
re-parse it.

If you have generated your own SeqRecords (or modified those from reading
a file), then it makes sense to save them somehow. The choice of file
format depends on the nature of annotation. The latest Biopython will now
record the features in a GenBank file, making that a reasonable choice -
but this does not cover per-letter-annotations. BioSQL has the same

> > Sorry about this,
> Don't worry. I think you are developing the system in a way that it
> will bring it to a better state... so, it isn't a problem at all.... 
> even better thanks a lot.
> Andrea



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