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

[bugzilla-daemon at portal.open-bio.org]

http://bugzilla.open-bio.org/show_bug.cgi?id=2883





------- Comment #5 from andrea at biodec.com  2009-07-23 04:47 EST -------

> You can probably hack the missing per letter annotation with something
> like record._per_letter_annotations = {}, 
Yes, i tried and it works... but there is no possibility to recover the 
seq... seqrecord.seq is not accessibile anymore....

> but it looks like there is no
> obvious way to get at the sequence information in the unpicked record.
> 
> 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'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?

> 
> 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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