[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 09:56:50 UTC 2009


------- Comment #7 from andrea at biodec.com  2009-07-23 05:56 EST -------
(In reply to comment #6)
> (In reply to comment #5)
> 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
> limitation.

yes, i'm testing some predictors. I do prediction and i compare the 
"newly predicted seqrecords" with the "previously correct predicted pickled
I've them (the correct ones) only in pickled seqrecord format. 
The correctly predicted seqrecord, before prediction were in fasta format, 
but after i parsed them (into seqrecord), i did prediction, and then 
i pickled them (during prediction i add to seqrecord features and annotations).

Actually i don't use per-letter-annotation despite the fact it seems 
interesting. But i didn't find any example in documentation (that
show how the dictionary is populated...) so i really don't know
how to use it.... even if i've, during prediction, a "per position
Also if the "per letter annotation" is not managed in the GenBank format
or in the BioSQL format (that i use a lot) i've to wait!!

I was thinking also to store the pssm information somewhere in the
seqrecord.... but this would be a very big change... (and also
manage to store it in BioSQL.... )... but it's better to stop
the discussion here or to move it... :-)


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