[Biopython-dev] [Bug 2390] Error importing Swiss Prot in BioSQL

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

http://bugzilla.open-bio.org/show_bug.cgi?id=2390





------- Comment #21 from Biosql at hotmail.com  2007-12-12 17:17 EST -------
(In reply to comment #20)
> Hi Jonathan,
> 
> I'm glad we've fixed the error for you.  Could you be a little more precise
> about what isn't working with getting Swiss Prot cross-references into BioSQL?
> 
> e.g. Pick a specific SwissProt record, and quote the lines from the file
> containing the cross-references.
> 
> That should be enough for me to try and track down what's going on.
> 
> By the way - if you want to work with BioSQL, you have to use SeqRecord objects
> (e.g. from the Bio.SeqIO parser), and not the Bio.SwissProt.SProt.Record
> objects.  This probably explains the error you mentioned using the RecordParser
> parser instead.
> 
> Peter
> 

Sorry for the lack of informations,

Here's an example : http://ca.expasy.org/uniprot/Q9CQD1.txt

All the sequences, ID line, AC lines and comments (cc lines) are being uploaded
in the database, but not the : DR lines (which I consider the most interesting
cross-references), the Pubmed references (R_ lines) and the Taxon of the
protein. 

I don't think that the FT lines can be uploaded too isn't ? 
If so, it would be awesome !

Just to clear things, this uploading pattern is not only related to this
protein (Rab5a) but for all the Swiss Prot proteins. 

Do you need anything else ?

Jonathan


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