[Biopython-dev] [Bug 2396] BioSQL loader does not store sequence level annotations dict

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

http://bugzilla.open-bio.org/show_bug.cgi?id=2396


biopython-bugzilla at maubp.freeserve.co.uk changed:

           What    |Removed                     |Added
----------------------------------------------------------------------------
             Status|NEW                         |RESOLVED
         Resolution|                            |FIXED




------- Comment #3 from biopython-bugzilla at maubp.freeserve.co.uk  2007-12-04 15:25 EST -------
I think I have fixed this now in CVS.

One related wrinkle is that if you had this:

record.annotations["example1"] == "string"
record.annotations["example2"] == ["alpha"]
record.annotations["example3"] == ["alpha", "beta"]

after loading and retreiving from BioSQL you have this:

record.annotations["example1"] == ["string"]
record.annotations["example2"] == ["alpha"]
record.annotations["example3"] == ["alpha", "beta"]

i.e. Everything becomes a list of strings.

It is difficult to see how to deal with this elegantly given the current BioSQL
schema.  One option is to treat single entries as either a list or a string
depending on the rank field in the database... I should probably take this up
with the BioSQL mailing list to see how/if this issue affects BioPerl/BioJava.


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