[Biopython-dev] SwissProt DE lines and bioentry.description field in BioSQL

Peter biopython at maubp.freeserve.co.uk
Sun May 24 10:42:14 UTC 2009

On Sun, May 24, 2009 at 5:10 AM, Michiel de Hoon <mjldehoon at yahoo.com> wrote:
> I suggest that for the short term, we store the DE lines as one
> string in the same way as Bioperl 1.5 and 1.6, until we decide
> on a more advanced way to treat these lines.


> Currently Bio.SeqIO and Bio.SwissProt use different ways to
> handle the DE lines, and neither of them agrees with Bioperl.

Well, Bio.SeqIO agrees with BioPerl modulo the white space -
but we might as well agree with the current BioPerl behaviour
until something is settled for storing more complex objects
than strings in BioSQL.

As I mentioned earlier, I'll be away for this week, so feel free
to press ahead with this.


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