[Biopython-dev] SeqIO circular

Peter Cock p.j.a.cock at googlemail.com
Thu May 3 17:50:55 UTC 2012

On Saturday, April 28, 2012, Matthias Bernt wrote:

> Dear developers,
> I would like to suggest a quick "fix" for the problem. Currently the
> parser just returns true per default for the circular property. This
> is a wrong piece of information for all circular sequences.
> Furthermore its not possible to detect if the parser did return true
> because it is its default value or if its really from the data. So I
> suggest to return None if the parser does not parse the information.
> What do you think? This should be possible with minimal effort.

The parsing side of this is trivial - the only piece missing is
how best to present the information in the SeqRecord for
BioSQL compatibility (and perhaps some extra work on our
BioSQL bindings). That requires someone to test where
BioPerl stores this in BioSQL (as that is the reference

Without that, a "quick fix" will mostly likely create a bug in
our BioSQL support - in that we wouldn't store the circular
field in the same way as the other Bio* implementations.


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