[Biopython-dev] SeqIO circular

Matthias Bernt MatatTHC at gmx.de
Sun Jul 15 13:56:33 UTC 2012


just wanted to ask if there is any new ideas wrt. this bug. I just
wanted to get the
residue type from a genbank file and realised that this is also not
parsed. This
reminded me of this bug.

While searching the web I found that the problem also affects others.


I would really like to see some progress here. And of course I would
like to help.
But I do not know how. I tried to dig in the bioperl sources - but the
problem is
that I don't speak perl.


2012/5/3 Peter Cock <p.j.a.cock at googlemail.com>:
> 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
> implementation).
> 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.
> Peter

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