[Biopython-dev] GSoC python variant update

Peter Cock p.j.a.cock at googlemail.com
Thu Aug 9 09:07:15 UTC 2012

On Wed, Aug 8, 2012 at 10:58 PM, Laurent Gautier <lgautier at gmail.com> wrote:
> What about making the design decision that string representations that are
> 1-based then, and go beyond making a kill switch by just kill the switch ?
> You'd document it, folks that want 0-based positions would cook their own
> function(s).
> I think that configuration modules can be very useful for an application ...

I agree that a module level config setting is unwise.

However, I'd much prefer the string representation was 0-based for
consistency, both internal to the module and with most of Biopython.
(The restriction module uses 1-based counting which I find very

You could still provide something like a format method to give a
string in common representations (e.g. GenBank/EMBL/INSDC
style location strings).


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