[Biopython-dev] [Wg-phyloinformatics] GSoC Weekly Update: PhyloXML for Biopython

[Peter]

On Mon, Jun 22, 2009 at 2:08 PM, Eric Talevich<eric.talevich at gmail.com> wrote:
>>
>> I can understand a +/- one to the start location (moving between
>> Python zero based counting and normal one based counts), but
>> why would the end location also change?
>>
>> Peter
>>
>
> Er, it wouldn't. Oops.
>
> On that note, how do you feel about specifying biology-style indexes in
> PhyloXML.ProteinDomain, and switching to zero-based indexes when converting
> to SeqFeature? Would it be better to use zero-based indexes in ProteinDomain
> and substract 1 from the start position during parsing?

Personally, within any Python object representation I would expect Python
style counting to be used (i.e. so the start and end could be used as is for
slicing the sequence). This would be consistent with the SeqFeature usage
in Biopython.

However, if your object is a simple naive representation of the raw data
from the file, you might arguably keep is as in the file (one based).
Whatever you do, please make it very explicit in the docstring.

Peter