[Biopython-dev] SearchIO HSP indexing

[Peter Cock]

On Sat, Feb 9, 2013 at 1:54 PM, Colin Archer <colin.aibn at gmail.com> wrote:
> Hi Peter,
>              Thanks for getting back to me so quickly.
>

Thank you - the main reason for including SearchIO in Biopython 1.61
as 'experimental code' is to get wider testing and feedback (hopefully
an approach that will work well and we can use this more in future for
other new code).

> I'm curious about the benefits of having these values in Python string
> slicing format? I haven't come across this very often, I'm used to seeing
> values systematically zero or one-based.

Once you're used to Python slicing it becomes very natural.

> Would it be easier to keep the range variables hit_range and hit_range_all
> in slicing format and the start and end variables in sequence position
> format so that they represent the actual BLAST results?

One reason for this is to be consistent across all the formats supported
in SearchIO, and since Biopython is a Python library following Python
norms seems most natural.

> I had a look at some of the code and I can't see the slicing format
> mentioned anywhere (Hsp.py, Hit.py, or blast_xml.py). It would probably be
> helpful to explain the values in Hsp.py as a ** mark on hsp_start, hsp_end,
> query_start, and query_end so that if people are interested they can have a
> look at the files and see what they mean.
>
> Thanks
> Colin

OK, so some clarification with examples in the docstrings is needed.
How about the Tutorial chapter?

Thanks,

Peter