[Biopython-dev] Fwd: SearchIO HSP indexing

[Colin Archer]

> 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've been using it for a couple months now and i definitely prefer it over
the existing parser.


>  > 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?
>
> I would definitely add comments to the Hsp.py file and if there is a
tutorial that people use, I would also update that as that would be the
first place most people would look.

I was wondering if there was any code in SearchIO to align high-scoring
segment pairs against the same hit? I see the fragmentation code but that
seems specific to BLAT results and when I look at the HSPFragments in the
QueryResult object it does not seem to combine multiple HSPs against the
same hit even if they are not overlapping.

Thanks
Colin