[Biopython] Getting 'raw_score' of a Blast hit

[Peter Cock]

On Thu, Jan 11, 2018 at 12:15 PM, Adam Sjøgren <asjo at koldfront.dk> wrote:
>   Hi,
>
>
> Peter writes:
>
>> Each of the HSPs will have its own raw score - it that not what you want?
>
> To be honest: I wasn't sure; I am porting pieces of old code, trying to
> match it as much as possible, more or less with my head under my arm.
>
> I see now that we use hsp.score in other similar places, so I think I
> can use hsp.score and be done with it.
>
> (It is a different value, though, right?)

I believe so when a single sequence has returned multiple HSPs,
but failed to immediately find a clear reference for this with the full
details.

https://www.ncbi.nlm.nih.gov/BLAST/tutorial/Altschul-1.html

>> Also you might find Bio.SearchIO more future proof over using Bio.Blast
>> (the later offers a more generic interface covering HMMER etc as well).
>
> Thanks for the hint, I'll have to look into why my colleague chose
> Bio.Blast.

Probably just timing - Biopython's Bio.SearchIO is comparatively new.

Peter