[Biopython] Getting 'raw_score' of a Blast hit

Peter Cock p.j.a.cock at googlemail.com
Wed Jan 10 14:59:54 UTC 2018

Hi Adam,

Each of the HSPs will have its own raw score - it that not what you want?

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).


On Wed, Jan 10, 2018 at 1:56 PM, Adam Sjøgren <asjo at koldfront.dk> wrote:
> In BioPerl the hit object I get from a Blast result has a field called
> 'raw_score':
>   name          hit name
>   length        Length of the Hit sequence
>   accession     accession (usually when this is a Genbank formatted id this will be an accession number - the part after the gb or emb )
>   description   hit description
>   algorithm     algorithm
>   raw_score     hit raw score
>   significance  hit significance
>   bits          hit bits
>   hsps          Resets the internal counter for next_hsp() so that the iterator will begin at the beginning of the list
>    - table 2.2: http://bioperl.org/howtos/SearchIO_HOWTO.html
> When I look at the fields on the equivalent object in BioPython,
> Bio.Blast.Record.Alignment, it has these fields:
>   hit_id     Hit identifier. (str)
>   hit_def    Hit definition. (str)
>   length     Length.  (int)
>   hsps       A list of HSP objects.
>    - http://biopython.org/DIST/docs/api/Bio.Blast.Record.Alignment-class.html
> Can I extract the 'raw_score' from somewhere else, or is a bit of new
> code in the Blast-module(s) needed?
>   Best regards,
>     Adam
> --
>  "He also no longer jokes about world domination; it          Adam Sjøgren
>   was only funny when it was obviously meant in jest."   asjo at koldfront.dk
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