[Biopython] Getting 'raw_score' of a Blast hit
p.j.a.cock at googlemail.com
Wed Jan 10 14:59:54 UTC 2018
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
> 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,
> "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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