[Biopython] Getting 'raw_score' of a Blast hit

Adam Sjøgren asjo at koldfront.dk
Wed Jan 10 13:56:23 UTC 2018

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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