[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
'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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