[BioRuby] Extracting identity from Bio::Blast::Report::Hit

Rob Syme rob.syme at gmail.com
Tue Nov 18 03:03:58 UTC 2008


Hi all,
I'm running a blast against a local database, but I'm only getting
some of the information back:

local_blast_factory = Bio::Blast.local('blastn','/home/.../sn15cds')
query = "TAT...sequence...TAA"
report = local_blast_factory.query(query)

report.each do |hit|
  puts hit.identity.class
end

Gives:
NilClass
NilClass

Most of the other variables (eg: query_def, definition, hsps) work
fine. I don't know why the identity information can't be extracted.
Are there particular arguments I need to give the blast factory so
that I can extract the identity information?
Thanks in advance.

-r



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