[BioRuby] Bio::Blast not fully functional?
Fredrik Johansson
fredjoha at bioreg.kyushu-u.ac.jp
Tue May 15 05:54:46 UTC 2007
Hello all,
I am reading in the tutorial at
http://dev.bioruby.org/wiki/en/?Tutorial.rd
about BLAST and I try to use it according to this tutorial (see the code
below).
However, many of the entries in the 'hit' variable in the code below
seems to be nil. hit.identity and hit.target_seq are for example two
methods that just answer nil when I call them. Am I missing something?
#!/usr/bin/env ruby
require 'bio'
factory = Bio::Blast.remote('blastp', 'nr-aa')
Bio::FlatFile.open(Bio::FastaFormat, '/home/fred/pdb/test.fasta.txt') do
|ff|
ff.each do |entry|
report = factory.query(entry)
report.each do |hit|
if hit.evalue < 0.001
puts hit.target_id
puts hit.target_seq
end
end
end
end
Thanks for any help!
Best regards,
Fredrik Johansson
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