Comments on: Standalone BLAST with Ruby (windows) http://biorelated.com/2007/10/03/standalone-blast-with-ruby-part-1/ Sat, 28 Jan 2012 06:27:28 +0000 hourly 1 http://wordpress.com/ By: yannick http://biorelated.com/2007/10/03/standalone-blast-with-ruby-part-1/#comment-202 Wed, 22 Jun 2011 12:35:54 +0000 http://biorelated.wordpress.com/2007/10/03/standalone-blast-with-ruby-part-1/#comment-202 You can also use ruby to set up a local BLAST server, much easier than would be using NCBI’s wwwblast.
Cheers!

]]> By: jan. http://biorelated.com/2007/10/03/standalone-blast-with-ruby-part-1/#comment-62 Thu, 24 Jan 2008 15:59:43 +0000 http://biorelated.wordpress.com/2007/10/03/standalone-blast-with-ruby-part-1/#comment-62 You can also use bioruby to run BLAST searches against local databases. Here’s a sample script:

#!/usr/bin/ruby
require 'bio'

factory = Bio::Blast.local('blastn', '/path/to/BLAST/database')
ff = Bio::FlatFile.open(Bio::FastaFormat, 'input_file.fa')
ff.each do |entry|
$stderr.puts "Searching..." + entry.definition
report = factory.query(entry)
report.each do |hit|
hit.each do |hsp|
puts hsp.query_from
end
end
end

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