Comments on: Standalone BLAST with Ruby http://biorelated.wordpress.com/2007/10/03/standalone-blast-with-ruby-part-1/ [bioinformatics,biology,ruby,rails].each do |b| puts b.blog end Wed, 14 Oct 2009 09:11:15 +0000 http://wordpress.com/ hourly 1 By: jan. http://biorelated.wordpress.com/2007/10/03/standalone-blast-with-ruby-part-1/#comment-62 jan. 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: <code> #!/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 </code> 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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