Ruby tips

batch_run.rb

#!/usr/bin/env ruby

ARGV[1..-1].each do |file|
  puts file
  `#{ARGV[0]} #{file}`
end


# Example
# ./batch_run.rb "tar zxvf" refseq_genomic.*.gz

extract_db_by_taxid.rb

#!/usr/bin/env ruby

if ARGV.size != 3
  $stderr.puts "Usage: #{$0} nr 9606 human.rna"
  exit
else
  db = ARGV[0]
  tax_id = ARGV[1]
  out = ARGV[2]
end

`blastdbcmd -db #{db} -entry all -outfmt "%g %T" | awk ' { if ($2 == #{tax_id}) { print $1 } } ' | blastdbcmd -db #{db} -entry_batch - -out #{out}`