Ruby script to blat search fasta sequence using qsub

qsub_blat.rb

#!/usr/bin/env ruby
# qsub parametres:
# Specify Ruby
#$ -S /usr/bin/ruby
# name for job
#$ -N blat
# pe request for slots, means processors, with
# minimum to maximum.
# e.g. 2    means two processors
#      2-   means 2 upto number of processor restricted by pe
#      2-8  means 2 upto 8 processors
#
# The number of slots / processors restriction can be retrieved by
# qmon under Parallel Environment Configuration choosing scampi and
# there by the number of Slots.
#
# ATTENTION: If the number of slots ist exceeded by single or
# maximum number, the job does not run.
#
#$ -pe hmp 6
#
# Written by Gisle Vestergaard
require 'pp'
require 'optparse'

ARGV << "--help" if ARGV.empty?

cmd_init = File.basename($0) + " " + ARGV.join(" ")

options = {}

OptionParser.new do |opts|
  opts.banner = "Usage: #{File.basename(__FILE__)} [options]"

  opts.on("-h", "--help", "Display this screen" ) do
    $stderr.puts opts
    exit
  end

  opts.on("-i", "--input_fasta <file>", String, "Input fasta sequence") do |o|
    options[:input_fasta] = o
  end
  
  opts.on("-d", "--database <file>", String, "Input database to search") do |o|
    options[:database] = o
  end

  opts.on("-t", "--type <file>", String, "Select blastp, blastn or blastx (default is blastn)") do |o|
    options[:type] = o
  end
  
  opts.on("-o", "--output directory <directory>", String, "Output directory") do |o|
    options[:out_lib] = o
  end

  opts.on("-f", "--outformat <string>", String, "blast8 for tabulated or blast for flat output for MEGAN et al. (default=flat)") do |o|
    options[:outfmt] = o
  end

end.parse!

options[:database] ||= '~/genomics/NCBI/Refseq/complete.nonredundant_protein.faa'
options[:out_lib] ||= File.basename(options[:input_fasta], ".*") + ".blat"
options[:type] ||= "blastn"
options[:outfmt] ||= blast

if options[:type] == "blastp"
  system 'blat -prot -out=' + options[:outfmt].to_s + ' ' + options[:database].to_s + ' ' + options[:input_fasta].to_s + ' ' + options[:out_lib].to_s
  elsif options[:type] == "blastn"
  system 'blat -prot -out=' + options[:outfmt].to_s + ' ' + options[:database].to_s + ' ' + options[:input_fasta].to_s + ' ' + options[:out_lib].to_s
end