Contents

#!/usr/bin/ruby

require 'fasta'
require 'optparse'

hash = {
  'shuffle' => {
    'method' => :aaseq_shuffle!,
    'file_postfix' => Fasta::SHUFF_FILE_POSTFIX,
  },
  'invert' => {
    'method' => :aaseq_invert!,
    'file_postfix' => Fasta::INV_FILE_POSTFIX,
  },
}

opt = {}
OptionParser.new do |opts|
  opts.on("-p", "--prefix PREFIX", "add prefix to protein header") {|v| opt['p'] = v } 
end.parse!
#opts = GetoptLong.new(["-p", "--prefix", GetoptLong::REQUIRED_ARGUMENT])


if ARGV.size < 2
  puts "
  usage: #{File.basename(__FILE__)} [-p <prefix>] <method> <file>.fasta ...

  AA seq's will be modified according to <method>.  Each file takes on a
  postfix (before the extension).
  
  -p prefix   each protein's header will take on a header prefix after the '>'.

  Method      FILE_POSTFIX (added before the file extension)
  shuffle     #{hash['shuffle']['file_postfix']}
  invert      #{hash['invert']['file_postfix']}
  "
  exit
end

prefix = nil; if opt.key?('p') then prefix = opt['p'] end
method = ARGV.shift

cmd_hash = nil
if hash.key?(method)
  cmd_hash = hash[method]
else
  puts "Not a defined method: #{method}"
  puts "type #{File.basename(__FILE__)} for usage"
  exit
end

ARGV.each do |fn|
  outfile = Fasta.modify_file(fn, cmd_hash['method'], cmd_hash['file_postfix'], prefix)
  puts "OUTPUT: #{outfile}"
end

Version data entries

3 entries across 3 versions & 1 rubygems

Version	Path
mspire-0.1.3	bin/fasta_mod.rb
mspire-0.1.5	bin/fasta_mod.rb
mspire-0.1.7	bin/fasta_mod.rb