Contents

#!/usr/bin/ruby

require 'fasta'
require 'optparse'

hash = {
  'shuffle' => {
    'method' => :aaseq_shuffle!,
    'protein_header_prefix' => Fasta::SHUFF_PREFIX,
    'file_postfix' => Fasta::CAT_SHUFF_FILE_POSTFIX,
  },
  'invert' => {
    'method' => :aaseq_invert!,
    'protein_header_prefix' => Fasta::INV_PREFIX,
    'file_postfix' => Fasta::CAT_INV_FILE_POSTFIX,
  },
}

opt = {}
OptionParser.new do |opts|
  opts.on("-f", "--fraction FLOAT", "fraction") {|v| opt['f'] = v }
end.parse!


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

  The AA seq's of (a fraction of) proteins will be modified according to
  <method> and concatenated to the end of the normal proteins.  Each modified
  protein's header takes on a header prefix after the '>'.  Each file takes on
  a postfix (before the extension).

  METHOD      PROT_PREFIX     FILE_POSTFIX
  shuffle     #{hash['shuffle']['protein_header_prefix']}          #{hash['shuffle']['file_postfix']}
  invert      #{hash['invert']['protein_header_prefix']}            #{hash['invert']['file_postfix']}
  "
  exit
end

method = ARGV.shift
opt_h = nil
if hash.key? method
  opth = hash[method]
else
  abort "invalid method! choose: #{hash.keys.join(", ")}"
end

fraction = 1; if opt.key?('f') then fraction = opt['f'] end

specific_method = opth['method']
file_postfix = opth['file_postfix']
protein_header_prefix = opth['protein_header_prefix']
#puts [file, specific_method, fraction, file_postfix, protein_header_prefix].join("*")

ARGV.each do |file|
  outfile = Fasta.modify_fraction_and_cat_to_file(file, specific_method, fraction, file_postfix, protein_header_prefix)
  puts "OUTPUT: #{outfile}"
end

Version data entries

3 entries across 3 versions & 1 rubygems

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