#!/opt/local/bin/ruby

################################
####
##
#     David Austin - UPENN
#     converts mzML to MGF format
#     set up to replicate msconvert but muuchh slower
#

require 'rubygems'
require 'mzml'


#first load nokogiri document

mzml =  MzML::Doc.new(ARGV[0])

#now loop through each spectrum.. sort first to be the same as msconvert

sorted_keys = mzml.parse_index_list[:spectrum].keys.sort{ |x,y| x.split('=')[3].to_i <=> y.split('=')[3].to_i }

sorted_keys.each do |k|
  s = mzml.spectrum(k)
  unless  s.precursor_list.nil? || s.precursor_list.empty?
    puts "BEGIN IONS"
    puts "TITLE=#{s.id}"
    puts "RTINSECONDS=#{s.retention_time}"
    puts "PEPMASS=#{s.precursor_mass} #{s.precursor_intensity}"
    0.upto(s.mz.length-1) do |i|
      puts "#{sprintf('%0.7f', s.mz[i]).to_f} #{sprintf('%0.2f', s.intensity[i]).to_f}"
    end
    puts "END IONS"
  end
end