require 'macroape'

module Macroape
  module CLI
    module FindThreshold
    
      def self.main(argv)
        help_string = %q{
          Command-line format::
          ruby find_threshold.rb <pat-file> [options]
                    or in linux
          cat <pat-file> | ruby find_threshold.rb .stdin [options]
                      or on windows
          type <pat-file> | ruby find_threshold.rb .stdin [options]

          Options:
            [-p <list of P-values>]
            [-d <discretization level>]
            [-b <background probabilities, ACGT - 4 numbers, space-delimited, sum should be equal to 1>]

          Output format:
            requested_pvalue_1 threshold_1 achieved_pvalue_1
            requested_pvalue_2 threshold_2 achieved_pvalue_2


          Example:
            ruby find_threshold.rb motifs/KLF4.pat -p 0.001 0.0001 0.0005 -d 1000 -b 0.4 0.3 0.2 0.1
        }
      
        if argv.empty? || ['-h', '--h', '-help', '--help'].any?{|help_option| argv.include?(help_option)}
          STDERR.puts help_string
          exit
        end
        
        background = [1,1,1,1]
        default_pvalues = [0.0005]
        discretization = 10000
        max_hash_size = 1000000
        data_model = argv.delete('--pcm') ? Bioinform::PCM : Bioinform::PWM      

        filename = argv.shift
        raise "No input. You'd specify input source: filename or .stdin" unless filename

        pvalues = []
        until argv.empty?
          case argv.shift
            when '-b'
              background = argv.shift(4).map(&:to_f)
            when '-m'
              max_hash_size = argv.shift.to_i
            when '-p'
              loop do
                begin
                  Float(argv.first)
                  pvalues << argv.shift.to_f
                rescue
                  raise StopIteration
                end
              end
            when '-d'
              discretization = argv.shift.to_f
            end
        end
        pvalues = default_pvalues if pvalues.empty?

        if filename == '.stdin'
          input = $stdin.read
        else
          raise "Error! File #{filename} doesn't exist" unless File.exist?(filename)
          input = File.read(filename)
        end
        pwm = data_model.new(input).to_pwm
        pwm.background!(background).max_hash_size!(max_hash_size).discrete!(discretization)

        pwm.thresholds(*pvalues) do |pvalue, threshold, real_pvalue|
          puts "#{pvalue}\t#{threshold / discretization}\t#{real_pvalue}"
        end
        
      rescue => err
        STDERR.puts "\n#{err}\n#{err.backtrace.first(5).join("\n")}\n\nUse -help option for help\n"
      end
      
    end
  end
end