require 'macroape'
require 'yaml'

module Macroape
  module CLI
    module PreprocessCollection
    
      def self.main(argv)
        help_string = %q{
        Command-line format:
          ruby preprocess_collection.rb <file or folder with PWMs or .stdin with PWMs> [options]

        Options:
          [-p <list of P-values>]
          [-d <rough discretization> <precise discretization>]
          [-b <background probabilities, ACGT - 4 numbers, space-delimited, sum should be equal to 1>]
          [-o <output file>]
          [--silent] - don't show current progress information during scan (by default this information's written into stderr)
          [--pcm] - treats your input motifs as PCM-s. Motifs are converted to PWMs internally so output is the same as for according PWMs

        The tool stores preprocessed Macroape collection to the specified YAML-file.

        Example:
          ruby preprocess_collection.rb ./motifs -p 0.001 0.0005 0.0001 -d 1 10 -b 0.2 0.3 0.2 0.3 -o collection.yaml
        }

        if argv.empty? || ['-h', '--h', '-help', '--help'].any?{|help_option| argv.include?(help_option)}
          STDERR.puts help_string
          exit
        end

        data_model = argv.delete('--pcm') ? Bioinform::PCM : Bioinform::PWM
        
        default_pvalues = [0.0005]
        background = [1,1,1,1]
        rough_discretization = 1
        precise_discretization = 10
        output_file =  'collection.yaml'
        max_hash_size = 1000000
        
        data_source = argv.shift
        
        raise "No input. You'd specify file or folder with pwms" unless data_source
        raise "Error! File or folder #{data_source} doesn't exist" unless Dir.exist?(data_source) || File.exist?(data_source) || data_source == '.stdin'

        pvalues = []
        silent = false
        until argv.empty?
          case argv.shift
            when '-b'
              background = argv.shift(4).map(&:to_f)
              raise 'background should be symmetric: p(A)=p(T) and p(G) = p(C)' unless background == background.reverse
            when '-p'
              loop do
                begin
                  Float(argv.first)
                  pvalues << argv.shift.to_f
                rescue
                  raise StopIteration
                end
              end
            when '-d'
              rough_discretization, precise_discretization = argv.shift(2).map(&:to_f).sort
            when '-o'
              output_file = argv.shift
            when '-m'
              max_hash_size = argv.shift.to_i
            when '--silent'
              silent = true
            end
        end
        pvalues = default_pvalues  if pvalues.empty?

        collection = Macroape::Collection.new(rough_discretization, precise_discretization, background, pvalues)
        
        if File.directory?(data_source)
            motifs = Dir.glob(File.join(data_source,'*')).map do |filename|
            pwm = data_model.new(File.read(filename))
            pwm.name ||= File.basename(filename, File.extname(filename))
            pwm
          end
        elsif File.file?(data_source)
          input = File.read(data_source)
          motifs = data_model.choose_parser(input).split_on_motifs(input, data_model)
        elsif data_source == '.stdin'
          input = $stdin.read
          motifs = data_model.choose_parser(input).split_on_motifs(input, data_model)
        else
          raise "Specified data source `#{data_source}` is neither directory nor file nor even .stdin"
        end
        
        pwms = motifs.map(&:to_pwm)
        
        pwms.each_with_index do |pwm,index|
          STDERR.puts "#{index + 1} -- Name: #{pwm.name}, Length: #{pwm.length}"  unless silent
          
          # When support of onefile collections is introduced - then here should be check if name exists.
          # Otherwise it should skip motif and tell you about this
          # Also two command line options to fail on skipping or to skip silently should be included

          info = {rough: {}, precise: {}}
          pwm.background!(background).max_hash_size!(max_hash_size)

          pwm.discrete(rough_discretization).thresholds(*pvalues) do |pvalue, threshold, real_pvalue|
            info[:rough][pvalue] = threshold / rough_discretization
          end

          pwm.discrete(precise_discretization).thresholds(*pvalues) do |pvalue, threshold, real_pvalue|
            info[:precise][pvalue] = threshold / precise_discretization
          end

          collection.add_pwm(pwm, info)
        end
        File.open(output_file,'w') do |f|
          f.puts(collection.to_yaml)
        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