##
# ADD TAXONOMIC DESCRIPTIONS TO OTU TABLE
#

module Lederhosen
  class CLI

    desc "add_names",
      "add names to otu abundance matrix using blat output"

    method_option :blat,   :type => :string, :required => true
    method_option :table,  :type => :string, :required => true
    method_option :level,  :type => :string, :required => true
    method_option :output, :type => :string, :required => false

    def add_names
      blat   = options[:blat]
      table  = options[:table]
      level  = options[:level]
      output = options[:output] || $stdout

      levels = { 'kingdom' => 0,
                 'domain'  => 0,
                 'phylum'  => 1,
                 'class'   => 2,
                 'order'   => 3,
                 'family'  => 4,
                 'genus'   => 5,
                 'species' => 6 }

      ohno "unknown level #{level}. try #{levels.keys.join(', ')}" unless levels.include? level

      ohai "adding names to #{table} using #{blat} @ #{levels[level]} (#{level}). Saving to #{output}"

      # Corresponds with the numbers used in the TaxCollector database
      # taxonomic descriptions
      level_no = levels[level]

      # map cluster_id to taxonomic description
      # default is the cluster_id itself in case
      # the cluster was not classified.
      clusterid_to_name = Hash.new { |h, k| h[k] = k }

      # map clusterid to name using blat output
      ohai "loading BLAT output from #{blat}"
      File.open(blat) do |handle|
        handle.each do |line|
          line = line.strip.split

          # Only get first match
          # TODO something smarter here

          cluster_id = "cluster-#{line[0].match(/cluster-(\d*)/)[1]}"
          next if clusterid_to_name.include? cluster_id

          taxonomic_description = line[1]

          # match by level_no
          # Example:
          # [0]Bacteria;[1]Actinobacteria;[2]Actinobacteria;[3]Acidimicrobiales;[4]Acidimicrobiaceae;[5]Acidimicrobium;[6]Acidimicrobium_ferrooxidans;
          # I want to match Actinobacteria given level_no = 2
          level_name = taxonomic_description.match(/\[#{level_no}\](\w*)[;\[]/)[1] rescue nil

          # keep cluster id if name is 'null' (bad taxonomic description)
          # but put paranthesis around it so I know
          level_name = "(#{cluster_id})" if level_name =~ /null/

          clusterid_to_name[cluster_id] = level_name
        end
      end

      ohai "#{clusterid_to_name.keys.size} clusters were identified"

      # load table, replace cluster names with taxonomic descriptions
      output = File.open(output, 'w') unless output == $stdout
      ohai "replacing names in #{table}"
      File.open(table) do |handle|

        # read in header, replace clusterids to names
        header = handle.gets.strip.split(',')
        header[1..-1] = header[1..-1].map { |x| clusterid_to_name[x] }

        # print new header
        output.puts header.join(',')

        # print rest of table
        handle.each { |l| output.print l }
      end

      # print status message
      ohai "Got #{clusterid_to_name.values.reject { |x| x =~ /cluster/ }.size} names (#{clusterid_to_name.keys.size} total)"
    end

  end
end