join_parents.rb

require 'set'

class Table
  def initialize(table_path, tax_name, tax_rank)
    @table = load_table(table_path, "\t")
    @names  = load_table(tax_name, "\t|\t").to_set
    @ranks  = load_table(tax_rank, "\t|\t").to_set
  end
  
  def load_table(path, chr)
    open(path).readlines.map{|ln| ln.chomp.split(chr) }
  end
  
  def join
    join_rank.map{|e| e.join("\t") }
  end
  
  def join_rank
    sname_col_list = @table.map{|e| e[3] }.drop(1).uniq
    col_to_rank    = snames2rank(sname_col_list).to_h
    @table.drop(1).map do |entry|
      sname_col = entry[3]
      p sname_col
      entry << col_to_rank[sname_col]
      entry.flatten
    end
  end
  
  def extract_sname_from_col(col)
    col.sub(/(mitoch|chloroplast|clone|plastid|complete).+$/,"").sub(/^\s+/,"").sub(/\s+$/,"")
  end
  
  def snames2rank(sname_col_list)
    sname_col_list.map do |sname_col|
      sname = extract_sname_from_col(sname_col)
      taxid = @names.select{|e| e[1] == sname }[0][0]
      parents = id2parents(taxid)
      [
        sname_col,
        [
          parents["genus"],
          parents["family"],
          parents["order"],
          parents["class"],
          parents["phylum"],
        ]
      ]
    end
  end
  
  def id2parents(taxid)
    id = taxid
    current_rank = ""
    ps = {}
    while current_rank != "kingdom"
      record = @ranks.select{|e| e[0] == id }[0]
      
      parent_id = record[1]
      parent_sname = id2name(parent_id)
      id = parent_id
      
      rank = record[2]
      current_rank = rank
      
      ps[rank] = parent_sname
    end
    ps
  end
  
  def id2name(taxid)
    @names.select{|e| e[0] == taxid }[0][1]
  end
end

if __FILE__ == $0
  puts Table.new(*ARGV).join
end