Class: Dphil::Csv2NexConverter

Inherits:
Object
  • Object
show all
Includes:
Converter
Defined in:
lib/dphil/converters/csv2nex.rb

Overview

CSV to NEXUS file converter class

Instance Method Summary collapse

Constructor Details

#initialize(csv_file, opts = {}) ⇒ Csv2NexConverter

Returns a new instance of Csv2NexConverter.



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# File 'lib/dphil/converters/csv2nex.rb', line 10

def initialize(csv_file, opts = {})
  opts = opts.to_h

  # Load csv file
  @csv = load_csv(csv_file, "r:bom|utf-8")
  @csv = @csv.transpose if opts[:transpose]

  # Load paup file
  if opts[:paup_data].nil?
    opts[:paup_data] = File.join(GEM_ROOT, "vendor", "default_commands.paup")
  end
  @paup = load_file(opts[:paup_data])
  @paup << "\n" unless @paup.blank? || @paup[-1] == "\n"
  @paup.indent!(2)
  @paup.freeze
end

Instance Method Details

#convert ⇒ Object

Perform the conversion and return a string result



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# File 'lib/dphil/converters/csv2nex.rb', line 28

def convert
  # Setup taxa information and orientation
  taxa_count = @csv.first.count
  character_count = @csv.count - 1
  taxa_labels = @csv.first.map { |name| name.to_s.strip.scrub.gsub(/[^A-Za-z0-9]/, "_") }

  # Generate labels and matrix
  character_labels = []
  character_matrix = taxa_labels.map { |t| [t] }
  (1..character_count).each do |r|
    row = @csv[r]
    token_hash = tokenize(row)
    character_label = (token_hash.map do |k, _|
      "'#{sanitize_char(k)}'"
    end).join(" ")
    character_labels << %(#{r} /#{character_label})
    row.each_with_index do |charstate, i|
      token = token_hash[sanitize_char(charstate)]
      character_matrix[i] << (token.nil? ? "-" : token[0])
    end
  end
  character_matrix.map! do |arr|
    "#{arr.shift} #{arr.join('')}"
  end

  # Return NEXUS output
  "    #NEXUS\n\n    BEGIN TAXA;\n      TITLE Manuscripts;\n      DIMENSIONS NTAX=\#{taxa_count};\n      TAXLABELS \#{taxa_labels.join(' ')};\n    END;\n\n    BEGIN CHARACTERS;\n      TITLE  Variant_Matrix;\n      DIMENSIONS  NCHAR=\#{character_count};\n      FORMAT DATATYPE = STANDARD RESPECTCASE GAP = - MISSING = ? SYMBOLS = \"\#{ALPHABET.join(' ')}\";\n      CHARSTATELABELS \#{character_labels.join(', ')};\n      MATRIX\n        \#{character_matrix.join(\"\\n    \")}\n    ;\n\n    END;\n\n    BEGIN ASSUMPTIONS;\n      OPTIONS DEFTYPE = UNORD;\n    END;\n\n    BEGIN PAUP;\n    \#{@paup}END;\n  NEXUS_EOF\nend\n"