Class: ViennaRna::Global::Rna

Inherits:
Object
  • Object
show all
Includes:
RnaExtensions
Defined in:
lib/vienna_rna/global/rna.rb

Instance Attribute Summary collapse

Class Method Summary collapse

Instance Method Summary collapse

Methods included from RnaExtensions

included

Constructor Details

#initialize(sequence: "", structure: "", second_structure: "", raw_data: {}) ⇒ Rna

Returns a new instance of Rna.



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# File 'lib/vienna_rna/global/rna.rb', line 48

def initialize(sequence: "", structure: "", second_structure: "", raw_data: {})
  @sequence, @raw_data = sequence.kind_of?(Rna) ? sequence.seq : sequence, raw_data

  [:structure, :second_structure].each do |structure_symbol|
    instance_variable_set(
      :"@#{structure_symbol}", 
      case structure_value = eval("#{structure_symbol}")
      when :empty then empty_structure
      when :mfe   then RNA(sequence).run(:fold).mfe_rna.structure
      when String then structure_value
      when Hash   then 
        if structure_value.keys.count > 1
          ViennaRna.debugger { "The following options hash has more than one key. This will probably produce unpredictable results: %s" % structure_value.inspect }
        end
        
        RNA(sequence).run(*structure_value.keys, *structure_value.values).mfe_rna.structure
      end
    )
  end

  if str && seq.length != str.length
    ViennaRna.debugger { "The sequence length (%d) doesn't match the structure length (%d)" % [seq, str].map(&:length) }
  end

  if str_2 && str_1.length != str_2.length
    ViennaRna.debugger { "The first structure length (%d) doesn't match the second structure length (%d)" % [str_1, str_2].map(&:length) }
  end
end

Instance Attribute Details

#raw_data ⇒ Object (readonly)

Returns the value of attribute raw_data.



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# File 'lib/vienna_rna/global/rna.rb', line 6

def raw_data
  @raw_data
end

#second_structure ⇒ Object (readonly) Also known as: str_2

Returns the value of attribute second_structure.



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# File 'lib/vienna_rna/global/rna.rb', line 6

def second_structure
  @second_structure
end

#sequence ⇒ Object (readonly) Also known as: seq

Returns the value of attribute sequence.



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# File 'lib/vienna_rna/global/rna.rb', line 6

def sequence
  @sequence
end

#structure ⇒ Object (readonly) Also known as: str, str_1

Returns the value of attribute structure.



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# File 'lib/vienna_rna/global/rna.rb', line 6

def structure
  @structure
end

Class Method Details

.init_from_array(array) ⇒ Object 



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# File 'lib/vienna_rna/global/rna.rb', line 26

def init_from_array(array)
  init_from_string(*array)
end

.init_from_fasta(string) ⇒ Object 



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# File 'lib/vienna_rna/global/rna.rb', line 30

def init_from_fasta(string)
  string = File.read(string).chomp if File.exist?(string)
  init_from_string(*string.split(/\n/).reject { |line| line.start_with?(">") }[0, 3])
end

.init_from_hash(hash) ⇒ Object 



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# File 'lib/vienna_rna/global/rna.rb', line 17

def init_from_hash(hash)
  new(
    sequence:         hash[:sequence]         || hash[:seq], 
    structure:        hash[:structure]        || hash[:str_1] || hash[:str], 
    second_structure: hash[:second_structure] || hash[:str_2], 
    raw_data:         hash
  )
end

.init_from_self(rna) ⇒ Object 



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# File 'lib/vienna_rna/global/rna.rb', line 35

def init_from_self(rna)
  # This happens when you call a ViennaRna library function with the output of something like ViennaRna::Fold.run(...).mfe
  new(
    sequence:         rna.sequence, 
    strucutre:        rna.structure, 
    second_strucutre: rna.second_structure, 
    raw_data:         rna.raw_data
  )
end

.init_from_string(sequence, structure = nil, second_structure = nil) ⇒ Object 



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# File 'lib/vienna_rna/global/rna.rb', line 9

def init_from_string(sequence, structure = nil, second_structure = nil)
  new(
    sequence:         sequence, 
    structure:        structure, 
    second_structure: second_structure
  )
end

Instance Method Details

#empty_structure ⇒ Object Also known as: empty_str 



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# File 'lib/vienna_rna/global/rna.rb', line 82

def empty_structure
  "." * seq.length
end

#inspect ⇒ Object 



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# File 'lib/vienna_rna/global/rna.rb', line 107

def inspect
  "#<%s>" % [
    "#{self.class.name}",
    ("#{seq[0, 20]   + (seq.length > 20   ? '...' : '')}"          if seq && !seq.empty?),
    ("#{str_1[0, 20] + (str_1.length > 20 ? ' [truncated]' : '')}" if str_1 && !str_1.empty?),
    ("#{str_2[0, 20] + (str_2.length > 20 ? ' [truncated]' : '')}" if str_2 && !str_1.empty?),
  ].compact.join(" ")
end

#run(package_name, options = {}) ⇒ Object 



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# File 'lib/vienna_rna/global/rna.rb', line 103

def run(package_name, options = {})
  ViennaRna::Package.lookup(package_name).run(self, options)
end

#temp_fa_file! ⇒ Object 



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# File 'lib/vienna_rna/global/rna.rb', line 99

def temp_fa_file!
  write_fa!(Tempfile.new("rna")).path
end

#write_fa!(filename, comment = nil) ⇒ Object 



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# File 'lib/vienna_rna/global/rna.rb', line 88

def write_fa!(filename, comment = nil)
  filename.tap do |filename|
    File.open(filename, ?w) do |file|
      file.write("> %s\n" % comment) if comment
      file.write("%s\n" % seq)       if seq
      file.write("%s\n" % str_1)     if str_1
      file.write("%s\n" % str_2)     if str_2
    end
  end
end