Class: ViennaRna::Rna

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

Instance Attribute Summary collapse

Class Method Summary collapse

Instance Method Summary collapse

Methods included from RnaExtensions

included

Constructor Details

#initialize(sequence, structure, raw_data = {}) ⇒ Rna

Returns a new instance of Rna.



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

def initialize(sequence, structure, raw_data = {})
  @sequence, @raw_data = sequence, raw_data
  
  @structure = case structure
  when :empty then empty_structure
  when :mfe   then ViennaRna::Fold.run(Rna.init_from_string(seq)).structure
  when String then structure
  end
end

Instance Attribute Details

#raw_data ⇒ Object (readonly)

Returns the value of attribute raw_data.



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# File 'lib/vienna_rna/modules/rna.rb', line 5

def raw_data
  @raw_data
end

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

Returns the value of attribute sequence.



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# File 'lib/vienna_rna/modules/rna.rb', line 5

def sequence
  @sequence
end

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

Returns the value of attribute structure.



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# File 'lib/vienna_rna/modules/rna.rb', line 5

def structure
  @structure
end

Class Method Details

.init_from_array(array) ⇒ Object 



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# File 'lib/vienna_rna/modules/rna.rb', line 16

def init_from_array(array)
  new(*array)
end

.init_from_fasta(string) ⇒ Object 



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# File 'lib/vienna_rna/modules/rna.rb', line 20

def init_from_fasta(string)
  init_from_string(*string.split(/\n/).reject { |line| line.start_with?(">") })
end

.init_from_hash(hash) ⇒ Object 



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# File 'lib/vienna_rna/modules/rna.rb', line 12

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

.init_from_self(rna) ⇒ Object 



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# File 'lib/vienna_rna/modules/rna.rb', line 24

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(rna.sequence, rna.structure, rna.raw_data)
end

.init_from_string(sequence, structure = nil) ⇒ Object 



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# File 'lib/vienna_rna/modules/rna.rb', line 8

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

Instance Method Details

#inspect ⇒ Object 



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# File 'lib/vienna_rna/modules/rna.rb', line 44

def inspect
  case [sequence.present?, structure.present?]
  when [true, true] then
    "#<#{self.class.name} #{seq[0, 20] + (seq.length > 20 ? '...' : '')} #{str[0, 20] + (str.length > 20 ? ' [truncated]' : '')}>"
  when [true, false] then
    "#<#{self.class.name} #{seq[0, 20] + (seq.length > 20 ? '...' : '')}>"
  when [false, false] then
    "#<#{self.class.name}>"
  end
end

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



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# File 'lib/vienna_rna/modules/rna.rb', line 65

def run(module_name, options = {})
  if rna_module = ViennaRna.const_missing("#{module_name}".camelize)
    rna_module.run(self, options)
  else
    raise ArgumentError.new("#{module_name} can't be resolved as an executable")
  end
end

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



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# File 'lib/vienna_rna/modules/rna.rb', line 55

def write_fa!(filename, comment = "")
  (File.basename(filename, ".fa") + ".fa").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)       if str
    end
  end
end