Class: Bioroebe::ReverseComplement

Inherits:
Sequence show all
Defined in:
lib/bioroebe/sequence/reverse_complement.rb

Overview

Bioroebe::ReverseComplement

Constant Summary collapse

DEFAULT_INPUT =
#

DEFAULT_INPUT

#
'AAAACCCGGT'

Constants inherited from Sequence

Sequence::REMOVE_INVALID_CHARACTERS, Sequence::SHALL_WE_UPCASE

Class Method Summary collapse

Instance Method Summary collapse

Methods inherited from Sequence

#automatic_support_for_nucleotides, #description?, #index, #infer_type, #is_DNA?, #is_RNA?, #is_a_protein?, #is_a_protein_now, #map, #n_uracil?, #randomize, #remove_invalid_entries_from_the_dna_sequence, #remove_invalid_entries_from_the_dna_sequence!, #return_string_nucleotides_or_aminoacids, #sanitize_dataset, #sanitize_rna, #save_sequence_to_this_file, sequence_from_file, #set_description, #set_dna, #set_protein, #set_rna, #set_save_file, #set_sequence, #set_type, #shall_we_upcase?, #size?, #to_genbank, #to_regexp, #type?

Methods inherited from RawSequence

#+, #<<, #[]=, #calculate_levensthein_distance, #chars?, #complement, #composition?, #count, #delete, #delete!, #downcase, #each_char, #empty?, #find_substring_indices, #first_position=, #freeze, #gsub, #gsub!, #include?, #insert_at_this_position, #prepend, #remove_n_characters_from_the_left_side, #reverse, #reverse!, #reverse_complement, #scan, #set_raw_sequence, #shuffle, #size?, #split, #start_with?, #strip, #subseq, #to_s, #to_str, #tr!, #upcase!

Constructor Details

#initialize(i = DEFAULT_INPUT, run_already = true) ⇒ ReverseComplement

#

initialize

#


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# File 'lib/bioroebe/sequence/reverse_complement.rb', line 38

def initialize(
    i           = DEFAULT_INPUT,
    run_already = true
  )
  reset
  set_sequence(i)
  # ======================================================================= #
  # === Handle blocks
  # ======================================================================= #
  if block_given?
    yielded = yield
    case yielded
    # ===================================================================== #
    # === :be_quiet
    # ===================================================================== #
    when :be_quiet
      @be_verbose = false
    end
  end
  run if run_already
end

Class Method Details

.[](i) ⇒ Object

#

Bioroebe::ReverseComplement[]

#


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# File 'lib/bioroebe/sequence/reverse_complement.rb', line 121

def self.[](i)
  sequence = new(i) { :be_quiet }.complement_sequence?
  return sequence
end

Instance Method Details

#complement? ⇒ Boolean Also known as: result?, complement_sequence?

#

complement?

#

Returns:

  • (Boolean) 


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# File 'lib/bioroebe/sequence/reverse_complement.rb', line 74

def complement?
  @complement
end

#report ⇒ Object

#

report (report tag)

#


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# File 'lib/bioroebe/sequence/reverse_complement.rb', line 82

def report
  e @complement if @be_verbose
end

#reset ⇒ Object

#

reset

#


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# File 'lib/bioroebe/sequence/reverse_complement.rb', line 63

def reset
  super()
  # ======================================================================= #
  # === @be_verbose
  # ======================================================================= #
  @be_verbose = true
end

#run ⇒ Object

#

run

#


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# File 'lib/bioroebe/sequence/reverse_complement.rb', line 89

def run
  _ = sequence?
  # ======================================================================= #
  # (1) Obtain the reverse:
  # ======================================================================= #
  _ = _.reverse
  # ======================================================================= #
  # (2) Build the complement to that reverse:
  # ======================================================================= #
  @complement = ''.dup
  chars = _.chars
  # ======================================================================= #
  # The following code will build the reverse-complement.
  # ======================================================================= #
  chars.each {|character|
    case character
    when 'A'
      @complement << 'T'
    when 'T','U'
      @complement << 'A'
    when 'C'
      @complement << 'G'
    when 'G'
      @complement << 'C'
    end
  }
  report if @be_verbose
end