Class: Bioroebe::DNA

Inherits:
Sequence show all
Includes:
NucleotideModule
Defined in:
lib/bioroebe/sequence/dna.rb

Overview

Bioroebe::DNA

Constant Summary

Constants inherited from Sequence

Sequence::REMOVE_INVALID_CHARACTERS, Sequence::SHALL_WE_UPCASE

Instance Method Summary collapse

Methods included from NucleotideModule

#allow_only_valid_dna, #at_percentage, #back_from_rna, #codon_to_aminoacid, #complementary_strand, complementary_strand, #cut_with_enzyme, #gc_percentage, #has_stop_codon?, #n_random_dna, #random, #remove_invalid_entries_from_the_dna_sequence, #to_aminoacid_sequence, #to_dna

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(this_sequence = 'ATCG') ⇒ DNA

#

initialize

#


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# File 'lib/bioroebe/sequence/dna.rb', line 35

def initialize(
    this_sequence  = 'ATCG'
  )
  reset
  super(
    this_sequence
  )
  set_dna_type # Make sure we have a DNA only.
end

Instance Method Details

#gc_percentage? ⇒ Boolean

#

gc_percentage?

Usage example:

x = Bioroebe::DNA.new('TTATTAAGTATTACG'); x.gc_percentage? # => "20.000"
#

Returns:

  • (Boolean) 


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# File 'lib/bioroebe/sequence/dna.rb', line 156

def gc_percentage?
  require 'bioroebe/calculate/calculate_gc_content.rb'
  Bioroebe.gc_content(string?)
end

#name_of_gene? ⇒ Boolean Also known as: name_of_gene, name?

#

name_of_gene?

#

Returns:

  • (Boolean) 


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# File 'lib/bioroebe/sequence/dna.rb', line 71

def name_of_gene?
  @name_of_the_gene
end

#reset ⇒ Object

#

reset

#


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# File 'lib/bioroebe/sequence/dna.rb', line 48

def reset
  super()
  # ======================================================================= #
  # === @name_of_the_gene
  # ======================================================================= #
  @name_of_the_gene = nil # No name is assigned by default.
end

#set_name_of_the_gene(i) ⇒ Object Also known as: name=, set_name, name_of_gene=, set_gene_name

#

set_name_of_the_gene

Use this method if you want to give the gene a specific name.

#


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# File 'lib/bioroebe/sequence/dna.rb', line 61

def set_name_of_the_gene(i)
  @name_of_the_gene = i
end

#to_aminoacids(i = string?, , ignore_stop_codons = true) ⇒ Object Also known as: to_aa, to_protein

#

to_aminoacids

This will convert the given DNA input into the corresponding aminoacid “output” - aka a translational output, following the regular conversion of DNA→mRNA→protein.

If the second argument to this method is true, then we will filter away all “STOP” elements.

#


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# File 'lib/bioroebe/sequence/dna.rb', line 97

def to_aminoacids(
    i                  = string?,
    ignore_stop_codons = true
  )
  i = [i].flatten
  # ======================================================================= #
  # === Handle blocks next
  # ======================================================================= #
  if block_given?
    yielded = yield
    # ===================================================================== #
    # We don't have to handle :frame1 since this is the default anyway.
    # ===================================================================== #
    case yielded
    when :frame2
      i.map! {|entry| entry[1..-1] }
    when :frame3
      i.map! {|entry| entry[2..-1] }
    end
  end
  i.map {|entry|
    if entry and (entry.size > 2) # Must check for at the least 3 nucleotides there.
      # =================================================================== #
      # Get a chunk of 3 nucleotides next. This will yield an array of
      # codons such as this one here:
      #
      #   ["GCC", "CAC", "AGG", "CAC", "AAC"]
      #
      # =================================================================== #
      codons = entry.scan(/.../)
      # =================================================================== #
      # Next, find the corresponding aminoacid for this codon.
      # =================================================================== #
      aminoacids = codons.map {|codon|
        result = ::Bioroebe.codon_to_aminoacid(codon)
        result
      }
      if ignore_stop_codons
        aminoacids.reject! {|inner_entry|
          inner_entry == 'STOP'
        }
      end
      result = aminoacids.join
      result # Return the result here.
    else
      entry
    end
  }
end

#to_rna ⇒ Object Also known as: to_RNA, to_T

#

to_rna

Convert the main sequence to RNA and return that result.

#


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# File 'lib/bioroebe/sequence/dna.rb', line 81

def to_rna
  string?.tr('T','U')
end