Module: Bioroebe::CodonTables

Defined in:
lib/bioroebe/codons/codon_tables.rb

Overview

CodonTables::CODON_TABLES

Constant Summary collapse

DEFINITIONS =
#

Bioroebe::CodonTables::DEFINITIONS

Some of the basic definitions are stored here.

The table in this .rb file was last updated manually in August 2021.

They can be found here:

https://www.ncbi.nlm.nih.gov/Taxonomy/Utils/wprintgc.cgi?mode=t

The numbers here are taken from the above URL.

#
{
   1 => 'Standard (Eukaryote)',
   2 => 'Vertebrate Mitochondrial',
   3 => 'Yeast Mitochondrial',
   4 => 'Mold, Protozoan, Coelenterate Mitochondrial and Mycoplasma/Spiroplasma',
   5 => 'Invertebrate Mitochondrial',
   6 => 'Ciliate Macronuclear and Dasycladacean',
   9 => 'Echinoderm Mitochondrial',
  10 => 'Euplotid Nuclear',
  11 => 'Bacteria',
  12 => 'Alternative Yeast Nuclear',
  13 => 'Ascidian Mitochondrial',
  14 => 'Flatworm Mitochondrial',
  15 => 'Blepharisma Macronuclear',
  16 => 'Chlorophycean Mitochondrial',
  21 => 'Trematode Mitochondrial',
  22 => 'Scenedesmus obliquus mitochondrial',
  23 => 'Thraustochytrium Mitochondrial',
  24 => 'Pterobranchia Mitochondrial Code',
  25 => 'Candidate Division SR1 and Gracilibacteria Code',
  26 => 'Pachysolen tannophilus Nuclear Code',
  27 => 'Karyorelict Nuclear',
  28 => 'Condylostoma Nuclear',
  29 => 'Mesodinium Nuclear',
  30 => 'Peritrich Nuclear',
  31 => 'Blastocrithidia Nuclear',
  33 => 'Cephalodiscidae Mitochondrial UAA-Tyr Code'
}

Class Method Summary collapse

Class Method Details

.definitions? ⇒ Boolean

#

Bioroebe::CodonTables.definitions?

#

Returns:

  • (Boolean) 


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# File 'lib/bioroebe/codons/codon_tables.rb', line 99

def self.definitions?
  DEFINITIONS
end

.human_codon_table? ⇒ Boolean

#

Bioroebe::CodonTables.human_codon_table?

#

Returns:

  • (Boolean) 


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# File 'lib/bioroebe/codons/codon_tables.rb', line 92

def self.human_codon_table?
  1
end

.title_for_entry_number?(i = 1) ⇒ Boolean

#

Bioroebe::CodonTables.title_for_entry_number?

#

Returns:

  • (Boolean) 


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# File 'lib/bioroebe/codons/codon_tables.rb', line 106

def self.title_for_entry_number?(i = 1)
  DEFINITIONS[i.to_i]
end