Module: Bioroebe::CodonTable

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

Class Method Summary collapse

Class Method Details

.[](i) ⇒ Object

#

Bioroebe::CodonTable[]

This method will return a Hash containing the codon table for the given organism/species at hand. It will NOT modify the main codon table in use.

For a list of these codons, see this page:

https://www.ncbi.nlm.nih.gov/Taxonomy/Utils/wprintgc.cgi?mode=t#SG1

To obtain the human codon table, do either of the following:

human_codon_table = Bioroebe::CodonTable[:human]
human_codon_table = Bioroebe::CodonTable[1]

Usage example:

Bioroebe::CodonTable[2]
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# File 'lib/bioroebe/codons/codon_table.rb', line 391

def self.[](i)
  ::Bioroebe.load_the_codon_table_dataset(i)
end

.by_name(i = 'Vertebrate Mitochondrial') ⇒ Object

#

Bioroebe::CodonTable.by_name

This method can be used to return the proper codon-table dataset. It will additionally change the main codon table in use for the Bioroebe “namespace”. If you wish to avoid this, consider using Bioroebe::CodonTable[] instead.

Usage example:

x = Bioroebe::CodonTable.by_name("Vertebrate Mitochondrial")
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# File 'lib/bioroebe/codons/codon_table.rb', line 408

def self.by_name(
    i = 'Vertebrate Mitochondrial'
  )
  ::Bioroebe.set_use_this_codon_table(i)
  return ::Bioroebe.codon_table_dataset?
end