class String

Public Instance Methods

count_ambiguities() click to toggle source

Monkey patching to count how many ambiguity codes are present in the string, for Nucleic Acids

# File lib/bio/BIOExtensions.rb, line 139
def count_ambiguities
  snps=0

  for i in (0..self.size-1)

    snps += 1 if !Bio::NucleicAcid.is_unambiguous(self[i])
  end
  snps
end
upper_case_count() click to toggle source

Counts how many bases are uppercase

# File lib/bio/BIOExtensions.rb, line 150
def upper_case_count
  match(/[^A-Z]*/).to_s.size
end