Nucleotide IUPAC symbol
IUPAC symbols are characters that can be used to represent a subset of nucleotides, for instance when the nucleotide at a given position is not precisely known. A IUPAC symbol is said ambiguous if it corresponds to a set of size at least 2.
Valid IUPAC symbols for nucleotides can be found here.
include Alphabet.S_intinclude Alphabet.S
with type t = private int
and type vector = private Linear_algebra.vec
and type matrix = private Linear_algebra.mat
and type 'a table = private 'a arraytype vector = private Linear_algebra.vectype matrix = private Linear_algebra.matval all : t listval to_int : t -> intval counts : t Core.Sequence.t -> int tablemodule Table : sig ... endmodule Vector : sig ... endval flat_profile : unit -> vectorval random_profile : Gsl.Rng.t -> float -> vectormodule Matrix : sig ... endval of_int : int -> t optionval of_int_exn : int -> tval of_char : char -> t optionof_char c returns the IUPAC symbol corresponding to the given character c. It returns None if the character is not a valid IUPAC nucleotide symbol.
Example:
let symbol = Iupac_nucleotide.of_char 'A' in
(* symbol = Some 0 *)val is_ambiguous : t -> boolis_ambiguous sym checks if the given IUPAC symbol sym represents an ambiguous nucleotide. It returns true if the symbol is ambiguous, and false otherwise.
Example:
let ambiguous = Iupac_nucleotide.is_ambiguous 4 in
(* ambiguous = true *)