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Module Biocaml_seq (.ml)

Nucleic acid sequences. A nucleic acid code is any of A, C, G, T, U, R, Y, K, M, S, W, B, D, H, V, N, or X. See IUB/IUPAC standards for further information. Gaps are not supported. Internal representation uses uppercase, but constructors are case-insensitive. By convention the first nucleic acid in a sequence is numbered 1.

module Biocaml_seq:
sig
type t
Type of a sequence
exception Bad of string
Raised to indicate ill-formed sequence.
val of_string : string -> t
Make sequence from string. Raise Bad if unsuccessful.
val of_buffer : Buffer.t -> t
Make sequence from buffer. Raise Bad if unsuccessful.
val nth : t -> int -> char
nth t i returns the ith nucleic acid in sequence t. Raise Failure if i is out of range.
val length : t -> int
Length of sequence.
val to_string : t -> string
Return string representation of sequence. Answer can be successfully converted back using of_string.
val is_nucleic_acid : char -> bool
True if given character represents one of the allowed nucleic acid codes, case-insensitive.
val slice : int -> int -> t -> t
slice first last t returns the sub-sequence, or slice, of t starting from index first to last (inclusive). Raise Failure if indices out of range or if first > last.
val fold_left : ('a -> char -> 'a) -> 'a -> t -> 'a
see String.fold_left.
val fold_lefti : ('a -> int -> char -> 'a) -> 'a -> t -> 'a
String.fold_lefti

Unsafe Sequences

val of_buffer_unsafe : Buffer.t -> t
val of_string_unsafe : string -> t
Make a sequence from given buffer or string. Every character in input should satisfy Biocaml_seq.is_nucleic_acid, else returned sequence is ill-formed and behavior of operations on it are undefined.
end