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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