package biocaml

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The OCaml Bioinformatics Library

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Dune Dependency

biocaml.org Readme Edit opam file Versions (5)

Authors

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biocaml@googlegroups.com

Sources

v0.11.0.tar.gz

md5=486aeb3e552dabae85839e2af30d6c52

sha512=4ed2df0b7cbd80bd6e29bd8fee9d2dacd9379ad0f4ff142bd8e16ade3f1507f6cc7cbe4c614943b8feb8fa4705935695cb458606b0da813dbf255b1e566a43cf

doc/biocaml.unix/Biocaml_unix/Seq/index.html

Module `Biocaml_unix.Seq`Source

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.

Sourcetype t

Type of a sequence

Sourceexception Bad of string

Raised to indicate ill-formed sequence.

Sourceval of_string : string -> t

Make sequence from string. Raise Bad if unsuccessful.

Sourceval of_buffer : Core_kernel.Buffer.t -> t

Make sequence from buffer. Raise Bad if unsuccessful.

Sourceval nth : t -> int -> char

nth t i returns the ith nucleic acid in sequence t. Raise Failure if i is out of range.

Sourceval length : t -> int

Length of sequence.

Sourceval to_string : t -> string

Return string representation of sequence. Answer can be successfully converted back using of_string.

Sourceval is_nucleic_acid : char -> bool

True if given character represents one of the allowed nucleic acid codes, case-insensitive.

Sourceval 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.

Sourceval fold_left : ('a -> char -> 'a) -> 'a -> t -> 'a

see String.fold_left.

Sourceval fold_lefti : ('a -> int -> char -> 'a) -> 'a -> t -> 'a

String.fold_lefti

Unsafe Sequences

Sourceval of_buffer_unsafe : Core_kernel.Buffer.t -> t

Sourceval of_string_unsafe : string -> t

Make a sequence from given buffer or string. Every character in input should satisfy is_nucleic_acid, else returned sequence is ill-formed and behavior of operations on it are undefined.

On This Page

Unsafe Sequences