bio_io 0.5.1 · OCaml Package

A record type for FASTA files.

Overview

Example 1

If you have a fasta file something like this:

>s1 apple pie
ACTG
actg

Then you would get a record something like this:

Fasta.Record.id record (* "s1" *) Fasta.Record.desc record
  (* Some "apple pie" *) Fasta.Record.seq record
(* "ACTGactg" *)

Example 2

If you have a fasta file something like this:

>s1
ACTG
actg

Then you would get a record something like this:

Fasta.Record.id record (* "s1" *) Fasta.Record.desc record (* None *)
  Fasta.Record.seq record
(* "ACTGactg" *)

Example 3

To change a part of the Fasta.Record use the with_* functions. E.g.,

Fasta.Record.with_id "apple" record

would change give you a t with the id set to "apple".

API

type t

include Sexplib0.Sexpable.S with type t := t

val t_of_sexp : Sexplib0.Sexp.t -> t

val sexp_of_t : t -> Sexplib0.Sexp.t

val create : 
  id:Base.string ->
  desc:Base.string Base.option ->
  seq:Base.string ->
  t

create ~id ~desc ~seq creates a new t. Shouldn't raise as literally any values of the correct type are accepted.

val of_header_exn : Base.string -> t

of_header_exn header returns a t from a FASTA header. May raise exceptions. Used internally for parsing FASTA files, but the code consuming the bio_io module probably won't need to use this function.

val of_header : Base.string -> t Base.Or_error.t

of_header header is like of_header_exn header except that it returns Or_error.t rather than raising exceptions.

val to_string : t -> Base.string

to_string t returns a string representation of t ready to print to a FASTA output file.

val to_string_nl : ?nl:Base.string -> t -> Base.string

to_string_nl t ~nl returns a string representation of t ready to print to a FASTA output file, including a trailing newline (nl) string. nl defaults to "\n".

val serialize : t -> Base.string

serialize t returns the Sexp of t as a string.

val equal : t -> t -> Base.bool

equal this other returns true if all fields of two ts are the same.

val (=) : t -> t -> Base.bool

Fasta.Record.(this = other) is like equal this other.

val id : t -> Base.string

id t returns the id of the t.

val desc : t -> Base.string Base.option

desc t returns the desc (description) of the t.

val seq : t -> Base.string

seq t returns the seq of the t.

val seq_length : t -> Base.int

seq_length t returns the length of the seq of t.

If you construct a record by hand (e.g., with create), and there are spaces or other weird characters in the sequences, they will be counted in the length. E.g.,

let r = Fasta.Record.create ~id:"apple" ~desc:None ~seq:"a a" in
assert (Int.(3 = Fasta.Record.seq_length r))

val with_id : Base.string -> t -> t

with_id new_id t returns a t with new_id instead of the original id.

val with_seq : Base.string -> t -> t

with_seq new_seq t returns a t with new_seq instead of the original seq.

val with_desc : Base.string Base.option -> t -> t

with_desc new_desc t returns a t with new_desc instead of the original desc.

package bio_io

Overview

Example 1

Example 2

Example 3

API