package bio_io

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Overview
API

package bio_io

bio_io
- Bio_io

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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 Ppx_sexp_conv_lib.Sexpable.S with type t := t

val t_of_sexp : Sexplib0.Sexp.t -> t

val sexp_of_t : t -> Sexplib0.Sexp.t

exception Exn of string

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

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

val serialize : t -> string

serialize t returns the Sexp of t as a string.

val equal : t -> t -> bool

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

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

Fasta_record.(this = other) is like equal this other.

val id : t -> string

id t returns the id of the t.

val desc : t -> string option

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

val seq : t -> string

seq t returns the seq of the t.

val with_id : string -> t -> t

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

val with_seq : string -> t -> t

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

val with_desc : string option -> t -> t

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