bio_io 0.6.0 · 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:

(* "s1" *)
Fasta.Record.id record;;

(* Some "apple pie" *)
Fasta.Record.desc record;;

(* "ACTGactg" *)
Fasta.Record.seq record

Example 2

If you have a fasta file something like this:

>s1
ACTG
actg

Then you would get a record something like this:

(* "s1" *)
Fasta.Record.id record;;

(* None *)
Fasta.Record.desc record;;

(* "ACTGactg" *)
Fasta.Record.seq record

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 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 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.

val rev : t -> t

rev t returns the reverse of t. I.e., the seq is reversed reversed.

val comp : t -> t

comp t returns the complement of t. I.e., the seq is complemented. Uses IUPAC conventions. Any "base" (char) that isn't part of the IUPAC passes through unchanged. Note that comp does not round-trip.

val rev_comp : t -> t

rev_comp t returns the reverse complement of t. I.e., the seq is reverse complemented. Uses IUPAC conventions. Any "base" (char) that isn't part of the IUPAC passes through unchanged. Note that rev_comp does not round-trip.

package bio_io

Overview

Example 1

Example 2

Example 3

API