package bio_io

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Module Fasta.RecordSource

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

Sourcetype t
include Sexplib0.Sexpable.S with type t := t
Sourceval t_of_sexp : Sexplib0.Sexp.t -> t
Sourceval sexp_of_t : t -> Sexplib0.Sexp.t
Sourceval 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.

Sourceval to_string : t -> Base.string

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

Sourceval 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".

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

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

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

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

Sourceval id : t -> Base.string

id t returns the id of the t.

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

Sourceval seq : t -> Base.string

seq t returns the seq of the t.

Sourceval 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))
Sourceval with_id : Base.string -> t -> t

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

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

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

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

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

Sourceval rev : t -> t

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

Sourceval 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.

Sourceval 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.