bio_io 0.7.0 (latest) · OCaml Package

A record type for FASTQ files.

Overview

Very similar to the Fasta.Record.t. See that module for more details.contents

Fields

For the "header" line, the id is everything up to the first space, and the desc is everything after. Note, that desc is optional. E.g.,

@this_is_the_id this is the desc
 ^^^^^^^^^^^^^^ ^^^^^^^^^^^^^^^^
 id ----------| Some desc -----|

The other possibly weird field is extra. It is simply everything on the line following the + (i.e., the third line of the 4 line FASTQ file).

It is currently NOT a parse error if the sequence length and quality string length are different lengths. This may change in the future.

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 ->
  qual:Base.string ->
  extra:Base.string Base.option ->
  t

create ~id ~desc ~seq ~qual ~extra 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 FASTQ 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 FASTQ 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

Fastq.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 qual : t -> Base.string

qual t returns the qual of t.

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

extra t returns the extra of the t if there is one. It is whatever is after the + line. Technically it should be the same ID+desc found in the header line, but this library just treats it as a blob of data.

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 =
  Fastq.Record.create ~id:"apple" ~desc:None ~seq:"a a" ~qual:". ."
    ~extra:None
in
assert (Int.(3 = Fastq.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 with_qual : Base.string -> t -> t

with_qual new_qual t returns a t with new_qual instead of the original qual.

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

with_extra new_extra t returns a t with new_extra instead of the original extra.

val rev : t -> t

rev t returns the reverse of t. I.e., the seq and the qual are 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, and the quality score is reversed to match it. 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

Fields

API