package biocaml

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The OCaml Bioinformatics Library

Install 

dune-project
 Dependency

biocaml.org Readme Edit opam file Versions (5)

Authors

  1. S
    Sebastien Mondet
  2. A
    Ashish Agarwal
  3. P
    Philippe Veber
  4. C
    Christophe Troestler
  5. S
    Sergei Lebedev
  6. D
    David Koppstein
  7. A
    Alexander Gryzlov
  8. F
    Francois Berenger

Maintainers

  1. B
    biocaml@googlegroups.com

Sources

v0.11.0.tar.gz
md5=486aeb3e552dabae85839e2af30d6c52
sha512=4ed2df0b7cbd80bd6e29bd8fee9d2dacd9379ad0f4ff142bd8e16ade3f1507f6cc7cbe4c614943b8feb8fa4705935695cb458606b0da813dbf255b1e566a43cf

doc/biocaml.unix/Biocaml_unix/Fastq/index.html

Module Biocaml_unix.FastqSource

FASTQ files. The FASTQ file format is repeated sequence of 4 lines:

\@name
sequence
+comment
qualities
...

The name line begins with an @ character, which is omitted in the parsed item type provided by this module. Any spaces after the @ are retained, but the specification implies that there shouldn't be any such spaces. Trailing whitespace is also retained since you should not normally have such files.

The comment line, which begins with a +, is handled similarly. The purpose of the comment line is unclear and it is rarely used. Also, "comment" may not be the correct term for this line.

The name line may be structured into two parts: a sequence identifier and an optional description. We provide a function split_name to parse such a value. However, an item's name field contains the unparsed string because it is unclear whether fastq files really follow this. Also the format of the description is unspecified. When it is provided, usually it has some additional structure, so the minimal amount of parsing done by split_name isn't too useful anyway.

Illumina uses a systematic format for the name line that serves as a unique sequence identifier. Use Illumina.sequence_id_of_string to parse an item's name field when you have fastq files produced by Casava version >= 1.8. Earlier versions of Casava returned a different format, which is not currently supported in this module (it could be easily added).

The qualities line is returned as a plain string, but it is required to be decodable as either Phred or Solexa scores. Modules Phred_score and Solexa_score can be used to parse as needed.

Older FASTQ files allowed the sequence and qualities strings to span multiple lines. This is discouraged and is not supported by this module.

Sourcetype item = {
  1. name : string;
  2. sequence : string;
  3. comment : string;
  4. qualities : string;
}
Sourceval sexp_of_item : item -> Ppx_sexp_conv_lib.Sexp.t
Sourceval item_of_sexp : Ppx_sexp_conv_lib.Sexp.t -> item
Sourceval split_name : string -> string * string option

Split a name string into a sequence identifier and an optional description. It is assumed that the given string is from an item's name field, i.e. that it doesn't contain a leading @ char.

Sourcemodule MakeIO (Future : Future.S) : sig ... end
include sig ... end
Sourceval write_file : ?perm:int -> ?append:bool -> string -> item Future_unix.Pipe.Reader.t -> unit Future_unix.Deferred.t
Sourcemodule Illumina : sig ... end

Low-level Printing

Sourceval item_to_string : item -> string

This function converts item values to strings that can be dumped to a file, i.e. they contain full-lines, including all end-of-line characters.

Sourceval name_of_line : ?pos:Pos.t -> Line.t -> string Core_kernel.Or_error.t

Low-level Parsing

Sourceval sequence_of_line : ?pos:Pos.t -> Line.t -> string
Sourceval comment_of_line : ?pos:Pos.t -> Line.t -> string Core_kernel.Or_error.t
Sourceval qualities_of_line : ?pos:Pos.t -> ?sequence:string -> Line.t -> string Core_kernel.Or_error.t

qualities sequence line parses given qualities line in the context of a previously parsed sequence. The sequence is needed to assure the correct number of quality scores are provided. If not provided, this check is omitted.