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

v0.10.0.tar.gz
md5=497e3f2f7128a6ca347d66848da38a3d
sha512=4a76ebbafda3bc944afaff40d69791dfe153a0638ef5d7e6e1bc962b7f991d9545cd0af2d7930b39f8b31dbf067d0603cfa03d9b7a49396ab1ae452df47fd1f3

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

Module Biocaml_unix.Gff

GFF files.

Versions 2 and 3 are supported. The only difference is the delimiter used for tag-value pairs in the attribute list: 3 uses an equal sign, and 2 uses a space. Version 3 also has additional requirements, e.g. the feature must be a sequence ontology term, but these are not checked.

More information:

GFF Item Types

type record = {
  1. seqname : string;
  2. source : string option;
  3. feature : string option;
  4. pos : int * int;
  5. score : float option;
  6. strand : [ `plus | `minus | `not_applicable | `unknown ];
  7. phase : int option;
  8. attributes : (string * string list) list;
}

The type of the GFF records/rows.

type item = [
  1. | `comment of string
  2. | `record of record
]

The items being output by the parser.

Error Types

module Error : sig ... end

The errors of the Gff module.

Tags.t

module Tags : sig ... end

In_channel.t Functions

exception Error of Error.t
val in_channel_to_item_stream : ?buffer_size:int -> ?filename:string -> ?tags:Tags.t -> Core_kernel.In_channel.t -> (item, [> Error.parsing ]) Core_kernel.result Stream.t

Parse an input-channel into item values.

val in_channel_to_item_stream_exn : ?buffer_size:int -> ?tags:Tags.t -> Core_kernel.In_channel.t -> item Stream.t

Like in_channel_to_item_stream but use exceptions for errors (raised within Stream.next).

To_string Function

val item_to_string : ?tags:Tags.t -> item -> string

Convert an item to a string.

Tfxm.t

module Transform : sig ... end

Lower-level stream transformations.

S-Expressions

val record_of_sexp : Sexplib.Sexp.t -> record
val sexp_of_record : record -> Sexplib.Sexp.t
val item_of_sexp : Sexplib.Sexp.t -> item
val sexp_of_item : item -> Sexplib.Sexp.t