package biocaml

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The OCaml Bioinformatics Library

Install

Dune Dependency

biocaml.org Readme Edit opam file Versions (5)

Authors

Maintainers

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:

Version 2: www.sanger.ac.uk/resources/software/gff/spec.html, gmod.org/wiki/GFF2
Version 3: www.sequenceontology.org/gff3.shtml, gmod.org/wiki/GFF3

GFF Item Types

type record = {

seqname : string;
source : string option;
feature : string option;
pos : int * int;
score : float option;
strand : [ `plus | `minus | `not_applicable | `unknown ];
phase : int option;
attributes : (string * string list) list;

}

The type of the GFF records/rows.

type item = [

| `comment of string
| `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

On This Page

GFF Item Types
Error Types
Tags.t
In_channel.t Functions
To_string Function
Tfxm.t
S-Expressions