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

v0.11.0.tar.gz

md5=486aeb3e552dabae85839e2af30d6c52

sha512=4ed2df0b7cbd80bd6e29bd8fee9d2dacd9379ad0f4ff142bd8e16ade3f1507f6cc7cbe4c614943b8feb8fa4705935695cb458606b0da813dbf255b1e566a43cf

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

Module `Biocaml_unix.Gff`Source

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

Sourcetype 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.

Sourcetype item = [

| `comment of string
| `record of record

]

The items being output by the parser.

Error Types

Sourcemodule Error : sig ... end

The errors of the Gff module.

`Tags.t`

Sourcemodule Tags : sig ... end

`In_channel.t` Functions

Sourceexception Error of Error.t

The exception raised by the *_exn functions.

Source

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.

Source

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

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

Convert an item to a string.

`Tfxm.t`

Sourcemodule Transform : sig ... end

Lower-level stream transformations.

S-Expressions

Sourceval record_of_sexp : Sexplib.Sexp.t -> record

Sourceval sexp_of_record : record -> Sexplib.Sexp.t

Sourceval item_of_sexp : Sexplib.Sexp.t -> item

Sourceval 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