Previous  Up  Next

Module Biocaml_gff (.ml)

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: 


module Biocaml_gff:
sig

GFF Item Types


type record = {
   seqname : string;
   source : string option;
   feature : string option;
   pos : int * int;
   score : float option;
   strand : [ `minus | `not_applicable | `plus | `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

The errors of the Gff module.
type parsing = [ `cannot_parse_float of Biocaml_pos.t * string
       | `cannot_parse_int of Biocaml_pos.t * string
       | `cannot_parse_strand of Biocaml_pos.t * string
       | `cannot_parse_string of Biocaml_pos.t * string
       | `empty_line of Biocaml_pos.t
       | `incomplete_input of Biocaml_pos.t * string list * string option
       | `wrong_attributes of Biocaml_pos.t * string
       | `wrong_row of Biocaml_pos.t * string
       | `wrong_url_escaping of Biocaml_pos.t * string ]
The possible parsing errors.
type t = parsing
The union of all the errors of this module.
val parsing_of_sexp : Sexplib.Sexp.t -> parsing
val sexp_of_parsing : parsing -> Sexplib.Sexp.t
val t_of_sexp : Sexplib.Sexp.t -> t
val sexp_of_t : t -> Sexplib.Sexp.t
end

Biocaml_tags.t 


module Tags:
sig
type t = {
   version : [ `three | `two ];
   allow_empty_lines : bool;
   sharp_comments : bool;
}
Additional format-information tags (c.f. Biocaml_tags).
val default : t
Default tags for a random Gff file: {version = `three; allow_empty_lines = false; sharp_comments = true}.
val of_string : string ->
       (t, [> `gff of [> `tags_of_string of exn ] ]) Core.Result.t
Parse tags (for now S-Expressions).
val to_string : t -> string
Serialize tags (for now S-Expressions).
val t_of_sexp : Sexplib.Sexp.t -> t
val sexp_of_t : t -> Sexplib.Sexp.t
end

In_channel.t Functions 


exception Error of Error.t
The exception raised by the *_exn functions.
val in_channel_to_item_stream : ?buffer_size:int ->
       ?filename:string ->
       ?tags:Tags.t ->
       Pervasives.in_channel ->
       (item, [> Error.parsing ]) Core.Result.t Stream.t
Parse an input-channel into item values.
val in_channel_to_item_stream_exn : ?buffer_size:int ->
       ?tags:Tags.t ->
       Pervasives.in_channel -> 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.

Biocaml_transform.t 


module Transform:
sig

Lower-level stream transformations.
val string_to_item : ?filename:string ->
       tags:Biocaml_gff.Tags.t ->
       unit ->
       (string, (Biocaml_gff.item, [> Biocaml_gff.Error.parsing ]) Core.Result.t)
       Biocaml_transform.t
Create a parsing Biocaml_transform.t for a given version.
val item_to_string : tags:Biocaml_gff.Tags.t ->
       unit -> (Biocaml_gff.item, string) Biocaml_transform.t
Create a printer for a given version.
end

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
end