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_internal_utils.Pos.t * string
 | `cannot_parse_int of Biocaml_internal_utils.Pos.t * string
 | `cannot_parse_strand of Biocaml_internal_utils.Pos.t * string
 | `cannot_parse_string of Biocaml_internal_utils.Pos.t * string
 | `empty_line of Biocaml_internal_utils.Pos.t
 | `incomplete_input of
 Biocaml_internal_utils.Pos.t * string list * string option
 | `wrong_attributes of Biocaml_internal_utils.Pos.t * string
 | `wrong_row of Biocaml_internal_utils.Pos.t * string
 | `wrong_url_escaping of Biocaml_internal_utils.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 ] ])
 Biocaml_internal_utils.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 ])
 Biocaml_internal_utils.Result.t Biocaml_internal_utils.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 Biocaml_internal_utils.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 ])
 Biocaml_internal_utils.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

AltStyle によって変換されたページ (->オリジナル) /