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Module Biocaml_gff (.ml)

module Biocaml_gff: sig .. end

GFF files. Parser silently skips comment lines, blank lines, and pragmas.

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.

type t = {

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 stream_item = [ `comment of string | `record of t ]

The items being output by the parser.

type parse_error = [ `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 tag = [ `pedantic | `version of [ `three | `two ] ]

val default_tags  : tag list

module Transform: sig .. end

val parse_error_of_sexp  : Sexplib.Sexp.t -> parse_error

val parse_error_of_sexp__  : Sexplib.Sexp.t -> parse_error

val sexp_of_parse_error  : parse_error -> Sexplib.Sexp.t

The possible parsing errors.

val tag_of_sexp  : Sexplib.Sexp.t -> tag

val tag_of_sexp__  : Sexplib.Sexp.t -> tag

val sexp_of_tag  : tag -> Sexplib.Sexp.t

Create a parsing Biocaml_transform.t for a given version.

Create a printer for a given version.