Previous  Up  Next

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.