package biocaml

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  1. GFF Item Types
package biocaml
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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:

GFF Item Types

type record = {
  1. seqname : string;
  2. source : string option;
  3. feature : string option;
  4. start_pos : int;
  5. stop_pos : int;
  6. score : float option;
  7. strand : [ `Plus | `Minus | `Not_stranded | `Unknown ];
  8. phase : int option;
  9. attributes : (string * string list) list;
}

The type of the GFF records/rows.

type item = [
  1. | `Comment of string
  2. | `Record of record
]

The items being output by the parser.

val record : ?source:string -> ?feature:string -> ?score:float -> ?strand:[ `Plus | `Minus | `Not_stranded | `Unknown ] -> ?phase:int -> ?attributes:(string * string list) list -> string -> int -> int -> record
val gff3_item_of_line : Line.t -> (item, [> `Msg of string ]) Pervasives.result
val line_of_item : [ `two | `three ] -> item -> Line.t