Module Biocaml_base.Gff

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

The type of the GFF records/rows.

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

The items being output by the parser.

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