Module Biocaml_gff

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.

exception Bad of string
Raised if there are any parse errrors.

type strand =
| Sense
| Antisense
| Unknown (*strand is relevant but unknown*)
| Unstranded (*strand is irrelevant*)

type attribute =
| TagValue of string * string (*name and value of an attribute*)
| Something of string (*attributes not in tag-value format*)

type row = {
   chr : string; (*chromosome name*)
   source : string; (*where annotation came from, e.g. a database or algorithm*)
   feature : string; (*the feature type, e.g. exon or gene*)
   pos : int * int; (*position*)
   score : float option; (*possible score, semantics not defined*)
   strand : strand; (*strand*)
   phase : int option; (*phase, should be 0,1, or 2 if feature = "CDS" or None otherwise but this is not checked*)
   attributes : attribute list; (*the attributes*)
Type of information on a row.
type t 
The type representing a GFF file.
val of_file : ?chr_map:(string -> string) ->
?version:int -> ?strict:bool -> string -> t
of_file file parses file. If strict=true, the default, Bad is raise on any errors. If strict=false, errors are silently skipped. Default version is 3, but you can also specify 2.
val of_list : row list -> t
val fold : ('a -> row -> 'a) -> 'a -> t -> 'a
val iter : (row -> unit) -> t -> unit
val fold_file : ?version:int ->
?strict:bool -> ('a -> row -> 'a) -> 'a -> string -> 'a
fold_file f init file accumulates the result of applying f to each row of file. Optional arguments version and strict are as in of_file.
val iter_file : ?version:int -> ?strict:bool -> (row -> unit) -> string -> unit
val to_list : t -> row list
val enum : t -> row BatEnum.t
val to_map : t -> row list Biocaml_std.StringMap.t
Partitions annotations by chromosome.
val map_of_file : ?version:int ->
?strict:bool -> string -> row list Biocaml_std.StringMap.t
val row_to_string : ?version:int -> row -> string
val to_channel : ?version:int -> t -> Pervasives.out_channel -> unit
val to_file : ?version:int -> t -> string -> unit

Operations Related to Attributes

val attribute_names : row -> string list
List of attributes defined for the given row.
val get_attribute : row -> string -> string
get_attribute r x returns the value of attribute x. Enclosing quotes if any are stripped off. Raise Failure if x is not defined exactly once.
val get_attributel : row -> string -> string list
get_attributel r x returns the values of the attribute named x in row r. A list is returned in case the same attribute is multiply defined. An empty list indicates that the requested attribute is undefined. See also get_attribute.
val has_attribute : row -> string -> bool
has_attribute r x returns true if attribute x is defined in r.
val add_attribute : string -> string -> row -> row
add_attribute x y r adds attribute x with value y in r. Any previous value of x is left unaltered. Use delete_attribute first if desired. See also set_attribute.
val set_attribute : string -> string -> row -> row
set_attribute x y r sets attribute x to y in r, deleting any previous values.
val delete_attribute : string -> row -> row
delete_attribute x r deletes all occurrences of attribute x in r.
val index_by_attribute : string -> t -> (string, row list) Hashtbl.t
index_by_attribute x returns a mapping from the values of attribute x to those rows with that value. Instead of an attribute, x can also be "CHR", "SOURCE", or "FEATURE" to index by values of the respective column.