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Module Biocaml_wig (.ml)

WIG data.

Internal representation of coordinates always assumes the first position on a chromosome is numbered 1. Also, integer ranges are always closed; the range [1, 10] is the set of integers from 1 to 10 inclusive of 1 and 10. WIG data can be in three formats---bed, variable-step, or fixed-step---and unfortunately each has different conventions as follows:

The inverse is done for printing routines. You are freed from these details if you always use this module to parse and print.

All parsers allow columns (fields) on a line to be separated by any combination of space, tab, or carriage return characters. Printers always separate columns with a single tab. Tag-value pairs must be in the form "tag=value" with no space around the '='.

module Biocaml_wig:
sig

Basic Types


type comment = [ `comment of string ] 
type variable_step = [ `variable_step_state_change of string * int option
       | `variable_step_value of int * float ] 
type fixed_step = [ `fixed_step_state_change of string * int * int * int option
       | `fixed_step_value of float ] 
type bed_graph_value = string * int * int * float 
type item = [ `bed_graph_value of bed_graph_value
       | `comment of string
       | `fixed_step_state_change of string * int * int * int option
       | `fixed_step_value of float
       | `variable_step_state_change of string * int option
       | `variable_step_value of int * float ]
The most general type that the default parser outputs. 
    type t = [comment | variable_step | fixed_step | `bed_graph_value of bed_graph_value ]

    


Error Types


module Error:
sig

The errors of the Wig module.
type parsing = [ `cannot_parse_key_values of Biocaml_internal_utils.Pos.t * string
       | `empty_line of Biocaml_internal_utils.Pos.t
       | `incomplete_input of
           Biocaml_internal_utils.Pos.t * string list * string option
       | `missing_chrom_value of Biocaml_internal_utils.Pos.t * string
       | `missing_start_value of Biocaml_internal_utils.Pos.t * string
       | `missing_step_value of Biocaml_internal_utils.Pos.t * string
       | `unrecognizable_line of Biocaml_internal_utils.Pos.t * string list
       | `wrong_bed_graph_value of Biocaml_internal_utils.Pos.t * string
       | `wrong_fixed_step_value of Biocaml_internal_utils.Pos.t * string
       | `wrong_span_value of Biocaml_internal_utils.Pos.t * string
       | `wrong_start_value of Biocaml_internal_utils.Pos.t * string
       | `wrong_step_value of Biocaml_internal_utils.Pos.t * string
       | `wrong_variable_step_value of Biocaml_internal_utils.Pos.t * string ]
The parsing errors.
val parsing_error_to_string : parsing -> string
Convert a parsing error to a string.
type to_bed_graph = [ `not_in_fixed_step_state | `not_in_variable_step_state ]
The errors encountered while transforming item values to bed-graph-only values.
type t = [ `cannot_parse_key_values of Biocaml_internal_utils.Pos.t * string
       | `empty_line of Biocaml_internal_utils.Pos.t
       | `incomplete_input of
           Biocaml_internal_utils.Pos.t * string list * string option
       | `missing_chrom_value of Biocaml_internal_utils.Pos.t * string
       | `missing_start_value of Biocaml_internal_utils.Pos.t * string
       | `missing_step_value of Biocaml_internal_utils.Pos.t * string
       | `not_in_fixed_step_state
       | `not_in_variable_step_state
       | `unrecognizable_line of Biocaml_internal_utils.Pos.t * string list
       | `wrong_bed_graph_value of Biocaml_internal_utils.Pos.t * string
       | `wrong_fixed_step_value of Biocaml_internal_utils.Pos.t * string
       | `wrong_span_value of Biocaml_internal_utils.Pos.t * string
       | `wrong_start_value of Biocaml_internal_utils.Pos.t * string
       | `wrong_step_value of Biocaml_internal_utils.Pos.t * string
       | `wrong_variable_step_value of Biocaml_internal_utils.Pos.t * string ]
The union of all errors.
val parsing_of_sexp : Sexplib.Sexp.t -> parsing
val sexp_of_parsing : parsing -> Sexplib.Sexp.t
val t_of_sexp : Sexplib.Sexp.t -> t
val sexp_of_t : t -> Sexplib.Sexp.t
val to_bed_graph_of_sexp : Sexplib.Sexp.t -> to_bed_graph
val sexp_of_to_bed_graph : to_bed_graph -> Sexplib.Sexp.t
end

Tags


module Tags:
sig
type t = {
   allow_empty_lines : bool;
   sharp_comments : bool;
}
Additional tags (c.f. Biocaml_tags).
val default : t
Default tags ({allow_empty_lines = false; sharp_comments = true}).
val of_string : string ->
       (t, [> `wig of [> `tags_of_string of exn ] ])
       Biocaml_internal_utils.Result.t
Parse tags (for now S-Expressions).
val to_string : t -> string
Serialize tags (for now S-Expressions).
val t_of_sexp : Sexplib.Sexp.t -> t
val sexp_of_t : t -> Sexplib.Sexp.t
end

In_channel Functions


exception Error of Error.t
The exceptions raised by the Wig module's *_exn functions.
val in_channel_to_item_stream : ?buffer_size:int ->
       ?filename:string ->
       ?tags:Tags.t ->
       Pervasives.in_channel ->
       (item, Error.t) Biocaml_internal_utils.Result.t
       Biocaml_internal_utils.Stream.t
Get a stream of item values out of an input-channel.
val in_channel_to_item_stream_exn : ?buffer_size:int ->
       ?filename:string ->
       ?tags:Tags.t ->
       Pervasives.in_channel -> item Biocaml_internal_utils.Stream.t
Do like in_channel_to_item_stream but each call to Stream.next may throw an exception.
val in_channel_to_bed_graph : ?buffer_size:int ->
       ?filename:string ->
       ?tags:Tags.t ->
       Pervasives.in_channel ->
       (bed_graph_value, Error.t)
       Biocaml_internal_utils.Result.t Biocaml_internal_utils.Stream.t
Get a stream of bed_graph_value values out of a WIG-file input-channel.
val in_channel_to_bed_graph_exn : ?buffer_size:int ->
       ?filename:string ->
       ?tags:Tags.t ->
       Pervasives.in_channel ->
       bed_graph_value Biocaml_internal_utils.Stream.t
Do like in_channel_to_bed_graph but each call to Stream.next may throw an exception.

To_string Functions


val item_to_string : ?tags:Tags.t -> item -> string
Convert an item to a string (including new line characters).

Note: the parsing of the Tags.t is staged, so storing let to_string = item_to_string ~tags only once could be slightly more efficient than calling item_to_string ~tags item many times.


Transform Creations


module Transform:
sig

Low-level Biocaml_transform.t.
val string_to_item : ?filename:string ->
       ?tags:Biocaml_wig.Tags.t ->
       unit ->
       (string,
        (Biocaml_wig.item, [> Biocaml_wig.Error.parsing ])
        Biocaml_internal_utils.Result.t)
       Biocaml_transform.t
Create the parsing Biocaml_transform.t. The parser is "best-effort" and stateless (i.e. a line containing "1000 42." will parsed succesfully as a `variable_step_value (1000, 42.) even if no "variableStep" was line present before).
val item_to_string : ?tags:Biocaml_wig.Tags.t ->
       unit -> (Biocaml_wig.item, string) Biocaml_transform.t
Create the transform that prints item values to strings.
val item_to_bed_graph : unit ->
       (Biocaml_wig.item,
        (Biocaml_wig.bed_graph_value, [> Biocaml_wig.Error.to_bed_graph ])
        Biocaml_internal_utils.Result.t)
       Biocaml_transform.t
Create a transform which converts `variable_step_value _ and `fixed_step_value _ values to `bed_graph_value _ values, using the current state. The `bed_graph_value _ items stay untouched and `comment _ values are ignored.
end

S-Expressions


val comment_of_sexp : Sexplib.Sexp.t -> comment
val sexp_of_comment : comment -> Sexplib.Sexp.t
val variable_step_of_sexp : Sexplib.Sexp.t -> variable_step
val sexp_of_variable_step : variable_step -> Sexplib.Sexp.t
val fixed_step_of_sexp : Sexplib.Sexp.t -> fixed_step
val sexp_of_fixed_step : fixed_step -> Sexplib.Sexp.t
val bed_graph_value_of_sexp : Sexplib.Sexp.t -> bed_graph_value
val sexp_of_bed_graph_value : bed_graph_value -> Sexplib.Sexp.t
val item_of_sexp : Sexplib.Sexp.t -> item
val sexp_of_item : item -> Sexplib.Sexp.t
end