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Module Biocaml_bed (.ml)

BED data files.

A BED file is in the format shown below, where columns must be separted by a tab character. 

    chrA   lo1   hi1
    chrA   lo2   hi2
    .      .     .
    .      .     .
    .      .     .
    chrB   lo1   hi1
    chrB   lo2   hi2
    .      .     .
    .      .     .
    .      .     .

The definition is that intervals are zero based and half-open. So by default the line "chrA lo hi" is parsed to the interval [lo + 1, hi] on chromosome chrA. Similarly, when printing, the default is to print [lo - 1, hi]. The optional argument increment_lo_hi allows changing this behavior for non-conformant files. In addition, the optional argument chr_map is a string -> string function that allows changing of the chromosome name to a specified format, and defaults to identity.

Some tools require that the set of intervals do not overlap within each chromosome. This is not enforced, but you can use any_overlap to verify this property when needed.

module Biocaml_bed:
sig

Item Types


type item = string * int * int * Biocaml_table.Row.t
The type of BED data stream items.

Tags: Describe The Format: TODO 


type parsing_spec = [ `enforce of Biocaml_table.Row.t_type | `strings ]
The specification of how to parse the remaining columns.

Error Types


module Error:
sig

Definitions of error types (with sexp)
type parsing_base = [ `wrong_format of
           [ `column_number | `float_of_string of string | `int_of_string of string ] *
           Biocaml_table.Row.t_type * string
       | `wrong_number_of_columns of Biocaml_table.Row.t ]
The parsing errors.
type parsing = [ `bed of parsing_base ]
The parsing errors.
type t = parsing
The union of all the errors.
val parsing_base_of_sexp : Sexplib.Sexp.t -> parsing_base
val sexp_of_parsing_base : parsing_base -> Sexplib.Sexp.t
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
end

In_channel Functions 


exception Error of Error.t
The exception raised by the *_exn functions.
val in_channel_to_item_stream : ?buffer_size:int ->
       ?more_columns:parsing_spec ->
       Pervasives.in_channel ->
       (item, [> Error.parsing ]) Core.Std.Result.t Stream.t
Parse an input-channel into item values.
val in_channel_to_item_stream_exn : ?buffer_size:int ->
       ?more_columns:parsing_spec ->
       Pervasives.in_channel -> item Stream.t
Like in_channel_to_item_stream but use exceptions for errors (raised within Stream.next).

Conversions to/from Line.t

See also Biocaml_line.t.

val item_of_line : how:parsing_spec ->
       Biocaml_lines.item ->
       (item, [> Error.parsing ]) Core.Std.Result.t
Basic parsing of a single line.
val item_to_line : item -> Biocaml_lines.item
Basic “printing” of one single item.

Transforms 


module Transform:
sig

Lower-level transforms of BED data-streams.
val string_to_item : ?more_columns:Biocaml_bed.parsing_spec ->
       unit ->
       (string,
        (string * int * int * Biocaml_table.Row.item array,
         [> Biocaml_bed.Error.parsing ])
        Core.Std.Result.t)
       Biocaml_transform.t
Create a Biocaml_transform.t-based parser, while providing the format of the additional columns (default `strings).
val item_to_string : unit -> (Biocaml_bed.item, string) Biocaml_transform.t
Create a Biocaml_transform.t which “prints” BED data (reminder: includes ends-of-line).
end

S-Expressions


val item_of_sexp : Sexplib.Sexp.t -> item
val sexp_of_item : item -> Sexplib.Sexp.t
val parsing_spec_of_sexp : Sexplib.Sexp.t -> parsing_spec
val sexp_of_parsing_spec : parsing_spec -> Sexplib.Sexp.t
end