Module Biocaml_wig (.ml)

module Biocaml_wig: sig .. end

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:

Bed format requires half-open intervals [low, high\) and numbers the first base as 0. Thus 1 is added to the low value when parsing. The line "chrI 0 10 3.14" is parsed to ("chrI", 1, 10, 3.14).
Variable-step format numbers the first position 1 and uses closed intervals. Thus no change is required. The line "1 3.14" is parsed to (1, 3.14).
Fixed-step format numbers the first position 1 and uses closed intervals. Thus no change is required. The header line "fixedStep chrom=chrI start=1 step=100 span=30" is parsed to ("chrI", 1, 100, 30).

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 '='.

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

Parsing and Printing

type t = [ `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 parse_error = [ `cannot_parse_key_values of Biocaml_pos.t * string
       | `empty_line of Biocaml_pos.t
       | `incomplete_input of Biocaml_pos.t * string list * string option
       | `missing_chrom_value of Biocaml_pos.t * string
       | `missing_start_value of Biocaml_pos.t * string
       | `missing_step_value of Biocaml_pos.t * string
       | `unrecognizable_line of Biocaml_pos.t * string list
       | `wrong_bed_graph_value of Biocaml_pos.t * string
       | `wrong_fixed_step_value of Biocaml_pos.t * string
       | `wrong_span_value of Biocaml_pos.t * string
       | `wrong_start_value of Biocaml_pos.t * string
       | `wrong_step_value of Biocaml_pos.t * string
       | `wrong_variable_step_value of Biocaml_pos.t * string ]

The parsing errors.

val parse_error_to_string : parse_error -> string

Convert a parse_error to a string.

type tag = [ `pedantic | `sharp_comments ]

val default_tags : tag list

module Transform: sig .. end

val comment_of_sexp : Sexplib.Sexp.t -> comment

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 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 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

Parsing and Printing

val t_of_sexp : Sexplib.Sexp.t -> t

val t_of_sexp__ : Sexplib.Sexp.t -> t

val sexp_of_t : t -> Sexplib.Sexp.t

The most general type that the default parser outputs.

val parse_error_of_sexp : Sexplib.Sexp.t -> parse_error

val parse_error_of_sexp__ : Sexplib.Sexp.t -> parse_error

val sexp_of_parse_error : parse_error -> Sexplib.Sexp.t

The parsing errors.

Convert a parse_error to a string.

val tag_of_sexp : Sexplib.Sexp.t -> tag

val tag_of_sexp__ : Sexplib.Sexp.t -> tag

val sexp_of_tag : tag -> Sexplib.Sexp.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).

Create the transform that prints t values to strings.

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 _ and `comment _ values stay untouched.