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Module Biocaml_table (.ml)

Generic “tables” (like CSV, TSV, Bed …).

module Biocaml_table:
sig

Table Rows/Lines 


module Row:
sig

Definition of rows
type item = [ `float of float | `int of int | `string of string ]
Type row elements (or “cells”).
type t = item array
A single row.
type item_type = [ `type_float | `type_int | `type_string ]
Definition of the type of a cell.
type t_type = item_type array
Definition of the type of a row.

Tags 


module Tags:
sig

Tags describe the actual format of the row stream. See also Biocaml_tags.t.
type t = [ `format of Biocaml_table.Row.t_type
       | `separator of char
       | `strict_about of [ `cell_type | `row_length ] ] list
The tags associated with table rows:
  • `separator c adds c in the list of separators used.
  • `strict_about something ensures that the format is fully compliant with something (example: otherwise the parser may ignore some errors to keep going).
  • `tail_format array describes the format of the columns of the row, if not provided everything is assumed to be `type_string. 

val separators : t -> char list
Get the list of separators defined in t.
val strict_row_length : t -> bool
Tell whether one should be strict about the minimal number of cells per row (defined with `format _).
val strict_cell_type : t -> bool
Tell whether one should be strict about the types of the cells (defined with `format _).
val format : t -> Biocaml_table.Row.t_type option
Get the defined format if any.
val default : t
The default tags define a loose TSV format.
val default_extension : t -> string
Give a file extension ("tsv", "csv", or "table").
val to_string : t -> string
Serialize tags.
val of_string : string ->
       (t, [> `table_row of [> `tags_of_string of exn ] ])
       Biocaml_internal_utils.Result.t
Parse the description of the tags (for now S-Expressions).
val t_of_sexp : Sexplib.Sexp.t -> t
val sexp_of_t : t -> Sexplib.Sexp.t
end

module Error:
sig
type line_parsing = [ `wrong_format of
           [ `column_number | `float_of_string of string | `int_of_string of string ] *
           Biocaml_table.Row.t_type * string ] 
type t = line_parsing 
val line_parsing_of_sexp : Sexplib.Sexp.t -> line_parsing
val sexp_of_line_parsing : line_parsing -> Sexplib.Sexp.t
val t_of_sexp : Sexplib.Sexp.t -> t
val sexp_of_t : t -> Sexplib.Sexp.t
end
val of_line : ?separators:char list ->
       ?strict_row_length:bool ->
       ?strict_cell_type:bool ->
       ?format:t_type ->
       Biocaml_internal_utils.Line.t ->
       (t, [> Error.line_parsing ])
       Biocaml_internal_utils.Result.t
Parse a Line.t into a row while specifying a format.
  • If format is None (the default), then all the elements are put in `string _ rows.
  • The default cell separators are [' '; '\t'].
  • If strict_row_length is true and format provided, then check that the number of columns is at least the one of the format.
  • If strict_cell_type is true and format provided, then check that each cell has the exactly right format.

val to_line : sep:string -> t -> Biocaml_internal_utils.Line.t
Write the row to a Line.t.

Transform.t Creations


module Transform:
sig
val line_to_item : ?tags:Biocaml_table.Row.Tags.t ->
       unit ->
       (Biocaml_lines.item,
        (Biocaml_table.Row.t,
         [> `table_row of Biocaml_table.Row.Error.line_parsing ])
        Biocaml_internal_utils.Result.t)
       Biocaml_transform.t
Create a Biocaml_transform.t that converts lines to table-rows according to the tags (default: Biocaml_table.Row.Tags.default).
val item_to_line : ?tags:Biocaml_table.Row.Tags.t ->
       unit -> (Biocaml_table.Row.t, Biocaml_lines.item) Biocaml_transform.t
Create a Biocaml_transform.t that converts rows to lines using the first separator in the tags or '\t' if none (default tags: Biocaml_table.Row.Tags.default).
end

S-Expressions 


val item_of_sexp : Sexplib.Sexp.t -> item
val sexp_of_item : item -> Sexplib.Sexp.t
val t_of_sexp : Sexplib.Sexp.t -> t
val sexp_of_t : t -> Sexplib.Sexp.t
val item_type_of_sexp : Sexplib.Sexp.t -> item_type
val sexp_of_item_type : item_type -> Sexplib.Sexp.t
val t_type_of_sexp : Sexplib.Sexp.t -> t_type
val sexp_of_t_type : t_type -> Sexplib.Sexp.t
end
end