Previous  Up  Next

Module Biocaml_track (.ml)

Track files in UCSC Genome Browser format. The following documentation assumes knowledge of concepts explained on the UCSC Genome Browser's website. Basically, a track file is one of several types of data (WIG, GFF, etc.), possibly preceded by comments, browser lines, and a track line. This module allows only a single data track within a file, although the UCSC specifies that multiple tracks may be provided together.

module Biocaml_track:
sig

Track lines define display attributes. They can be thought of as lists of attribute-value pairs. For forward compatibility, this module allows arbitrary attributes to be set. However, the following lists known attributes and specifies restrictions on their values:

Item Types


type t = [ `browser of
           [ `hide of [ `all ]
           | `position of string * int * int
           | `unknown of string ]
       | `comment of string
       | `track of (string * string) list ]
The type of the parser "track" lines.
type 'a content = [ `content of 'a ]
The "content" lines of the files.

Error Types


module Error:
sig
type parsing = [ `incomplete_input of Biocaml_pos.t * string list * string option
       | `wrong_browser_position of Biocaml_pos.t * string
       | `wrong_key_value_format of (string * string) list * string * string ]
The parsing errors that can happen while parsing Track-specific content.
type t = parsing
The union of all the 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
end

Low-level transforms.


module Transform:
sig

Low-level transforms.
val string_to_string_content : ?filename:string ->
       unit ->
       (string,
        ([ `browser of
             [ `hide of [ `all ]
             | `position of string * int * int
             | `unknown of string ]
         | `comment of string
         | `content of string
         | `track of (string * string) list ], [> Biocaml_track.Error.parsing ])
        Core.Result.t)
       Biocaml_transform.t
Create a parser that gets the "track", comment, and "browser" lines and puts the other lines in `content _.
val string_content_to_string : ?add_content_new_line:bool ->
       unit ->
       ([ `browser of
            [ `hide of [ `all ]
            | `position of string * int * int
            | `unknown of string ]
        | `comment of string
        | `content of string
        | `track of (string * string) list ], string)
       Biocaml_transform.t
Create a printer for track files containing `content line lines.
val string_to_wig : ?filename:string ->
       unit ->
       (string,
        ([ `bed_graph_value of Biocaml_wig.bed_graph_value
         | `browser of
             [ `hide of [ `all ]
             | `position of string * int * int
             | `unknown of string ]
         | `comment of string
         | `fixed_step_state_change of string * int * int * int option
         | `fixed_step_value of float
         | `track of (string * string) list
         | `variable_step_state_change of string * int option
         | `variable_step_value of int * float ],
         [> `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_browser_position of Biocaml_pos.t * string
          | `wrong_fixed_step_value of Biocaml_pos.t * string
          | `wrong_key_value_format of (string * string) list * string * 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 ])
        Core.Result.t)
       Biocaml_transform.t
Create a composite parser for UCSC WIG files.
val wig_to_string : unit ->
       ([ `bed_graph_value of Biocaml_wig.bed_graph_value
        | `browser of
            [ `hide of [ `all ]
            | `position of string * int * int
            | `unknown of string ]
        | `comment of string
        | `fixed_step_state_change of string * int * int * int option
        | `fixed_step_value of float
        | `track of (string * string) list
        | `variable_step_state_change of string * int option
        | `variable_step_value of int * float ], string)
       Biocaml_transform.t
Create a printer for track files containing WIG lines.
val string_to_gff : ?filename:string ->
       tags:Biocaml_gff.Tags.t ->
       unit ->
       (string,
        ([ `browser of
             [ `hide of [ `all ]
             | `position of string * int * int
             | `unknown of string ]
         | `comment of string
         | `record of Biocaml_gff.record
         | `track of (string * string) list ],
         [> `cannot_parse_float of Biocaml_pos.t * string
          | `cannot_parse_int of Biocaml_pos.t * string
          | `cannot_parse_strand of Biocaml_pos.t * string
          | `cannot_parse_string of Biocaml_pos.t * string
          | `empty_line of Biocaml_pos.t
          | `incomplete_input of Biocaml_pos.t * string list * string option
          | `wrong_attributes of Biocaml_pos.t * string
          | `wrong_browser_position of Biocaml_pos.t * string
          | `wrong_key_value_format of (string * string) list * string * string
          | `wrong_row of Biocaml_pos.t * string
          | `wrong_url_escaping of Biocaml_pos.t * string ])
        Core.Result.t)
       Biocaml_transform.t
Create a composite parser for UCSC GFF files.
val gff_to_string : tags:Biocaml_gff.Tags.t ->
       unit ->
       ([ `browser of
            [ `hide of [ `all ]
            | `position of string * int * int
            | `unknown of string ]
        | `comment of string
        | `record of Biocaml_gff.record
        | `track of (string * string) list ], string)
       Biocaml_transform.t
Create a printer for track files containing GFF lines.
val string_to_bed : ?filename:string ->
       ?more_columns:Biocaml_bed.parsing_spec ->
       unit ->
       (string,
        ([ `browser of
             [ `hide of [ `all ]
             | `position of string * int * int
             | `unknown of string ]
         | `comment of string
         | `content of Biocaml_bed.item
         | `track of (string * string) list ],
         [> `bed of Biocaml_bed.Error.parsing_base
          | `incomplete_input of Biocaml_pos.t * string list * string option
          | `wrong_browser_position of Biocaml_pos.t * string
          | `wrong_key_value_format of (string * string) list * string * string ])
        Core.Result.t)
       Biocaml_transform.t
Create a composite parser for UCSC Bed(Graph) files.
val bed_to_string : unit ->
       ([ `browser of
            [ `hide of [ `all ]
            | `position of string * int * int
            | `unknown of string ]
        | `comment of string
        | `content of Biocaml_bed.item
        | `track of (string * string) list ], string)
       Biocaml_transform.t
Create a printer for track files containing Bed(Graph) lines.
end
end