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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:

name - string enclosed in double quotes if there are spaces; recommended to use only alphanumeric characters and length less than 15 characters but this is not enforced
description - string enclosed in double quotes if there are spaces; recommended to use only alphanumeric characters and length less than 60 characters but this is not enforced
visibility - "hide", "dense", "full", "pack", or "squish"; if type=wiggle_0 then "hide", "dense", or "full"; can also use integer value where 0 = "hide", 1 = "dense", 2 = "full", 3 = "pack", 4 = "squish"
color - "R,G,B" where each of R, G, and B are integers between 0 and 255
altColor - "R,G,B" where each of R, G, and B are integers between 0 and 255
itemRgb - "On" is the only allowed value
useScore - 0 or 1
group - string
priority - integer
autoScale - "on" or "off"
gridDefault - "on" or "off"
maxHeightPixels - "max:default:min" where each of max, default, and min are integers
graphType - "bar" or "points"
viewLimits - "lower:upper" where each of lower and upper are integers
yLineMark - floating point value
yLineOnOff - "on" or "off"
windowingFunction - "maximum", "mean", or "minimum"
smoothingWindow - "off" or an integer between 2 and 16
db - should be a valid UCSC assembly ID, but currently any string is accepted
offset - integer
url - string
htmlUrl - string
type - "wiggle_0" is the only value currently supported, leaving this attribute unset handles other track types

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_internal_utils.Pos.t * string list * string option
 | `wrong_browser_position of Biocaml_internal_utils.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 ])
 Biocaml_internal_utils.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_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_browser_position of Biocaml_internal_utils.Pos.t * string
 | `wrong_fixed_step_value of Biocaml_internal_utils.Pos.t * string
 | `wrong_key_value_format of (string * string) list * string * 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 ])
 Biocaml_internal_utils.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_internal_utils.Pos.t * string
 | `cannot_parse_int of Biocaml_internal_utils.Pos.t * string
 | `cannot_parse_strand of Biocaml_internal_utils.Pos.t * string
 | `cannot_parse_string 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
 | `wrong_attributes of Biocaml_internal_utils.Pos.t * string
 | `wrong_browser_position of Biocaml_internal_utils.Pos.t * string
 | `wrong_key_value_format of (string * string) list * string * string
 | `wrong_row of Biocaml_internal_utils.Pos.t * string
 | `wrong_url_escaping of Biocaml_internal_utils.Pos.t * string ])
 Biocaml_internal_utils.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_internal_utils.Pos.t * string list * string option
 | `wrong_browser_position of Biocaml_internal_utils.Pos.t * string
 | `wrong_key_value_format of (string * string) list * string * string ])
 Biocaml_internal_utils.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