Biocaml 0.4-dev : Biocaml

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.

Module Biocaml_track.Transform (.ml)