Source file bed.ml

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type parser_error = [ `Bed_parser_error of int * string ]
[@@deriving sexp]

module Field = Table.Field

type item = string * int * int * string list

let item_of_line l =
  let open Result in
  match Line.split l ~on:'\t' with
  | chrom :: chrom_start :: chrom_end :: others ->
    Field.(parse ~ctx:"chrom_start" int) chrom_start >>= fun chrom_start ->
    Field.(parse ~ctx:"chrom_end" int) chrom_end >>| fun chrom_end ->
    chrom, chrom_start, chrom_end, others
  | _ -> Error "Expected at least 3 fields separated by tab characters"

let line_of_item (chr, start_pos, stop_pos, others) =
  String.concat ~sep:"\t" (chr :: Int.to_string start_pos :: Int.to_string stop_pos :: others)
  |> Line.of_string_unsafe

module Bed3 = struct
  type item = {
    chrom : string ;
    chrom_start : int ;
    chrom_end : int ;
    others : string array ;
  }
  [@@deriving sexp]
end

module Bed4 = struct
  type item = {
    chrom : string ;
    chrom_start : int ;
    chrom_end : int ;
    name : string ;
    others : string array ;
  }
  [@@deriving sexp]

end

module Bed5_raw = struct
  type item = {
    chrom : string ;
    chrom_start : int ;
    chrom_end : int ;
    name : string ;
    score : int ;
    others : string list ;
  }
  [@@deriving sexp]

  let make ~chrom ~chrom_start ~chrom_end ~name ~score ?(others = []) () =
    let open Result in
    Field.(parse ~ctx:"chrom" string_with_no_sep) chrom >>= fun chrom ->
    Field.(parse ~ctx:"name" string_with_no_sep) name >>= fun name ->
    Field.(parse_all string_with_no_sep) others >>= fun others ->
    Ok { chrom ; chrom_start ; chrom_end ; name ; score ; others }

  let set_score it score = { it with score }

  let item_of_line l =
    let open Result in
    match Line.split l ~on:'\t' with
    | chrom :: chrom_start :: chrom_end :: name :: score :: others ->
      Field.(parse ~ctx:"chrom_start" int) chrom_start >>= fun chrom_start ->
      Field.(parse ~ctx:"chrom_end" int) chrom_end >>= fun chrom_end ->
      Field.(parse ~ctx:"score" int) score >>= fun score ->
      (* don't call [make] to avoid unnecessary checks*)
      Ok { chrom ; chrom_start ; chrom_end ; name ; score ; others }
    | _ -> Error "Expected at least 5 fields separated by tab characters"

  let line_of_item it =
    it.chrom ::
    Int.to_string it.chrom_start ::
    Int.to_string it.chrom_end ::
    it.name ::
    Int.to_string it.score ::
    it.others
    |> String.concat ~sep:"\t"
    |> Line.of_string_unsafe
end

module Bed5 = struct
  include Bed5_raw

  let make ~chrom ~chrom_start ~chrom_end ~name ~score ?(others = []) () =
    let open Result in
    Field.(parse ~ctx:"chrom" string_with_no_sep) chrom >>= fun chrom ->
    Field.(parse ~ctx:"name" string_with_no_sep) name >>= fun name ->
    Field.(parse_all ~ctx:"others" string_with_no_sep) others >>= fun others ->
    Ok { chrom ; chrom_start ; chrom_end ; name ; score ; others }

  let item_of_line l =
    let open Result in
    match Line.split l ~on:'\t' with
    | chrom :: chrom_start :: chrom_end :: name :: score :: others ->
      Field.(parse ~ctx:"chrom_start" positive_int) chrom_start >>= fun chrom_start ->
      Field.(parse ~ctx:"chrom_end" positive_int) chrom_end >>= fun chrom_end ->
      Field.(parse ~ctx:"score" (bounded_int ~lo:0 ~hi:1000)) score >>= fun score ->
      (* don't call [make] to avoid unnecessary checks*)
      Ok { chrom ; chrom_start ; chrom_end ; name ; score ; others }
    | _ -> Error "Expected at least 5 fields separated by tab characters"

  let line_of_item = Bed5_raw.line_of_item
end