From dd38d0d1dda2be42bf280aeca110542f2f2fef1b Mon Sep 17 00:00:00 2001 From: Calvin Date: Tue, 28 May 2013 10:47:11 -0400 Subject: removed files --- src/nbc/tabulate.ml | 190 ---------------------------------------------------- 1 file changed, 190 deletions(-) delete mode 100644 src/nbc/tabulate.ml (limited to 'src/nbc/tabulate.ml') diff --git a/src/nbc/tabulate.ml b/src/nbc/tabulate.ml deleted file mode 100644 index dbfbe43..0000000 --- a/src/nbc/tabulate.ml +++ /dev/null @@ -1,190 +0,0 @@ -let (|>) a b = b a -let car, cdr = fst, snd -let odd n = n land 1 = 1 -let even n = not (odd n) -module ExtArray = ExtArray.Array -module ExtList = ExtList.List -module ExtString = ExtString.String -module Program = struct - let name = "Naive Bayes Classifier - Tabulate" - let version = "1.0" -end -let chop_extra s = ExtString.strip ~chars:"_- " s -let any_alphanumeric s = - let e = String.length s in - let rec loop i = - if i = e then false - else match s.[i] with - 'a'..'z' | 'A'..'Z' | '0'..'9' -> true - | _ -> loop (i + 1) - in loop 0 -let guess_prefix filenames = - let s = - List.map Misc.basename_without_extension filenames - |> Misc.longest_common_substring |> chop_extra - in - if any_alphanumeric s then s - else "" -module Options = struct - let parser = OptParse.OptParser.make ~version:Program.version () - let genomes = - let option = OptParse.StdOpt.str_option ~metavar:"file" () in - OptParse.OptParser.add parser ~short_name:'g' ~long_name:"genome-list" option; - (fun () -> match OptParse.Opt.opt option with - Some x -> x - | None -> - OptParse.OptParser.usage parser (); - exit 1 - ) - let columns = - let option = OptParse.StdOpt.int_option ~default:200 () in - OptParse.OptParser.add parser ~short_name:'c' ~long_name:"columns" option; - (fun () -> OptParse.Opt.get option) - let template = - let option = OptParse.StdOpt.str_option ~metavar:"template" - ~default:"$prefix-$n.csv.gz" () in - OptParse.OptParser.add parser ~short_name:'t' ~long_name:"output-template" option; - (fun () -> OptParse.Opt.get option) - let given_prefix = - let x = ref None in - OptParse.StdOpt.str_callback ~metavar:"prefix" (fun s -> x := Some s) - |> OptParse.OptParser.add parser ~short_name:'p' - ~long_name:"output-prefix"; - (fun () -> !x) - let files = OptParse.OptParser.parse_argv parser - let prefix = match given_prefix () with - None -> ( - match guess_prefix files with - "" -> "table" - | s -> s - ) | Some x -> x - let string_of_int n = Printf.sprintf "%08u" n - let output n = template () |> Misc.substitute ["prefix", prefix; "n", string_of_int n] -end - -exception Collide of string * string * string -let match_files_to_genomes genomes files = - let g = Array.of_list genomes in - let gl = Array.length g in - let gi = Array.init gl (fun i -> i) in - Array.sort (fun ai bi -> compare (String.length g.(bi)) (String.length g.(ai))) gi; - let gf = Array.make gl None in - List.iter (fun file -> - try ( - let i = ExtArray.find (fun i -> ExtString.exists file g.(i)) gi in - match gf.(i) with - None -> gf.(i) <- Some file - | Some other_file -> raise (Collide (g.(i), other_file, file)) - ) with Not_found -> () (* file does not match any genomes *) - ) files; - let r = ref [] in - for i = gl - 1 downto 0 do - match gf.(i) with - None -> () (* no file matches a given genome *) - | Some file -> r := (g.(i), file) :: !r - done; - !r - -let columns = Options.columns () -let genomes, files = - let genomes = Misc.io_of_file (Options.genomes ()) |> Misc.enum_of_lines - |> ExtList.of_enum in - let g, f = match_files_to_genomes genomes Options.files |> List.split in - Array.of_list g, - f |> List.map (fun x -> x, x |> open_in |> IO.input_channel) |> Array.of_list - -let newfile, newline, cell, finish = - let i = ref 0 in - let open_file () = - i := !i + 1; - let filename = Options.output !i in - Gzip.open_out filename - in - let c = ref None in - let force_out () = - match !c with - None -> - let d = open_file () in - c := Some d; - d - | Some d -> d - in - let start_of_line = ref true in - (* newfile *) (fun () -> - (match !c with - Some c -> Gzip.close_out c - | None -> ()); - i := !i + 1; - c := None - ), - (* newline *) (fun () -> - let c = force_out () in - Gzip.output_char c '\n'; - start_of_line := true - ), - (* cell *) (fun s -> - let c = force_out () in - if not !start_of_line then Gzip.output_char c ','; - Gzip.output c s 0 (String.length s); - start_of_line := false - ), - (* finish *) (fun () -> - match !c with - Some c -> Gzip.close_out c - | None -> () - ) - -let read_two_fields (filename, c) = - let line = IO.read_line c in - match Misc.split2 line with - Some x -> x - | None -> - Printf.eprintf "\ - There is something wrong with the file %s. \ - The offending line is:\n%s\n" filename line; - exit 1 - -let output_file () = - newfile (); - let yes_we_have_input = - let x = ref false in - (fun () -> - if !x then () - else ( - cell "names"; - x := true - ) - ) - in - let a = Array.make columns "" in - let rec loop i = - if i < columns then ( - try ( - let name, datum = read_two_fields files.(0) in - yes_we_have_input (); - cell name; - a.(i) <- datum; - loop (i + 1) - ) with IO.No_more_input -> - if i > 0 then Array.sub a 0 i - else raise End_of_file - ) else a - in - let a = loop 0 in - let these_columns = Array.length a in - newline (); - cell genomes.(0); - for i = 0 to these_columns - 1 do cell a.(i) done; - newline (); - for i = 1 to Array.length genomes - 1 do - cell genomes.(i); - for j = 0 to these_columns - 1 do - let _, datum = read_two_fields files.(i) in - cell datum - done; - newline () - done - -let () = - try while true do output_file () done - with End_of_file -> finish () -- cgit v1.2.3