nbc added

1 files changed, 190 insertions, 0 deletions

diff --git a/src/nbc/tabulate.ml b/src/nbc/tabulate.ml
new file mode 100644
index 0000000..dbfbe43
--- /dev/null
+++ b/src/nbc/tabulate.ml
@@ -0,0 +1,190 @@
+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 ()