nbc added

1 files changed, 60 insertions, 0 deletions

diff --git a/src/nbc/count.ml b/src/nbc/count.ml
new file mode 100644
index 0000000..bd97b7b
--- /dev/null
+++ b/src/nbc/count.ml
@@ -0,0 +1,60 @@
+module ExtArray = ExtArray.Array
+let (|>) a b = b a
+
+module Options = struct
+	let parser = OptParse.OptParser.make ~version:"1.0" ()
+	let per_word =
+		let option = OptParse.StdOpt.str_option ~metavar:"file" () in
+		OptParse.OptParser.add parser ~short_name:'w' ~long_name:"per-word"
+			~help:"file to store per-word counts in" option;
+		(fun () -> match OptParse.Opt.opt option with
+			Some x -> x
+			| None ->
+				OptParse.OptParser.usage parser ();
+				exit 1
+		)
+	let total =
+		let option = OptParse.StdOpt.str_option ~metavar:"file" () in
+		OptParse.OptParser.add parser ~short_name:'t' ~long_name:"total"
+			~help:"file to store total count in" option;
+		(fun () -> match OptParse.Opt.opt option with
+			Some x -> x
+			| None ->
+				OptParse.OptParser.usage parser ();
+				exit 1
+		)
+	let order =
+		let option = OptParse.StdOpt.int_option ~default:15 () in
+		OptParse.OptParser.add parser ~short_name:'r' ~long_name:"order" option;
+		(fun () -> OptParse.Opt.get option)
+	let files = OptParse.OptParser.parse_argv parser
+	let total = total ()
+	let per_word = per_word ()
+	let order = order ()
+end
+
+let load_file order judy total name =
+	Misc.io_of_gzip name |> Fasta.enum_words order
+	|> Enum.fold (fun word total ->
+		Judy.bump judy word;
+		Judy.bump judy (Gene.reverse word);
+		total + 2
+	) total
+let load_files order names =
+	let judy = Judy.create () in
+	List.fold_left (load_file order judy) 0 names, judy
+let gzip_output_string c s = Gzip.output c s 0 (String.length s)
+let () =
+	let total_words, judy = load_files Options.order Options.files in
+	(
+		let c = open_out Options.total in
+		output_string c (string_of_int total_words ^ "\n");
+		close_out c
+	); (
+		let c = Gzip.open_out Options.per_word in
+		Judy.iter (fun word count ->
+			gzip_output_string c
+				(String.concat "" [string_of_int count; " "; word; "\n"])
+		) judy;
+		Gzip.close_out c
+	)