nbc added

1 files changed, 98 insertions, 0 deletions

diff --git a/src/nbc/main.sml b/src/nbc/main.sml
new file mode 100644
index 0000000..361d9ca
--- /dev/null
+++ b/src/nbc/main.sml
@@ -0,0 +1,98 @@
+structure Main = struct
+
+fun |> (x, f) = f x
+infix |>
+
+val order = Options.order
+val genomes = case Options.genomes of
+	SOME x => x |> TextIO.openIn |> Misc.sequenceLines
+	| NONE => Options.genomesDir |> Misc.sortedDirectoryNoPrefix |> Sequence.fromList
+fun input () =
+	case Fasta.sequence (Gzip.openIn Options.input) of
+		NONE => Fail.fail "input file is not FASTA format"
+		| SOME x =>
+			Sequence.map (fn (header, data) =>
+				(header, String.map Char.toUpper data)
+			) x
+fun output genome =
+	let
+		fun inner format = case format of
+			Options.Matlab {variable, file} =>
+				let
+					val matlab = Matlab.openOut file
+					val doubleArray = Matlab.beginDoubleArray (matlab, variable)
+				in {
+					write = fn (_, score) =>
+						Matlab.writeDouble (doubleArray, score)
+					, close = fn () => (
+						Matlab.concludeDoubleArray doubleArray
+						; Matlab.closeOut matlab
+					)
+				} end
+			| Options.Text filename =>
+				let
+					val gzip = Gzip.openOut filename
+				in {
+					write = fn (header, score) =>
+						TextIO.output (
+							gzip
+							, Real.fmt (StringCvt.FIX (SOME 8)) score
+						)
+					, close = fn () => TextIO.closeOut gzip
+				} end
+			| Options.Dual {text, matlab} =>
+				let
+					val text = inner (Options.Text text)
+					val matlab = inner (Options.Matlab matlab)
+				in {
+					write = fn x => (
+						#write text x
+						; #write matlab x
+					), close = fn () => (
+						#close text ()
+						; #close matlab ()
+					)
+				} end
+	in
+		inner (Options.output genome)
+	end
+fun totalWords (genome, order) =
+        let
+		val name = Options.totalWords (genome, order)
+		val input = TextIO.openIn name
+	in
+		(case Option.mapPartial Real.fromString (Misc.inputLine input) of
+			NONE => Fail.fail ("could not read number from " ^ name)
+			| SOME r => r
+		) before TextIO.closeIn input
+	end
+
+val () =
+	Sequence.app (fn gname =>
+		let
+			val {write, close} = output gname
+			val totalWords = totalWords (gname, order)
+			val genome = (
+				Stopwatch.start ("Loading genome " ^ gname)
+				; Genome.load (gname, order)
+				before Stopwatch.finish ()
+			)
+		in
+			Stopwatch.start ("Scoring fragments")
+			; input () |> Sequence.app (fn (header, fragment) =>
+				write (
+					header
+					, Score.score (
+						order
+						, Options.missConstant
+						, fn nmer => Genome.get (genome, nmer)
+						, totalWords
+						, fragment
+					)
+				)
+			); Stopwatch.finish ()
+			; close ()
+		end
+	) genomes
+
+end