From b632667ce57af89691407bb8668e1512775278ae Mon Sep 17 00:00:00 2001
From: Calvin <calvin@EESI>
Date: Fri, 15 Mar 2013 15:26:20 -0400
Subject: nbc added

---
 src/nbc/probabilities-by-read.sml | 210 ++++++++++++++++++++++++++++++++++++++
 1 file changed, 210 insertions(+)
 create mode 100644 src/nbc/probabilities-by-read.sml

(limited to 'src/nbc/probabilities-by-read.sml')

diff --git a/src/nbc/probabilities-by-read.sml b/src/nbc/probabilities-by-read.sml
new file mode 100644
index 0000000..acd8041
--- /dev/null
+++ b/src/nbc/probabilities-by-read.sml
@@ -0,0 +1,210 @@
+local
+	fun usage result = (
+		TextIO.output (
+			TextIO.stdErr
+			, CommandLine.name ()
+		^ " <order> <input FASTA> <file of nmers to count>\n"
+		); OS.Process.exit result
+	)
+in
+	val (order, input, toCount) = case CommandLine.arguments () of
+		[order, input, toCount] => (case Int.fromString order of
+			NONE => usage OS.Process.failure
+			| SOME order => (order, input, toCount)
+		) | ["--help"] => usage OS.Process.success
+		| _ => usage OS.Process.failure
+end
+
+datatype result = Success | Failure
+fun warn message = TextIO.output (
+	TextIO.stdErr
+	, (
+		"warning: "
+		^ message
+		^ "\n"
+	)
+)
+
+signature NMER_TABLE = sig
+	type nmer
+	type table
+
+	(*
+		Create the table. Only the provided nmers will be counted.
+	*)
+	val create: nmer list -> table
+
+	(*
+		Increment the count for a given nmer. If the nmer was
+		not provided at table creation, do nothing.
+	*)
+	val bump: table * nmer -> unit
+
+	(*
+		Reset all counts to zero. Do not change the list of
+		nmers to count.
+	*)
+	val clear: table -> unit
+
+	(*
+		Apply a function to all nmers and their counts, in
+		lexicographic order.
+	*)
+	val app: (nmer * int -> unit) -> table -> unit
+end
+
+functor NmerTable (Nmer: NMER)
+:> NMER_TABLE where type nmer = Nmer.nmer
+= struct
+	structure HashTable = HashTableFn (
+		type hash_key = Nmer.nmer
+		val hashVal = Nmer.hash
+		val sameKey = Nmer.equal
+	)
+	exception NotFound
+	type nmer = Nmer.nmer
+	type table = {
+		indexes: int HashTable.hash_table
+		, counts: int array
+		, nmers: nmer vector
+	}
+	fun create list =
+		let
+			val indexes = HashTable.mkTable (1024, NotFound)
+			val nmers =
+				let
+					val array = Array.fromList list
+				in
+					ArrayQSort.sort Nmer.compare array
+					; Array.vector array
+				end
+		in
+			Vector.appi (fn (index, nmer) =>
+				HashTable.insert indexes (nmer, index)
+			) nmers
+			; {
+				indexes = indexes
+				, nmers = nmers
+				, counts = Array.array (
+					Vector.length nmers
+					, 0
+				)
+			}
+		end
+	fun bump ({indexes, nmers = _, counts}, nmer) =
+		case HashTable.find indexes nmer of
+			NONE => ()
+			| SOME index => Array.update (
+				counts
+				, index
+				, Array.sub (counts, index) + 1
+			)
+	fun clear {indexes = _, nmers = _, counts} =
+		Array.modify (fn _ => 0) counts
+	fun app execute {indexes = _, nmers, counts} =
+		Vector.appi (fn (index, nmer) =>
+			execute (nmer, Array.sub (counts, index))
+		) nmers
+end
+
+functor Input (
+	structure Nmer: NMER
+	structure NmerTable: NMER_TABLE
+	sharing type Nmer.nmer = NmerTable.nmer
+) = SingleSidedFasta (
+	structure Nmer = Nmer
+	structure File = struct
+		type argument = NmerTable.table
+		type file = argument
+		type read = Int64.int ref
+		type nmer = Nmer.nmer
+		datatype result = datatype result
+		exception NotFound
+		fun startFile table = table
+		fun startRead (table, _) = ref (0: Int64.int)
+		fun nmer (table, (total: Int64.int ref), nmer) = (
+			total := !total + 1
+			; NmerTable.bump (table, nmer)
+		)
+		fun put string = TextIO.output (TextIO.stdOut, string)
+		fun stopRead (table, total) =
+			let
+				val realFromInt64 =
+					Real.fromLargeInt o Int64.toLarge
+				val realTotal = realFromInt64 (!total)
+				val toString = Real.fmt (
+					StringCvt.FIX (SOME 17)
+				)
+				fun probability count = real count / realTotal
+				infix |>
+				fun argument |> function = function argument
+				val first = ref true
+			in
+				NmerTable.app (fn (nmer, count) => (
+					if !first then first := false
+					else put "\t"
+					; count
+						|> probability
+						|> toString
+						|> put
+				)) table
+				; put "\n"
+				; NmerTable.clear table
+				; total := 0
+			end
+		fun stopFile _ = Success
+		fun invalidFormat _ = Failure
+	end
+)
+
+structure Nmer = Nmer (
+	val order = order
+	structure Word = Word64
+)
+structure NmerTable = NmerTable (Nmer)
+structure Input = Input (
+	structure Nmer = Nmer
+	structure NmerTable = NmerTable
+)
+
+val table =
+	let
+		fun build collect goose = case collect goose of
+			NONE => nil
+			| SOME egg =>
+				egg :: build collect goose
+		fun chopEnd string = String.extract (
+			string
+			, 0
+			, SOME (size string - (
+				if String.isSuffix "\r\n" string
+				then 2
+				else 1
+			))
+		)
+		val line = Option.map chopEnd o TextIO.inputLine
+		val lines = build line
+		val instream = TextIO.openIn toCount
+		fun fromStringWithWarning string =
+			case Nmer.fromString string of
+				NONE => (
+					warn (
+						string
+						^ " is not a valid nmer"
+					); NONE
+				) | someNmer => someNmer
+		val nmers = List.mapPartial
+			fromStringWithWarning
+			(lines instream)
+	in
+		TextIO.closeIn instream
+		; NmerTable.create nmers
+	end
+
+val () = case Input.process (table, TextIO.openIn input) of
+	Failure => (
+		TextIO.output (
+			TextIO.stdErr
+			, "input is not valid FASTA\n"
+		); OS.Process.exit OS.Process.failure
+	) | Success => ()
-- 
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