diff options
Diffstat (limited to 'src/nbc/probabilities-by-read.sml')
| -rw-r--r-- | src/nbc/probabilities-by-read.sml | 210 |
1 files changed, 0 insertions, 210 deletions
diff --git a/src/nbc/probabilities-by-read.sml b/src/nbc/probabilities-by-read.sml deleted file mode 100644 index acd8041..0000000 --- a/src/nbc/probabilities-by-read.sml +++ /dev/null @@ -1,210 +0,0 @@ -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 => () |