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Diffstat (limited to 'src/nbc/options.sml')
| -rw-r--r-- | src/nbc/options.sml | 202 |
1 files changed, 0 insertions, 202 deletions
diff --git a/src/nbc/options.sml b/src/nbc/options.sml deleted file mode 100644 index 907c95a..0000000 --- a/src/nbc/options.sml +++ /dev/null @@ -1,202 +0,0 @@ -signature OPTIONS = sig - val order: int - val input: string - val genomesDir: string - val genomes: string option - val genomeText: int * string -> string - val totalWords: string * int -> string - val missConstant: real - datatype output = - Matlab of {variable: string, file: string} - | Text of string - | Dual of {text: string, matlab: {variable: string, file: string}} - val output: string -> output - val arguments: string list -end - -structure Options :> OPTIONS = struct - fun |> (x, f) = f x - infix |> - datatype outformat = Otext | Omatlab | Odual - local - val order = ref 15 - val fasta = ref NONE - val genomesDir = ref "/var/lib/genomes" - val genomes = ref NONE - val genomeText = ref "$genomes_dir/$genome/${order}perword.gz" - val totalWords = ref "$genomes_dir/$genome/${order}total" - val missConstant = ref (1.0 / 26067530.0 / 1000000.0) - val outFormat = ref Otext - val variable = ref "ps_g" - val outFile = ref "$input-$order-$genome.$extension" - fun withDefault (description, default) = concat ( - description - :: " (" - :: (case default of - NONE => ["no default)"] - | SOME x => ["default: ", x, ")"]) - ) - val options = [ - { - short = "r", long = ["order"] - , help = withDefault - ("Set the length of words used in matches", NONE) - , desc = GetOpt.ReqArg ( - fn x => case Int.fromString x of - NONE => Fail.fail - "given order is not a valid integer" - | SOME y => order := y - , "integer" - ) - }, { - short = "a", long = ["fasta-input"] - , help = "FASTA input file" - , desc = GetOpt.ReqArg (fn x => fasta := SOME x, "filename") - }, { - short = "j", long = ["genomes-dir"] - , help = withDefault ( - "Set the directory where genomes are stored" - , SOME (!genomesDir) - ), desc = GetOpt.ReqArg (fn x => genomesDir := x, "directory") - }, { - short = "g", long = ["genome-list"] - , help = withDefault ( - "Read genomes from this file, one per line" - , !genomes - ), desc = GetOpt.ReqArg (fn x => genomes := SOME x, "filename") - }, { - short = "w", long = ["genome-text"] - , help = withDefault ( - "Filename to read per-word counts from" - , SOME (!genomeText) - ), desc = GetOpt.ReqArg (fn x => genomeText := x, "filename") - }, { - short = "t", long = ["total-words"] - , help = withDefault ( - "Filename to read total word counts from" - , SOME (!totalWords) - ), desc = GetOpt.ReqArg (fn x => totalWords := x, "filename") - }, { - short = "k", long = ["miss-constant"] - , help = withDefault ( - "Set the constant used for scoring missing words" - , SOME (Real.toString (!missConstant)) - ), desc = GetOpt.ReqArg ( - fn x => (case Real.fromString x of - SOME y => missConstant := y - | NONE => Fail.fail - "given miss constant is not a valid number" - ), "number" - ) - }, { - short = "x", long = ["text"] - , help = "Select gzipped text output (default)" - , desc = GetOpt.NoArg (fn () => outFormat := Otext) - }, { - short = "m", long = ["matlab"] - , help = "Select Matlab binary output" - , desc = GetOpt.NoArg (fn () => outFormat := Omatlab) - }, { - short = "u", long = ["dual"] - , help = "Select both gzipped text and Matlab binary output" - , desc = GetOpt.NoArg (fn () => outFormat := Odual) - }, { - short = "v", long = ["variable"] - , help = withDefault ( - "Set Matlab output variable" - , SOME (!variable) - ), desc = GetOpt.ReqArg (fn x => variable := x, "name") - }, { - short = "o", long = ["output-file"] - , help = withDefault ( - "Set output filename(s)" - , SOME (!outFile) - ), desc = GetOpt.ReqArg (fn x => outFile := x, "filename") - } - ] - val optionsWithHelp = { - short = "h", long = ["help"] - , help = "Display help" - , desc = GetOpt.NoArg (fn () => ( - print ( - GetOpt.usageInfo { - header = "score <options>" - , options = options - } ^ "\n" - ); OS.Process.exit OS.Process.success - )) - } :: options - in - val (_, arguments) = GetOpt.getOpt { - argOrder = GetOpt.Permute - , options = optionsWithHelp - , errFn = print - } (CommandLine.arguments ()) - val order = !order - val input = case !fasta of - NONE => Fail.fail "No input file given" - | SOME x => x - val genomesDir = !genomesDir - val genomes = !genomes - val genomeText = fn (order, genome) => ( - case - Misc.substitute [ - ("genomes_dir", genomesDir) - , ("genome", genome) - , ("order", Int.toString order) - ] (!genomeText) - of - NONE => Fail.fail "bad per-word count filename syntax" - | SOME x => x - ) - val totalWords = fn (genome, order) => ( - case - Misc.substitute [ - ("genomes_dir", genomesDir) - , ("genome", genome) - , ("order", Int.toString order) - ] (!totalWords) - of - NONE => Fail.fail "bad total word count filename syntax" - | SOME x => x - ) - val missConstant = !missConstant - datatype output = - Matlab of {variable: string, file: string} - | Text of string - | Dual of {text: string, matlab: {variable: string, file: string}} - fun output genome = - let - val common = [ - ("input", Misc.basenameWithoutExtension input) - , ("order", Int.toString order) - , ("genome", genome) - ] - fun textName () = - case Misc.substitute - (("extension", "txt.gz") :: common) (!outFile) - of - NONE => Fail.fail "bad text output filename syntax" - | SOME x => x - fun matlabName () = - case Misc.substitute - (("extension", "mat") :: common) (!outFile) - of - NONE => Fail.fail "bad Matlab output filename syntax" - | SOME x => x - in - case !outFormat of - Otext => Text (textName ()) - | Omatlab => Matlab { - variable = !variable - , file = matlabName () - } | Odual => Dual { - text = textName () - , matlab = { - variable = !variable - , file = matlabName () - } - } - end - end -end |