diff options
Diffstat (limited to 'src/nbc/options.sml')
| -rw-r--r-- | src/nbc/options.sml | 202 |
1 files changed, 202 insertions, 0 deletions
diff --git a/src/nbc/options.sml b/src/nbc/options.sml new file mode 100644 index 0000000..907c95a --- /dev/null +++ b/src/nbc/options.sml @@ -0,0 +1,202 @@ +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 |