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|
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
|
