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|
signature FILE = sig
type argument
type file
type read
type nmer
type result
val startFile: argument -> file
val startRead: file * string -> read
val nmer: file * read * nmer -> unit
val stopRead: file * read -> unit
val stopFile: file -> result
val invalidFormat: file -> result
end
signature FASTA = sig
type argument
type result
val process: argument * TextIO.instream -> result
end
functor AgnosticFasta (
structure Nmer: NMER
structure File: FILE
sharing type Nmer.nmer = File.nmer
structure Sides: sig
include NMER_SIDES
type file
type read
val process: file * read * sides -> unit
end
sharing type Nmer.base = Sides.sidesBase
sharing type Nmer.nmer = Sides.sidesNmer
sharing type File.read = Sides.read
sharing type File.file = Sides.file
) :> FASTA
where type argument = File.argument
where type result = File.result
= struct
type argument = File.argument
type result = File.result
val beforeHeaderBeginningOfLine = ParseState.create ()
val beforeHeaderMiddleOfLine = ParseState.create ()
val afterHeaderBeginningOfLine = ParseState.create ()
val afterHeaderMiddleOfLine = ParseState.create ()
fun inputLineButDiscardNewline instream =
Option.map (fn line =>
String.extract (line, 0, SOME (size line - 1))
) (TextIO.inputLine instream)
datatype z = datatype ParseState.whichCharacters (* This | Any *)
local
fun header (instream, (file, sides)) =
case inputLineButDiscardNewline instream of
NONE => File.invalidFormat file
| SOME header => ParseState.enter (
afterHeaderBeginningOfLine
, instream
, (
file
, File.startRead (
file
, header
), sides
)
)
fun space (instream, (file, sides)) = ParseState.enter (
beforeHeaderMiddleOfLine
, instream
, (file, sides)
)
fun newline (instream, (file, sides)) = ParseState.enter (
beforeHeaderBeginningOfLine
, instream
, (file, sides)
)
fun invalidFormat (_, (file, _)) = File.invalidFormat file
in
val () = ParseState.build {
state = beforeHeaderBeginningOfLine
, characters = [
(These [#">"], header)
, (These [#"\n"], newline)
, (These [#" ", #"\t", #"\r"], space)
, (Any, invalidFormat)
], endOfFile = invalidFormat
}
val () = ParseState.build {
state = beforeHeaderMiddleOfLine
, characters = [
(These [#"\n"], newline)
, (These [#" ", #"\t", #"\r"], space)
, (Any, invalidFormat)
], endOfFile = invalidFormat
}
end
local
fun base base (instream, (file, read, sides)) = (
Sides.put (sides, base)
;
if Sides.isFull sides then
Sides.process (file, read, sides)
else ()
; ParseState.enter (
afterHeaderMiddleOfLine
, instream
, (file, read, sides)
)
)
fun space (instream, (file, read, sides)) = (
ParseState.enter (
afterHeaderMiddleOfLine
, instream
, (file, read, sides)
)
)
fun other (instream, (file, read, sides)) = (
Sides.clear sides
; ParseState.enter (
afterHeaderMiddleOfLine
, instream
, (file, read, sides)
)
)
fun newline (instream, (file, read, sides)) =
ParseState.enter (
afterHeaderBeginningOfLine
, instream
, (file, read, sides)
)
fun header (instream, (file, read, sides)) = (
File.stopRead (file, read)
; Sides.clear sides
; case inputLineButDiscardNewline instream of
NONE => File.invalidFormat file
| SOME header => ParseState.enter (
afterHeaderBeginningOfLine
, instream
, (
file
, File.startRead (
file
, header
), sides
)
)
)
fun success (_, (file, read, _)) = (
File.stopRead (file, read)
; File.stopFile file
)
in
val () = ParseState.build {
state = afterHeaderBeginningOfLine
, characters = [
(These [#"A", #"a"], base Nmer.a)
, (These [#"C", #"c"], base Nmer.c)
, (These [#"G", #"g"], base Nmer.g)
, (These [#"T", #"t"], base Nmer.t)
, (These [#">"], header)
, (These [#"\n"], newline)
, (These [#" ", #"\t", #"\r"], space)
, (Any, other)
], endOfFile = success
}
val () = ParseState.build {
state = afterHeaderMiddleOfLine
, characters = [
(These [#"A", #"a"], base Nmer.a)
, (These [#"C", #"c"], base Nmer.c)
, (These [#"G", #"g"], base Nmer.g)
, (These [#"T", #"t"], base Nmer.t)
, (These [#" ", #"\t", #"\r"], space)
, (These [#"\n"], newline)
, (Any, other)
], endOfFile = success
}
end
fun process (argument, instream) = ParseState.enter (
beforeHeaderBeginningOfLine
, instream
, (File.startFile argument, Sides.create ())
)
end
functor SingleSidedFasta (
structure Nmer: NMER
structure File: FILE
sharing type Nmer.nmer = File.nmer
) = AgnosticFasta (
structure Nmer = Nmer
structure File = File
structure Sides = struct
type read = File.read
type file = File.file
open Nmer.Single
fun process (file, read, sides) =
File.nmer (file, read, forward sides)
end
)
functor DoubleSidedFasta (
structure Nmer: NMER
structure File: FILE
sharing type Nmer.nmer = File.nmer
) = AgnosticFasta (
structure Nmer = Nmer
structure File = File
structure Sides = struct
type read = File.read
type file = File.file
open Nmer.Double
fun process (file, read, sides) = (
File.nmer (file, read, forward sides)
; File.nmer (file, read, reverse sides)
)
end
)
functor TestFile (Nmer: NMER) = struct
type argument = unit
type nmer = Nmer.nmer
type read = {header: string, nmers: nmer list ref}
type file = {header: string, nmers: string list} list ref
type result = string
fun startFile () = ref nil
fun stopFile file = String.concatWith ";" (
map (fn {header, nmers} =>
header
^ ":"
^ String.concatWith "," (rev nmers)
) (rev (!file))
)
fun startRead (_, header) =
{header = header, nmers = ref nil}
fun nmer (_, {header = _, nmers}, nmer) =
nmers := nmer :: !nmers
fun stopRead (file, {header, nmers = ref nmers}) =
file := {
header = header
, nmers = map Nmer.toString nmers
} :: !file
fun invalidFormat _ = "invalid format"
end
functor Test () = struct
structure Nmer1 = Nmer (
val order = 1
structure Word = Word32
)
structure File1 = TestFile (Nmer1)
structure SingleFasta1 = SingleSidedFasta (
structure Nmer = Nmer1
structure File = File1
)
fun test process input () = process ((), TextIO.openString input)
val single1 = test SingleFasta1.process
structure Nmer2 = Nmer (
val order = 2
structure Word = Word32
)
structure File2 = TestFile (Nmer2)
structure SingleFasta2 = SingleSidedFasta (
structure Nmer = Nmer2
structure File = File2
)
val single2 = test SingleFasta2.process
structure DoubleFasta1 = DoubleSidedFasta (
structure Nmer = Nmer1
structure File = File1
)
val double1 = test DoubleFasta1.process
structure DoubleFasta2 = DoubleSidedFasta (
structure Nmer = Nmer2
structure File = File2
)
val double2 = test DoubleFasta2.process
val () = Test.list [
{
description = "single 1: A"
, function = single1 ">foo\nA\n"
, expectedResult = "foo:A"
}, {
description = "single 1: AG"
, function = single1 ">foo\nAG\n"
, expectedResult = "foo:A,G"
}, {
description = "single 2: A"
, function = single2 ">foo\nA\n"
, expectedResult = "foo:"
}, {
description = "single 2: CTGAG"
, function = single2 ">foo\nCTGAG\n"
, expectedResult = "foo:CT,TG,GA,AG"
}, {
description = "double 1: C"
, function = double1 ">bar\nC\n"
, expectedResult = "bar:C,G"
}, {
description = "double 2: T"
, function = double2 ">baz\nT\n"
, expectedResult = "baz:"
}, {
description = "double 2: GC"
, function = double2 ">quux\nGC\n"
, expectedResult = "quux:GC,GC"
}, {
description = "double 2: CCC\\nC\\nCT"
, function = double2 ">goo\nCCC\nC\nCT\n"
, expectedResult = "goo:CC,GG,CC,GG,CC,GG,CC,GG,CT,AG"
}, {
description = "double 2: CC\\nC*\\nT"
, function = double2 ">goo\nCC\nC*\nT\n"
, expectedResult = "goo:CC,GG,CC,GG"
}, {
description = "double 2: foo CATGAC goo TACCAG"
, function = double2
">foo\nCATGAC\n>goo\nTACCAG\n"
, expectedResult = (
"foo:CA,TG,AT,AT,TG,CA,GA,TC,AC,GT"
^ ";goo:TA,TA,AC,GT,CC,GG,CA,TG,AG,CT"
)
}
]
end
|