{-# LANGUAGE OverloadedStrings #-}
{-# LANGUAGE TemplateHaskell #-}
module SLynx.Simulate.Simulate
( simulateCmd,
)
where
import Control.Applicative ((<|>))
import Control.Monad
import Control.Monad.IO.Class
import Control.Monad.Logger
import Control.Monad.Trans.Class
import Control.Monad.Trans.Reader (ask)
import qualified Data.ByteString.Builder as BB
import qualified Data.ByteString.Lazy.Char8 as BL
import Data.List
import Data.Maybe
import qualified Data.Set as Set
import qualified Data.Text as T
import qualified Data.Text.Lazy as LT
import qualified Data.Text.Lazy.Encoding as LT
import qualified Data.Vector as V
import qualified Data.Vector.Storable as VS
import qualified Data.Vector.Unboxed as U
import ELynx.Data.Alphabet.Alphabet as A
import qualified ELynx.Data.MarkovProcess.AminoAcid as MA
import ELynx.Data.MarkovProcess.GammaRateHeterogeneity
import qualified ELynx.Data.MarkovProcess.MixtureModel as MM
import qualified ELynx.Data.MarkovProcess.PhyloModel as MP
import qualified ELynx.Data.MarkovProcess.RateMatrix as MR
import qualified ELynx.Data.MarkovProcess.SubstitutionModel as MS
import qualified ELynx.Data.Sequence.Sequence as Seq hiding
( name,
)
import ELynx.Export.Sequence.Fasta
import ELynx.Import.MarkovProcess.EDMModelPhylobayes
import ELynx.Import.MarkovProcess.SiteprofilesPhylobayes
import ELynx.Simulate.MarkovProcessAlongTree
import ELynx.Tools
import ELynx.Tree
import SLynx.Simulate.Options
import SLynx.Simulate.PhyloModel
import System.Random.MWC
import Text.Printf
getDistLine :: Int -> MR.StationaryDistribution -> BB.Builder
getDistLine :: Int -> StationaryDistribution -> Builder
getDistLine Int
i StationaryDistribution
d =
Int -> Builder
BB.intDec Int
i
Builder -> Builder -> Builder
forall a. Semigroup a => a -> a -> a
<> Char -> Builder
BB.char8 Char
' '
Builder -> Builder -> Builder
forall a. Semigroup a => a -> a -> a
<> Builder
s
where
s :: Builder
s = [Builder] -> Builder
forall a. Monoid a => [a] -> a
mconcat ([Builder] -> Builder) -> [Builder] -> Builder
forall a b. (a -> b) -> a -> b
$ Builder -> [Builder] -> [Builder]
forall a. a -> [a] -> [a]
intersperse (Char -> Builder
BB.char8 Char
' ') ([Builder] -> [Builder]) -> [Builder] -> [Builder]
forall a b. (a -> b) -> a -> b
$ (Double -> Builder) -> [Double] -> [Builder]
forall a b. (a -> b) -> [a] -> [b]
map Double -> Builder
BB.doubleDec ([Double] -> [Builder]) -> [Double] -> [Builder]
forall a b. (a -> b) -> a -> b
$ StationaryDistribution -> [Double]
forall a. Storable a => Vector a -> [a]
VS.toList StationaryDistribution
d
writeSiteDists :: [Int] -> V.Vector MR.StationaryDistribution -> ELynx SimulateArguments ()
writeSiteDists :: [Int]
-> Vector StationaryDistribution -> ELynx SimulateArguments ()
writeSiteDists [Int]
componentIs Vector StationaryDistribution
ds = do
Maybe FilePath
mbn <- GlobalArguments -> Maybe FilePath
outFileBaseName (GlobalArguments -> Maybe FilePath)
-> (Arguments SimulateArguments -> GlobalArguments)
-> Arguments SimulateArguments
-> Maybe FilePath
forall b c a. (b -> c) -> (a -> b) -> a -> c
. Arguments SimulateArguments -> GlobalArguments
forall a. Arguments a -> GlobalArguments
global (Arguments SimulateArguments -> Maybe FilePath)
-> ReaderT
(Arguments SimulateArguments)
(LoggingT IO)
(Arguments SimulateArguments)
-> ReaderT
(Arguments SimulateArguments) (LoggingT IO) (Maybe FilePath)
forall (f :: * -> *) a b. Functor f => (a -> b) -> f a -> f b
<$> ReaderT
(Arguments SimulateArguments)
(LoggingT IO)
(Arguments SimulateArguments)
forall (m :: * -> *) r. Monad m => ReaderT r m r
ask
case Maybe FilePath
mbn of
Maybe FilePath
Nothing -> () -> ELynx SimulateArguments ()
forall (m :: * -> *) a. Monad m => a -> m a
return ()
Just FilePath
bn -> IO () -> ELynx SimulateArguments ()
forall (m :: * -> *) a. MonadIO m => IO a -> m a
liftIO (IO () -> ELynx SimulateArguments ())
-> IO () -> ELynx SimulateArguments ()
forall a b. (a -> b) -> a -> b
$ FilePath -> ByteString -> IO ()
BL.writeFile (FilePath
bn FilePath -> FilePath -> FilePath
forall a. Semigroup a => a -> a -> a
<> FilePath
".sitedists") ByteString
output
where
dsPaml :: Vector StationaryDistribution
dsPaml = (StationaryDistribution -> StationaryDistribution)
-> Vector StationaryDistribution -> Vector StationaryDistribution
forall a b. (a -> b) -> Vector a -> Vector b
V.map StationaryDistribution -> StationaryDistribution
MA.alphaToPamlVec Vector StationaryDistribution
ds
lns :: [Builder]
lns = [Int -> StationaryDistribution -> Builder
getDistLine Int
i StationaryDistribution
d | (Int
i, Int
c) <- [Int] -> [Int] -> [(Int, Int)]
forall a b. [a] -> [b] -> [(a, b)]
zip [Int
1 ..] [Int]
componentIs, let d :: StationaryDistribution
d = Vector StationaryDistribution
dsPaml Vector StationaryDistribution -> Int -> StationaryDistribution
forall a. Vector a -> Int -> a
V.! Int
c]
output :: ByteString
output = Builder -> ByteString
BB.toLazyByteString (Builder -> ByteString) -> Builder -> ByteString
forall a b. (a -> b) -> a -> b
$ [Builder] -> Builder
forall a. Monoid a => [a] -> a
mconcat ([Builder] -> Builder) -> [Builder] -> Builder
forall a b. (a -> b) -> a -> b
$ Builder -> [Builder] -> [Builder]
forall a. a -> [a] -> [a]
intersperse (Char -> Builder
BB.char8 Char
'\n') [Builder]
lns
simulateAlignment ::
(HasLength e, HasName a) =>
MP.PhyloModel ->
Tree e a ->
Int ->
GenIO ->
ELynx SimulateArguments ()
simulateAlignment :: PhyloModel
-> Tree e a -> Int -> GenIO -> ELynx SimulateArguments ()
simulateAlignment PhyloModel
pm Tree e a
t' Int
n GenIO
g = do
let t :: Tree Double
t = Length -> Double
fromLength (Length -> Double) -> (e -> Length) -> e -> Double
forall b c a. (b -> c) -> (a -> b) -> a -> c
. e -> Length
forall e. HasLength e => e -> Length
getLen (e -> Double) -> Tree e -> Tree Double
forall (f :: * -> *) a b. Functor f => (a -> b) -> f a -> f b
<$> Tree e a -> Tree e
forall e a. Tree e a -> Tree e
toTreeBranchLabels Tree e a
t'
[[Int]]
leafStates <- case PhyloModel
pm of
MP.SubstitutionModel SubstitutionModel
sm -> IO [[Int]]
-> ReaderT (Arguments SimulateArguments) (LoggingT IO) [[Int]]
forall (m :: * -> *) a. MonadIO m => IO a -> m a
liftIO (IO [[Int]]
-> ReaderT (Arguments SimulateArguments) (LoggingT IO) [[Int]])
-> IO [[Int]]
-> ReaderT (Arguments SimulateArguments) (LoggingT IO) [[Int]]
forall a b. (a -> b) -> a -> b
$ Int
-> StationaryDistribution
-> ExchangeabilityMatrix
-> Tree Double
-> GenIO
-> IO [[Int]]
simulateAndFlattenPar Int
n StationaryDistribution
d ExchangeabilityMatrix
e Tree Double
t GenIO
g
where
d :: StationaryDistribution
d = SubstitutionModel -> StationaryDistribution
MS.stationaryDistribution SubstitutionModel
sm
e :: ExchangeabilityMatrix
e = SubstitutionModel -> ExchangeabilityMatrix
MS.exchangeabilityMatrix SubstitutionModel
sm
MP.MixtureModel MixtureModel
mm -> do
([Int]
cs, [[Int]]
ss) <- IO ([Int], [[Int]])
-> ReaderT
(Arguments SimulateArguments) (LoggingT IO) ([Int], [[Int]])
forall (m :: * -> *) a. MonadIO m => IO a -> m a
liftIO (IO ([Int], [[Int]])
-> ReaderT
(Arguments SimulateArguments) (LoggingT IO) ([Int], [[Int]]))
-> IO ([Int], [[Int]])
-> ReaderT
(Arguments SimulateArguments) (LoggingT IO) ([Int], [[Int]])
forall a b. (a -> b) -> a -> b
$ Int
-> Vector Double
-> Vector StationaryDistribution
-> Vector ExchangeabilityMatrix
-> Tree Double
-> GenIO
-> IO ([Int], [[Int]])
simulateAndFlattenMixtureModelPar Int
n Vector Double
ws Vector StationaryDistribution
ds Vector ExchangeabilityMatrix
es Tree Double
t GenIO
g
[Int]
-> Vector StationaryDistribution -> ELynx SimulateArguments ()
writeSiteDists [Int]
cs Vector StationaryDistribution
ds
[[Int]]
-> ReaderT (Arguments SimulateArguments) (LoggingT IO) [[Int]]
forall (m :: * -> *) a. Monad m => a -> m a
return [[Int]]
ss
where
ws :: Vector Double
ws = MixtureModel -> Vector Double
MM.getWeights MixtureModel
mm
ds :: Vector StationaryDistribution
ds = (SubstitutionModel -> StationaryDistribution)
-> Vector SubstitutionModel -> Vector StationaryDistribution
forall a b. (a -> b) -> Vector a -> Vector b
V.map SubstitutionModel -> StationaryDistribution
MS.stationaryDistribution (Vector SubstitutionModel -> Vector StationaryDistribution)
-> Vector SubstitutionModel -> Vector StationaryDistribution
forall a b. (a -> b) -> a -> b
$ MixtureModel -> Vector SubstitutionModel
MM.getSubstitutionModels MixtureModel
mm
es :: Vector ExchangeabilityMatrix
es = (SubstitutionModel -> ExchangeabilityMatrix)
-> Vector SubstitutionModel -> Vector ExchangeabilityMatrix
forall a b. (a -> b) -> Vector a -> Vector b
V.map SubstitutionModel -> ExchangeabilityMatrix
MS.exchangeabilityMatrix (Vector SubstitutionModel -> Vector ExchangeabilityMatrix)
-> Vector SubstitutionModel -> Vector ExchangeabilityMatrix
forall a b. (a -> b) -> a -> b
$ MixtureModel -> Vector SubstitutionModel
MM.getSubstitutionModels MixtureModel
mm
let leafNames :: [Name]
leafNames = (a -> Name) -> [a] -> [Name]
forall a b. (a -> b) -> [a] -> [b]
map a -> Name
forall a. HasName a => a -> Name
getName ([a] -> [Name]) -> [a] -> [Name]
forall a b. (a -> b) -> a -> b
$ Tree e a -> [a]
forall e a. Tree e a -> [a]
leaves Tree e a
t'
code :: Alphabet
code = PhyloModel -> Alphabet
MP.getAlphabet PhyloModel
pm
alph :: Set Character
alph = AlphabetSpec -> Set Character
A.all (AlphabetSpec -> Set Character) -> AlphabetSpec -> Set Character
forall a b. (a -> b) -> a -> b
$ Alphabet -> AlphabetSpec
alphabetSpec Alphabet
code
sequences :: [Sequence]
sequences =
[ ByteString -> ByteString -> Alphabet -> Characters -> Sequence
Seq.Sequence (Name -> ByteString
fromName Name
sName) ByteString
"" Alphabet
code ([Character] -> Characters
forall a. Unbox a => [a] -> Vector a
U.fromList ([Character] -> Characters) -> [Character] -> Characters
forall a b. (a -> b) -> a -> b
$ (Int -> Character) -> [Int] -> [Character]
forall a b. (a -> b) -> [a] -> [b]
map (Int -> Set Character -> Character
forall a. Int -> Set a -> a
`Set.elemAt` Set Character
alph) [Int]
ss)
| (Name
sName, [Int]
ss) <- [Name] -> [[Int]] -> [(Name, [Int])]
forall a b. [a] -> [b] -> [(a, b)]
zip [Name]
leafNames [[Int]]
leafStates
]
output :: ByteString
output = [Sequence] -> ByteString
sequencesToFasta [Sequence]
sequences
$(Int
FilePath
LogLevel
FilePath -> Text
FilePath -> FilePath -> FilePath -> (Int, Int) -> (Int, Int) -> Loc
Text -> Text
Loc -> Text -> LogLevel -> Text -> ELynx SimulateArguments ()
(Text -> ELynx SimulateArguments ())
-> (Text -> Text) -> Text -> ELynx SimulateArguments ()
forall a. a -> a
forall b c a. (b -> c) -> (a -> b) -> a -> c
forall (m :: * -> *) msg.
(MonadLogger m, ToLogStr msg) =>
Loc -> Text -> LogLevel -> msg -> m ()
pack :: FilePath -> Text
monadLoggerLog :: forall (m :: * -> *) msg.
(MonadLogger m, ToLogStr msg) =>
Loc -> Text -> LogLevel -> msg -> m ()
id :: forall a. a -> a
. :: forall b c a. (b -> c) -> (a -> b) -> a -> c
logInfo) Text
""
FilePath -> ByteString -> FilePath -> ELynx SimulateArguments ()
forall a.
Reproducible a =>
FilePath -> ByteString -> FilePath -> ELynx a ()
out FilePath
"simulated multi sequence alignment" ByteString
output FilePath
".fasta"
summarizeEDMComponents :: [EDMComponent] -> BL.ByteString
summarizeEDMComponents :: [EDMComponent] -> ByteString
summarizeEDMComponents [EDMComponent]
cs =
FilePath -> ByteString
BL.pack (FilePath -> ByteString) -> FilePath -> ByteString
forall a b. (a -> b) -> a -> b
$
FilePath
"Empiricial distribution mixture model with "
FilePath -> FilePath -> FilePath
forall a. [a] -> [a] -> [a]
++ Int -> FilePath
forall a. Show a => a -> FilePath
show ([EDMComponent] -> Int
forall (t :: * -> *) a. Foldable t => t a -> Int
length [EDMComponent]
cs)
FilePath -> FilePath -> FilePath
forall a. [a] -> [a] -> [a]
++ FilePath
" components."
reportModel :: MP.PhyloModel -> ELynx SimulateArguments ()
reportModel :: PhyloModel -> ELynx SimulateArguments ()
reportModel PhyloModel
m = do
GlobalArguments
as <- Arguments SimulateArguments -> GlobalArguments
forall a. Arguments a -> GlobalArguments
global (Arguments SimulateArguments -> GlobalArguments)
-> ReaderT
(Arguments SimulateArguments)
(LoggingT IO)
(Arguments SimulateArguments)
-> ReaderT
(Arguments SimulateArguments) (LoggingT IO) GlobalArguments
forall (f :: * -> *) a b. Functor f => (a -> b) -> f a -> f b
<$> ReaderT
(Arguments SimulateArguments)
(LoggingT IO)
(Arguments SimulateArguments)
forall (m :: * -> *) r. Monad m => ReaderT r m r
ask
if GlobalArguments -> Bool
writeElynxFile GlobalArguments
as
then
( do
let bn :: Maybe FilePath
bn = GlobalArguments -> Maybe FilePath
outFileBaseName GlobalArguments
as
case Maybe FilePath
bn of
Maybe FilePath
Nothing ->
$(Int
FilePath
LogLevel
FilePath -> Text
FilePath -> FilePath -> FilePath -> (Int, Int) -> (Int, Int) -> Loc
Text -> Text
Loc -> Text -> LogLevel -> Text -> ELynx SimulateArguments ()
(Text -> ELynx SimulateArguments ())
-> (Text -> Text) -> Text -> ELynx SimulateArguments ()
forall a. a -> a
forall b c a. (b -> c) -> (a -> b) -> a -> c
forall (m :: * -> *) msg.
(MonadLogger m, ToLogStr msg) =>
Loc -> Text -> LogLevel -> msg -> m ()
pack :: FilePath -> Text
monadLoggerLog :: forall (m :: * -> *) msg.
(MonadLogger m, ToLogStr msg) =>
Loc -> Text -> LogLevel -> msg -> m ()
id :: forall a. a -> a
. :: forall b c a. (b -> c) -> (a -> b) -> a -> c
logInfo)
Text
"No output file provided; omit writing machine-readable phylogenetic model."
Just FilePath
_ ->
FilePath -> ByteString -> FilePath -> ELynx SimulateArguments ()
forall a.
Reproducible a =>
FilePath -> ByteString -> FilePath -> ELynx a ()
out FilePath
"model definition (machine readable)" (FilePath -> ByteString
BL.pack (PhyloModel -> FilePath
forall a. Show a => a -> FilePath
show PhyloModel
m) ByteString -> ByteString -> ByteString
forall a. Semigroup a => a -> a -> a
<> ByteString
"\n") FilePath
".model.gz"
)
else $(Int
FilePath
LogLevel
FilePath -> Text
FilePath -> FilePath -> FilePath -> (Int, Int) -> (Int, Int) -> Loc
Text -> Text
Loc -> Text -> LogLevel -> Text -> ELynx SimulateArguments ()
(Text -> ELynx SimulateArguments ())
-> (Text -> Text) -> Text -> ELynx SimulateArguments ()
forall a. a -> a
forall b c a. (b -> c) -> (a -> b) -> a -> c
forall (m :: * -> *) msg.
(MonadLogger m, ToLogStr msg) =>
Loc -> Text -> LogLevel -> msg -> m ()
pack :: FilePath -> Text
monadLoggerLog :: forall (m :: * -> *) msg.
(MonadLogger m, ToLogStr msg) =>
Loc -> Text -> LogLevel -> msg -> m ()
id :: forall a. a -> a
. :: forall b c a. (b -> c) -> (a -> b) -> a -> c
logInfo) Text
"No elynx file required; omit writing machine-readable phylogenetic model."
pretty :: Length -> String
pretty :: Length -> FilePath
pretty = FilePath -> Double -> FilePath
forall r. PrintfType r => FilePath -> r
printf FilePath
"%.5f" (Double -> FilePath) -> (Length -> Double) -> Length -> FilePath
forall b c a. (b -> c) -> (a -> b) -> a -> c
. Length -> Double
fromLength
prettyRow :: String -> String -> BL.ByteString
prettyRow :: FilePath -> FilePath -> ByteString
prettyRow FilePath
name FilePath
val = Int -> ByteString -> ByteString
alignLeft Int
33 ByteString
n ByteString -> ByteString -> ByteString
forall a. Semigroup a => a -> a -> a
<> Int -> ByteString -> ByteString
alignRight Int
8 ByteString
v
where
n :: ByteString
n = FilePath -> ByteString
BL.pack FilePath
name
v :: ByteString
v = FilePath -> ByteString
BL.pack FilePath
val
summarizeLengths :: HasLength e => Tree e a -> BL.ByteString
summarizeLengths :: Tree e a -> ByteString
summarizeLengths Tree e a
t =
ByteString -> [ByteString] -> ByteString
BL.intercalate
ByteString
"\n"
[ FilePath -> FilePath -> ByteString
prettyRow FilePath
"Origin height: " (FilePath -> ByteString) -> FilePath -> ByteString
forall a b. (a -> b) -> a -> b
$ Length -> FilePath
pretty Length
h,
FilePath -> FilePath -> ByteString
prettyRow FilePath
"Average distance origin to leaves: " (FilePath -> ByteString) -> FilePath -> ByteString
forall a b. (a -> b) -> a -> b
$ Length -> FilePath
pretty Length
h',
FilePath -> FilePath -> ByteString
prettyRow FilePath
"Total branch length: " (FilePath -> ByteString) -> FilePath -> ByteString
forall a b. (a -> b) -> a -> b
$ Length -> FilePath
pretty Length
b
]
where
n :: Int
n = [a] -> Int
forall (t :: * -> *) a. Foldable t => t a -> Int
length ([a] -> Int) -> [a] -> Int
forall a b. (a -> b) -> a -> b
$ Tree e a -> [a]
forall e a. Tree e a -> [a]
leaves Tree e a
t
h :: Length
h = Tree e a -> Length
forall e a. HasLength e => Tree e a -> Length
height Tree e a
t
h' :: Length
h' = [Length] -> Length
forall (t :: * -> *) a. (Foldable t, Num a) => t a -> a
sum (Tree e a -> [Length]
forall e a. HasLength e => Tree e a -> [Length]
distancesOriginLeaves Tree e a
t) Length -> Length -> Length
forall a. Fractional a => a -> a -> a
/ Int -> Length
forall a b. (Integral a, Num b) => a -> b
fromIntegral Int
n
b :: Length
b = Tree e a -> Length
forall e a. HasLength e => Tree e a -> Length
totalBranchLength Tree e a
t
summarizeSM :: MS.SubstitutionModel -> [BL.ByteString]
summarizeSM :: SubstitutionModel -> [ByteString]
summarizeSM SubstitutionModel
sm =
(FilePath -> ByteString) -> [FilePath] -> [ByteString]
forall a b. (a -> b) -> [a] -> [b]
map FilePath -> ByteString
BL.pack ([FilePath] -> [ByteString]) -> [FilePath] -> [ByteString]
forall a b. (a -> b) -> a -> b
$
(Alphabet -> FilePath
forall a. Show a => a -> FilePath
show (SubstitutionModel -> Alphabet
MS.alphabet SubstitutionModel
sm) FilePath -> FilePath -> FilePath
forall a. [a] -> [a] -> [a]
++ FilePath
" substitution model: " FilePath -> FilePath -> FilePath
forall a. [a] -> [a] -> [a]
++ SubstitutionModel -> FilePath
MS.name SubstitutionModel
sm FilePath -> FilePath -> FilePath
forall a. [a] -> [a] -> [a]
++ FilePath
".") FilePath -> [FilePath] -> [FilePath]
forall a. a -> [a] -> [a]
:
[FilePath
"Parameters: " FilePath -> FilePath -> FilePath
forall a. [a] -> [a] -> [a]
++ [Double] -> FilePath
forall a. Show a => a -> FilePath
show (SubstitutionModel -> [Double]
MS.params SubstitutionModel
sm) FilePath -> FilePath -> FilePath
forall a. [a] -> [a] -> [a]
++ FilePath
"." | Bool -> Bool
not ([Double] -> Bool
forall (t :: * -> *) a. Foldable t => t a -> Bool
null (SubstitutionModel -> [Double]
MS.params SubstitutionModel
sm))]
[FilePath] -> [FilePath] -> [FilePath]
forall a. [a] -> [a] -> [a]
++ case SubstitutionModel -> Alphabet
MS.alphabet SubstitutionModel
sm of
Alphabet
DNA ->
[ FilePath
"Stationary distribution: "
FilePath -> FilePath -> FilePath
forall a. [a] -> [a] -> [a]
++ Int -> StationaryDistribution -> FilePath
dispv Int
precision (SubstitutionModel -> StationaryDistribution
MS.stationaryDistribution SubstitutionModel
sm)
FilePath -> FilePath -> FilePath
forall a. [a] -> [a] -> [a]
++ FilePath
".",
FilePath
"Exchangeability matrix:\n"
FilePath -> FilePath -> FilePath
forall a. [a] -> [a] -> [a]
++ Int -> Int -> ExchangeabilityMatrix -> FilePath
dispmi Int
2 Int
precision (SubstitutionModel -> ExchangeabilityMatrix
MS.exchangeabilityMatrix SubstitutionModel
sm)
FilePath -> FilePath -> FilePath
forall a. [a] -> [a] -> [a]
++ FilePath
".",
FilePath
"Scale: " FilePath -> FilePath -> FilePath
forall a. [a] -> [a] -> [a]
++ Double -> FilePath
forall a. Show a => a -> FilePath
show (Int -> Double -> Double
roundN Int
precision (Double -> Double) -> Double -> Double
forall a b. (a -> b) -> a -> b
$ SubstitutionModel -> Double
MS.totalRate SubstitutionModel
sm) FilePath -> FilePath -> FilePath
forall a. [a] -> [a] -> [a]
++ FilePath
"."
]
Alphabet
Protein ->
[ FilePath
"Stationary distribution: "
FilePath -> FilePath -> FilePath
forall a. [a] -> [a] -> [a]
++ Int -> StationaryDistribution -> FilePath
dispv Int
precision (SubstitutionModel -> StationaryDistribution
MS.stationaryDistribution SubstitutionModel
sm)
FilePath -> FilePath -> FilePath
forall a. [a] -> [a] -> [a]
++ FilePath
".",
FilePath
"Scale: " FilePath -> FilePath -> FilePath
forall a. [a] -> [a] -> [a]
++ Double -> FilePath
forall a. Show a => a -> FilePath
show (Int -> Double -> Double
roundN Int
precision (Double -> Double) -> Double -> Double
forall a b. (a -> b) -> a -> b
$ SubstitutionModel -> Double
MS.totalRate SubstitutionModel
sm) FilePath -> FilePath -> FilePath
forall a. [a] -> [a] -> [a]
++ FilePath
"."
]
Alphabet
_ ->
FilePath -> [FilePath]
forall a. HasCallStack => FilePath -> a
error
FilePath
"Extended character sets are not supported with substitution models."
summarizeMMComponent :: MM.Component -> [BL.ByteString]
summarizeMMComponent :: Component -> [ByteString]
summarizeMMComponent Component
c =
FilePath -> ByteString
BL.pack FilePath
"Weight: "
ByteString -> ByteString -> ByteString
forall a. Semigroup a => a -> a -> a
<> (Builder -> ByteString
BB.toLazyByteString (Builder -> ByteString)
-> (Double -> Builder) -> Double -> ByteString
forall b c a. (b -> c) -> (a -> b) -> a -> c
. Double -> Builder
BB.doubleDec (Double -> ByteString) -> Double -> ByteString
forall a b. (a -> b) -> a -> b
$ Component -> Double
MM.weight Component
c) ByteString -> [ByteString] -> [ByteString]
forall a. a -> [a] -> [a]
:
SubstitutionModel -> [ByteString]
summarizeSM (Component -> SubstitutionModel
MM.substModel Component
c)
summarizeMM :: MM.MixtureModel -> [BL.ByteString]
summarizeMM :: MixtureModel -> [ByteString]
summarizeMM MixtureModel
m =
[ FilePath -> ByteString
BL.pack (FilePath -> ByteString) -> FilePath -> ByteString
forall a b. (a -> b) -> a -> b
$ FilePath
"Mixture model: " FilePath -> FilePath -> FilePath
forall a. [a] -> [a] -> [a]
++ MixtureModel -> FilePath
MM.name MixtureModel
m FilePath -> FilePath -> FilePath
forall a. [a] -> [a] -> [a]
++ FilePath
".",
FilePath -> ByteString
BL.pack (FilePath -> ByteString) -> FilePath -> ByteString
forall a b. (a -> b) -> a -> b
$ FilePath
"Number of components: " FilePath -> FilePath -> FilePath
forall a. [a] -> [a] -> [a]
++ Int -> FilePath
forall a. Show a => a -> FilePath
show Int
n FilePath -> FilePath -> FilePath
forall a. [a] -> [a] -> [a]
++ FilePath
"."
]
[ByteString] -> [ByteString] -> [ByteString]
forall a. [a] -> [a] -> [a]
++ [ByteString]
detail
where
n :: Int
n = Vector Component -> Int
forall (t :: * -> *) a. Foldable t => t a -> Int
length (Vector Component -> Int) -> Vector Component -> Int
forall a b. (a -> b) -> a -> b
$ MixtureModel -> Vector Component
MM.components MixtureModel
m
detail :: [ByteString]
detail =
if Int
n Int -> Int -> Bool
forall a. Ord a => a -> a -> Bool
<= Int
100
then
[[ByteString]] -> [ByteString]
forall (t :: * -> *) a. Foldable t => t [a] -> [a]
concat
[ FilePath -> ByteString
BL.pack (FilePath
"Component " FilePath -> FilePath -> FilePath
forall a. [a] -> [a] -> [a]
++ Int -> FilePath
forall a. Show a => a -> FilePath
show Int
i FilePath -> FilePath -> FilePath
forall a. [a] -> [a] -> [a]
++ FilePath
":") ByteString -> [ByteString] -> [ByteString]
forall a. a -> [a] -> [a]
: Component -> [ByteString]
summarizeMMComponent Component
c
| (Int
i, Component
c) <- [Int] -> [Component] -> [(Int, Component)]
forall a b. [a] -> [b] -> [(a, b)]
zip [Int
1 :: Int ..] (Vector Component -> [Component]
forall a. Vector a -> [a]
V.toList (Vector Component -> [Component])
-> Vector Component -> [Component]
forall a b. (a -> b) -> a -> b
$ MixtureModel -> Vector Component
MM.components MixtureModel
m)
]
else []
summarizePM :: MP.PhyloModel -> [BL.ByteString]
summarizePM :: PhyloModel -> [ByteString]
summarizePM (MP.MixtureModel MixtureModel
mm) = MixtureModel -> [ByteString]
summarizeMM MixtureModel
mm
summarizePM (MP.SubstitutionModel SubstitutionModel
sm) = SubstitutionModel -> [ByteString]
summarizeSM SubstitutionModel
sm
simulateCmd :: ELynx SimulateArguments ()
simulateCmd :: ELynx SimulateArguments ()
simulateCmd = do
SimulateArguments
l <- Arguments SimulateArguments -> SimulateArguments
forall a. Arguments a -> a
local (Arguments SimulateArguments -> SimulateArguments)
-> ReaderT
(Arguments SimulateArguments)
(LoggingT IO)
(Arguments SimulateArguments)
-> ReaderT
(Arguments SimulateArguments) (LoggingT IO) SimulateArguments
forall (f :: * -> *) a b. Functor f => (a -> b) -> f a -> f b
<$> ReaderT
(Arguments SimulateArguments)
(LoggingT IO)
(Arguments SimulateArguments)
forall (m :: * -> *) r. Monad m => ReaderT r m r
ask
let treeFile :: FilePath
treeFile = SimulateArguments -> FilePath
argsTreeFile SimulateArguments
l
$(Int
FilePath
LogLevel
FilePath -> Text
FilePath -> FilePath -> FilePath -> (Int, Int) -> (Int, Int) -> Loc
Text -> Text
Loc -> Text -> LogLevel -> Text -> ELynx SimulateArguments ()
(Text -> ELynx SimulateArguments ())
-> (Text -> Text) -> Text -> ELynx SimulateArguments ()
forall a. a -> a
forall b c a. (b -> c) -> (a -> b) -> a -> c
forall (m :: * -> *) msg.
(MonadLogger m, ToLogStr msg) =>
Loc -> Text -> LogLevel -> msg -> m ()
pack :: FilePath -> Text
monadLoggerLog :: forall (m :: * -> *) msg.
(MonadLogger m, ToLogStr msg) =>
Loc -> Text -> LogLevel -> msg -> m ()
id :: forall a. a -> a
. :: forall b c a. (b -> c) -> (a -> b) -> a -> c
logInfo) Text
""
$(Int
FilePath
LogLevel
FilePath -> Text
FilePath -> FilePath -> FilePath -> (Int, Int) -> (Int, Int) -> Loc
Text -> Text
Loc -> Text -> LogLevel -> Text -> ELynx SimulateArguments ()
(Text -> ELynx SimulateArguments ())
-> (Text -> Text) -> Text -> ELynx SimulateArguments ()
forall a. a -> a
forall b c a. (b -> c) -> (a -> b) -> a -> c
forall (m :: * -> *) msg.
(MonadLogger m, ToLogStr msg) =>
Loc -> Text -> LogLevel -> msg -> m ()
pack :: FilePath -> Text
monadLoggerLog :: forall (m :: * -> *) msg.
(MonadLogger m, ToLogStr msg) =>
Loc -> Text -> LogLevel -> msg -> m ()
id :: forall a. a -> a
. :: forall b c a. (b -> c) -> (a -> b) -> a -> c
logInfo) (Text -> ELynx SimulateArguments ())
-> Text -> ELynx SimulateArguments ()
forall a b. (a -> b) -> a -> b
$ FilePath -> Text
T.pack (FilePath -> Text) -> FilePath -> Text
forall a b. (a -> b) -> a -> b
$ FilePath
"Read tree from file '" FilePath -> FilePath -> FilePath
forall a. [a] -> [a] -> [a]
++ FilePath
treeFile FilePath -> FilePath -> FilePath
forall a. [a] -> [a] -> [a]
++ FilePath
"'."
Tree Phylo Name
tree <- IO (Tree Phylo Name)
-> ReaderT
(Arguments SimulateArguments) (LoggingT IO) (Tree Phylo Name)
forall (m :: * -> *) a. MonadIO m => IO a -> m a
liftIO (IO (Tree Phylo Name)
-> ReaderT
(Arguments SimulateArguments) (LoggingT IO) (Tree Phylo Name))
-> IO (Tree Phylo Name)
-> ReaderT
(Arguments SimulateArguments) (LoggingT IO) (Tree Phylo Name)
forall a b. (a -> b) -> a -> b
$ Parser (Tree Phylo Name) -> FilePath -> IO (Tree Phylo Name)
forall a. Parser a -> FilePath -> IO a
parseFileWith (NewickFormat -> Parser (Tree Phylo Name)
newick NewickFormat
Standard) FilePath
treeFile
let t' :: Tree Length Name
t' = (FilePath -> Tree Length Name)
-> (Tree Length Name -> Tree Length Name)
-> Either FilePath (Tree Length Name)
-> Tree Length Name
forall a c b. (a -> c) -> (b -> c) -> Either a b -> c
either FilePath -> Tree Length Name
forall a. HasCallStack => FilePath -> a
error Tree Length Name -> Tree Length Name
forall a. a -> a
id (Either FilePath (Tree Length Name) -> Tree Length Name)
-> Either FilePath (Tree Length Name) -> Tree Length Name
forall a b. (a -> b) -> a -> b
$ Tree Phylo Name -> Either FilePath (Tree Length Name)
forall a. Tree Phylo a -> Either FilePath (Tree Length a)
phyloToLengthTree Tree Phylo Name
tree
$(Int
FilePath
LogLevel
FilePath -> Text
FilePath -> FilePath -> FilePath -> (Int, Int) -> (Int, Int) -> Loc
Text -> Text
Loc -> Text -> LogLevel -> Text -> ELynx SimulateArguments ()
(Text -> ELynx SimulateArguments ())
-> (Text -> Text) -> Text -> ELynx SimulateArguments ()
forall a. a -> a
forall b c a. (b -> c) -> (a -> b) -> a -> c
forall (m :: * -> *) msg.
(MonadLogger m, ToLogStr msg) =>
Loc -> Text -> LogLevel -> msg -> m ()
pack :: FilePath -> Text
monadLoggerLog :: forall (m :: * -> *) msg.
(MonadLogger m, ToLogStr msg) =>
Loc -> Text -> LogLevel -> msg -> m ()
id :: forall a. a -> a
. :: forall b c a. (b -> c) -> (a -> b) -> a -> c
logInfo) (Text -> ELynx SimulateArguments ())
-> Text -> ELynx SimulateArguments ()
forall a b. (a -> b) -> a -> b
$ FilePath -> Text
T.pack (FilePath -> Text) -> FilePath -> Text
forall a b. (a -> b) -> a -> b
$ FilePath
"Number of leaves: " FilePath -> FilePath -> FilePath
forall a. [a] -> [a] -> [a]
++ Int -> FilePath
forall a. Show a => a -> FilePath
show ([Name] -> Int
forall (t :: * -> *) a. Foldable t => t a -> Int
length ([Name] -> Int) -> [Name] -> Int
forall a b. (a -> b) -> a -> b
$ Tree Length Name -> [Name]
forall e a. Tree e a -> [a]
leaves Tree Length Name
t')
$(Int
FilePath
LogLevel
FilePath -> Text
FilePath -> FilePath -> FilePath -> (Int, Int) -> (Int, Int) -> Loc
Text -> Text
Loc -> Text -> LogLevel -> Text -> ELynx SimulateArguments ()
(Text -> ELynx SimulateArguments ())
-> (Text -> Text) -> Text -> ELynx SimulateArguments ()
forall a. a -> a
forall b c a. (b -> c) -> (a -> b) -> a -> c
forall (m :: * -> *) msg.
(MonadLogger m, ToLogStr msg) =>
Loc -> Text -> LogLevel -> msg -> m ()
pack :: FilePath -> Text
monadLoggerLog :: forall (m :: * -> *) msg.
(MonadLogger m, ToLogStr msg) =>
Loc -> Text -> LogLevel -> msg -> m ()
id :: forall a. a -> a
. :: forall b c a. (b -> c) -> (a -> b) -> a -> c
logInfo) (Text -> ELynx SimulateArguments ())
-> Text -> ELynx SimulateArguments ()
forall a b. (a -> b) -> a -> b
$ Text -> Text
LT.toStrict (Text -> Text) -> Text -> Text
forall a b. (a -> b) -> a -> b
$ ByteString -> Text
LT.decodeUtf8 (ByteString -> Text) -> ByteString -> Text
forall a b. (a -> b) -> a -> b
$ Tree Length Name -> ByteString
forall e a. HasLength e => Tree e a -> ByteString
summarizeLengths Tree Length Name
t'
let edmFile :: Maybe FilePath
edmFile = SimulateArguments -> Maybe FilePath
argsEDMFile SimulateArguments
l
let sProfileFiles :: Maybe [FilePath]
sProfileFiles = SimulateArguments -> Maybe [FilePath]
argsSiteprofilesFiles SimulateArguments
l
$(Int
FilePath
LogLevel
FilePath -> Text
FilePath -> FilePath -> FilePath -> (Int, Int) -> (Int, Int) -> Loc
Text -> Text
Loc -> Text -> LogLevel -> Text -> ELynx SimulateArguments ()
(Text -> ELynx SimulateArguments ())
-> (Text -> Text) -> Text -> ELynx SimulateArguments ()
forall a. a -> a
forall b c a. (b -> c) -> (a -> b) -> a -> c
forall (m :: * -> *) msg.
(MonadLogger m, ToLogStr msg) =>
Loc -> Text -> LogLevel -> msg -> m ()
pack :: FilePath -> Text
monadLoggerLog :: forall (m :: * -> *) msg.
(MonadLogger m, ToLogStr msg) =>
Loc -> Text -> LogLevel -> msg -> m ()
id :: forall a. a -> a
. :: forall b c a. (b -> c) -> (a -> b) -> a -> c
logInfo) Text
""
$(Int
FilePath
LogLevel
FilePath -> Text
FilePath -> FilePath -> FilePath -> (Int, Int) -> (Int, Int) -> Loc
Text -> Text
Loc -> Text -> LogLevel -> Text -> ELynx SimulateArguments ()
(Text -> ELynx SimulateArguments ())
-> (Text -> Text) -> Text -> ELynx SimulateArguments ()
forall a. a -> a
forall b c a. (b -> c) -> (a -> b) -> a -> c
forall (m :: * -> *) msg.
(MonadLogger m, ToLogStr msg) =>
Loc -> Text -> LogLevel -> msg -> m ()
pack :: FilePath -> Text
monadLoggerLog :: forall (m :: * -> *) msg.
(MonadLogger m, ToLogStr msg) =>
Loc -> Text -> LogLevel -> msg -> m ()
id :: forall a. a -> a
. :: forall b c a. (b -> c) -> (a -> b) -> a -> c
logDebug) Text
"Read EDM file or siteprofile files."
Bool -> ELynx SimulateArguments () -> ELynx SimulateArguments ()
forall (f :: * -> *). Applicative f => Bool -> f () -> f ()
when (Maybe FilePath -> Bool
forall a. Maybe a -> Bool
isJust Maybe FilePath
edmFile Bool -> Bool -> Bool
&& Maybe [FilePath] -> Bool
forall a. Maybe a -> Bool
isJust Maybe [FilePath]
sProfileFiles) (ELynx SimulateArguments () -> ELynx SimulateArguments ())
-> ELynx SimulateArguments () -> ELynx SimulateArguments ()
forall a b. (a -> b) -> a -> b
$
FilePath -> ELynx SimulateArguments ()
forall a. HasCallStack => FilePath -> a
error FilePath
"Got both: --edm-file and --siteprofile-files."
Maybe [EDMComponent]
edmCs <- case Maybe FilePath
edmFile of
Maybe FilePath
Nothing -> Maybe [EDMComponent]
-> ReaderT
(Arguments SimulateArguments) (LoggingT IO) (Maybe [EDMComponent])
forall (m :: * -> *) a. Monad m => a -> m a
return Maybe [EDMComponent]
forall a. Maybe a
Nothing
Just FilePath
edmF -> do
$(Int
FilePath
LogLevel
FilePath -> Text
FilePath -> FilePath -> FilePath -> (Int, Int) -> (Int, Int) -> Loc
Text -> Text
Loc -> Text -> LogLevel -> Text -> ELynx SimulateArguments ()
(Text -> ELynx SimulateArguments ())
-> (Text -> Text) -> Text -> ELynx SimulateArguments ()
forall a. a -> a
forall b c a. (b -> c) -> (a -> b) -> a -> c
forall (m :: * -> *) msg.
(MonadLogger m, ToLogStr msg) =>
Loc -> Text -> LogLevel -> msg -> m ()
pack :: FilePath -> Text
monadLoggerLog :: forall (m :: * -> *) msg.
(MonadLogger m, ToLogStr msg) =>
Loc -> Text -> LogLevel -> msg -> m ()
id :: forall a. a -> a
. :: forall b c a. (b -> c) -> (a -> b) -> a -> c
logInfo) Text
"Read EDM file."
IO (Maybe [EDMComponent])
-> ReaderT
(Arguments SimulateArguments) (LoggingT IO) (Maybe [EDMComponent])
forall (m :: * -> *) a. MonadIO m => IO a -> m a
liftIO (IO (Maybe [EDMComponent])
-> ReaderT
(Arguments SimulateArguments) (LoggingT IO) (Maybe [EDMComponent]))
-> IO (Maybe [EDMComponent])
-> ReaderT
(Arguments SimulateArguments) (LoggingT IO) (Maybe [EDMComponent])
forall a b. (a -> b) -> a -> b
$ [EDMComponent] -> Maybe [EDMComponent]
forall a. a -> Maybe a
Just ([EDMComponent] -> Maybe [EDMComponent])
-> IO [EDMComponent] -> IO (Maybe [EDMComponent])
forall (f :: * -> *) a b. Functor f => (a -> b) -> f a -> f b
<$> Parser [EDMComponent] -> FilePath -> IO [EDMComponent]
forall a. Parser a -> FilePath -> IO a
parseFileWith Parser [EDMComponent]
phylobayes FilePath
edmF
ELynx SimulateArguments ()
-> ([EDMComponent] -> ELynx SimulateArguments ())
-> Maybe [EDMComponent]
-> ELynx SimulateArguments ()
forall b a. b -> (a -> b) -> Maybe a -> b
maybe
(() -> ELynx SimulateArguments ()
forall (m :: * -> *) a. Monad m => a -> m a
return ())
($(Int
FilePath
LogLevel
FilePath -> Text
FilePath -> FilePath -> FilePath -> (Int, Int) -> (Int, Int) -> Loc
Text -> Text
Loc -> Text -> LogLevel -> Text -> ELynx SimulateArguments ()
(Text -> ELynx SimulateArguments ())
-> (Text -> Text) -> Text -> ELynx SimulateArguments ()
forall a. a -> a
forall b c a. (b -> c) -> (a -> b) -> a -> c
forall (m :: * -> *) msg.
(MonadLogger m, ToLogStr msg) =>
Loc -> Text -> LogLevel -> msg -> m ()
pack :: FilePath -> Text
monadLoggerLog :: forall (m :: * -> *) msg.
(MonadLogger m, ToLogStr msg) =>
Loc -> Text -> LogLevel -> msg -> m ()
id :: forall a. a -> a
. :: forall b c a. (b -> c) -> (a -> b) -> a -> c
logInfo) (Text -> ELynx SimulateArguments ())
-> ([EDMComponent] -> Text)
-> [EDMComponent]
-> ELynx SimulateArguments ()
forall b c a. (b -> c) -> (a -> b) -> a -> c
. Text -> Text
LT.toStrict (Text -> Text)
-> ([EDMComponent] -> Text) -> [EDMComponent] -> Text
forall b c a. (b -> c) -> (a -> b) -> a -> c
. ByteString -> Text
LT.decodeUtf8 (ByteString -> Text)
-> ([EDMComponent] -> ByteString) -> [EDMComponent] -> Text
forall b c a. (b -> c) -> (a -> b) -> a -> c
. [EDMComponent] -> ByteString
summarizeEDMComponents)
Maybe [EDMComponent]
edmCs
Maybe [EDMComponent]
sProfiles <- case Maybe [FilePath]
sProfileFiles of
Maybe [FilePath]
Nothing -> Maybe [EDMComponent]
-> ReaderT
(Arguments SimulateArguments) (LoggingT IO) (Maybe [EDMComponent])
forall (m :: * -> *) a. Monad m => a -> m a
return Maybe [EDMComponent]
forall a. Maybe a
Nothing
Just [FilePath]
fns -> do
$(Int
FilePath
LogLevel
FilePath -> Text
FilePath -> FilePath -> FilePath -> (Int, Int) -> (Int, Int) -> Loc
Text -> Text
Loc -> Text -> LogLevel -> Text -> ELynx SimulateArguments ()
(Text -> ELynx SimulateArguments ())
-> (Text -> Text) -> Text -> ELynx SimulateArguments ()
forall a. a -> a
forall b c a. (b -> c) -> (a -> b) -> a -> c
forall (m :: * -> *) msg.
(MonadLogger m, ToLogStr msg) =>
Loc -> Text -> LogLevel -> msg -> m ()
pack :: FilePath -> Text
monadLoggerLog :: forall (m :: * -> *) msg.
(MonadLogger m, ToLogStr msg) =>
Loc -> Text -> LogLevel -> msg -> m ()
id :: forall a. a -> a
. :: forall b c a. (b -> c) -> (a -> b) -> a -> c
logInfo) (Text -> ELynx SimulateArguments ())
-> Text -> ELynx SimulateArguments ()
forall a b. (a -> b) -> a -> b
$
FilePath -> Text
T.pack (FilePath -> Text) -> FilePath -> Text
forall a b. (a -> b) -> a -> b
$
FilePath
"Read siteprofiles from "
FilePath -> FilePath -> FilePath
forall a. [a] -> [a] -> [a]
++ Int -> FilePath
forall a. Show a => a -> FilePath
show ([FilePath] -> Int
forall (t :: * -> *) a. Foldable t => t a -> Int
length [FilePath]
fns)
FilePath -> FilePath -> FilePath
forall a. [a] -> [a] -> [a]
++ FilePath
" file(s)."
$(Int
FilePath
LogLevel
FilePath -> Text
FilePath -> FilePath -> FilePath -> (Int, Int) -> (Int, Int) -> Loc
Text -> Text
Loc -> Text -> LogLevel -> Text -> ELynx SimulateArguments ()
(Text -> ELynx SimulateArguments ())
-> (Text -> Text) -> Text -> ELynx SimulateArguments ()
forall a. a -> a
forall b c a. (b -> c) -> (a -> b) -> a -> c
forall (m :: * -> *) msg.
(MonadLogger m, ToLogStr msg) =>
Loc -> Text -> LogLevel -> msg -> m ()
pack :: FilePath -> Text
monadLoggerLog :: forall (m :: * -> *) msg.
(MonadLogger m, ToLogStr msg) =>
Loc -> Text -> LogLevel -> msg -> m ()
id :: forall a. a -> a
. :: forall b c a. (b -> c) -> (a -> b) -> a -> c
logDebug) (Text -> ELynx SimulateArguments ())
-> Text -> ELynx SimulateArguments ()
forall a b. (a -> b) -> a -> b
$ FilePath -> Text
T.pack (FilePath -> Text) -> FilePath -> Text
forall a b. (a -> b) -> a -> b
$ FilePath
"The file names are:" FilePath -> FilePath -> FilePath
forall a. [a] -> [a] -> [a]
++ [FilePath] -> FilePath
forall a. Show a => a -> FilePath
show [FilePath]
fns
[[EDMComponent]]
xs <- IO [[EDMComponent]]
-> ReaderT
(Arguments SimulateArguments) (LoggingT IO) [[EDMComponent]]
forall (m :: * -> *) a. MonadIO m => IO a -> m a
liftIO (IO [[EDMComponent]]
-> ReaderT
(Arguments SimulateArguments) (LoggingT IO) [[EDMComponent]])
-> IO [[EDMComponent]]
-> ReaderT
(Arguments SimulateArguments) (LoggingT IO) [[EDMComponent]]
forall a b. (a -> b) -> a -> b
$ (FilePath -> IO [EDMComponent])
-> [FilePath] -> IO [[EDMComponent]]
forall (t :: * -> *) (m :: * -> *) a b.
(Traversable t, Monad m) =>
(a -> m b) -> t a -> m (t b)
mapM (Parser [EDMComponent] -> FilePath -> IO [EDMComponent]
forall a. Parser a -> FilePath -> IO a
parseFileWith Parser [EDMComponent]
siteprofiles) [FilePath]
fns
Maybe [EDMComponent]
-> ReaderT
(Arguments SimulateArguments) (LoggingT IO) (Maybe [EDMComponent])
forall (m :: * -> *) a. Monad m => a -> m a
return (Maybe [EDMComponent]
-> ReaderT
(Arguments SimulateArguments) (LoggingT IO) (Maybe [EDMComponent]))
-> Maybe [EDMComponent]
-> ReaderT
(Arguments SimulateArguments) (LoggingT IO) (Maybe [EDMComponent])
forall a b. (a -> b) -> a -> b
$ [EDMComponent] -> Maybe [EDMComponent]
forall a. a -> Maybe a
Just ([EDMComponent] -> Maybe [EDMComponent])
-> [EDMComponent] -> Maybe [EDMComponent]
forall a b. (a -> b) -> a -> b
$ [[EDMComponent]] -> [EDMComponent]
forall (t :: * -> *) a. Foldable t => t [a] -> [a]
concat [[EDMComponent]]
xs
ELynx SimulateArguments ()
-> ([EDMComponent] -> ELynx SimulateArguments ())
-> Maybe [EDMComponent]
-> ELynx SimulateArguments ()
forall b a. b -> (a -> b) -> Maybe a -> b
maybe
(() -> ELynx SimulateArguments ()
forall (m :: * -> *) a. Monad m => a -> m a
return ())
($(Int
FilePath
LogLevel
FilePath -> Text
FilePath -> FilePath -> FilePath -> (Int, Int) -> (Int, Int) -> Loc
Text -> Text
Loc -> Text -> LogLevel -> Text -> ELynx SimulateArguments ()
(Text -> ELynx SimulateArguments ())
-> (Text -> Text) -> Text -> ELynx SimulateArguments ()
forall a. a -> a
forall b c a. (b -> c) -> (a -> b) -> a -> c
forall (m :: * -> *) msg.
(MonadLogger m, ToLogStr msg) =>
Loc -> Text -> LogLevel -> msg -> m ()
pack :: FilePath -> Text
monadLoggerLog :: forall (m :: * -> *) msg.
(MonadLogger m, ToLogStr msg) =>
Loc -> Text -> LogLevel -> msg -> m ()
id :: forall a. a -> a
. :: forall b c a. (b -> c) -> (a -> b) -> a -> c
logInfo) (Text -> ELynx SimulateArguments ())
-> ([EDMComponent] -> Text)
-> [EDMComponent]
-> ELynx SimulateArguments ()
forall b c a. (b -> c) -> (a -> b) -> a -> c
. Text -> Text
LT.toStrict (Text -> Text)
-> ([EDMComponent] -> Text) -> [EDMComponent] -> Text
forall b c a. (b -> c) -> (a -> b) -> a -> c
. ByteString -> Text
LT.decodeUtf8 (ByteString -> Text)
-> ([EDMComponent] -> ByteString) -> [EDMComponent] -> Text
forall b c a. (b -> c) -> (a -> b) -> a -> c
. [EDMComponent] -> ByteString
summarizeEDMComponents)
Maybe [EDMComponent]
sProfiles
let edmCsOrSiteprofiles :: Maybe [EDMComponent]
edmCsOrSiteprofiles = Maybe [EDMComponent]
edmCs Maybe [EDMComponent]
-> Maybe [EDMComponent] -> Maybe [EDMComponent]
forall (f :: * -> *) a. Alternative f => f a -> f a -> f a
<|> Maybe [EDMComponent]
sProfiles
$(Int
FilePath
LogLevel
FilePath -> Text
FilePath -> FilePath -> FilePath -> (Int, Int) -> (Int, Int) -> Loc
Text -> Text
Loc -> Text -> LogLevel -> Text -> ELynx SimulateArguments ()
(Text -> ELynx SimulateArguments ())
-> (Text -> Text) -> Text -> ELynx SimulateArguments ()
forall a. a -> a
forall b c a. (b -> c) -> (a -> b) -> a -> c
forall (m :: * -> *) msg.
(MonadLogger m, ToLogStr msg) =>
Loc -> Text -> LogLevel -> msg -> m ()
pack :: FilePath -> Text
monadLoggerLog :: forall (m :: * -> *) msg.
(MonadLogger m, ToLogStr msg) =>
Loc -> Text -> LogLevel -> msg -> m ()
id :: forall a. a -> a
. :: forall b c a. (b -> c) -> (a -> b) -> a -> c
logInfo) Text
"Read model string."
let ms :: Maybe FilePath
ms = SimulateArguments -> Maybe FilePath
argsSubstitutionModelString SimulateArguments
l
mm :: Maybe FilePath
mm = SimulateArguments -> Maybe FilePath
argsMixtureModelString SimulateArguments
l
mws :: Maybe [Double]
mws = SimulateArguments -> Maybe [Double]
argsMixtureWeights SimulateArguments
l
eitherPhyloModel' :: Either FilePath PhyloModel
eitherPhyloModel' = Maybe FilePath
-> Maybe FilePath
-> Maybe [Double]
-> Maybe [EDMComponent]
-> Either FilePath PhyloModel
getPhyloModel Maybe FilePath
ms Maybe FilePath
mm Maybe [Double]
mws Maybe [EDMComponent]
edmCsOrSiteprofiles
PhyloModel
phyloModel' <- case Either FilePath PhyloModel
eitherPhyloModel' of
Left FilePath
err -> LoggingT IO PhyloModel
-> ReaderT (Arguments SimulateArguments) (LoggingT IO) PhyloModel
forall (t :: (* -> *) -> * -> *) (m :: * -> *) a.
(MonadTrans t, Monad m) =>
m a -> t m a
lift (LoggingT IO PhyloModel
-> ReaderT (Arguments SimulateArguments) (LoggingT IO) PhyloModel)
-> LoggingT IO PhyloModel
-> ReaderT (Arguments SimulateArguments) (LoggingT IO) PhyloModel
forall a b. (a -> b) -> a -> b
$ FilePath -> LoggingT IO PhyloModel
forall a. HasCallStack => FilePath -> a
error FilePath
err
Right PhyloModel
pm -> PhyloModel
-> ReaderT (Arguments SimulateArguments) (LoggingT IO) PhyloModel
forall (m :: * -> *) a. Monad m => a -> m a
return PhyloModel
pm
let maybeGammaParams :: Maybe GammaRateHeterogeneityParams
maybeGammaParams = SimulateArguments -> Maybe GammaRateHeterogeneityParams
argsGammaParams SimulateArguments
l
PhyloModel
phyloModel <- case Maybe GammaRateHeterogeneityParams
maybeGammaParams of
Maybe GammaRateHeterogeneityParams
Nothing -> do
$(Int
FilePath
LogLevel
FilePath -> Text
FilePath -> FilePath -> FilePath -> (Int, Int) -> (Int, Int) -> Loc
Text -> Text
Loc -> Text -> LogLevel -> Text -> ELynx SimulateArguments ()
(Text -> ELynx SimulateArguments ())
-> (Text -> Text) -> Text -> ELynx SimulateArguments ()
forall a. a -> a
forall b c a. (b -> c) -> (a -> b) -> a -> c
forall (m :: * -> *) msg.
(MonadLogger m, ToLogStr msg) =>
Loc -> Text -> LogLevel -> msg -> m ()
pack :: FilePath -> Text
monadLoggerLog :: forall (m :: * -> *) msg.
(MonadLogger m, ToLogStr msg) =>
Loc -> Text -> LogLevel -> msg -> m ()
id :: forall a. a -> a
. :: forall b c a. (b -> c) -> (a -> b) -> a -> c
logInfo) (Text -> ELynx SimulateArguments ())
-> Text -> ELynx SimulateArguments ()
forall a b. (a -> b) -> a -> b
$
Text -> Text
LT.toStrict (Text -> Text) -> Text -> Text
forall a b. (a -> b) -> a -> b
$
ByteString -> Text
LT.decodeUtf8 (ByteString -> Text) -> ByteString -> Text
forall a b. (a -> b) -> a -> b
$
[ByteString] -> ByteString
BL.unlines ([ByteString] -> ByteString) -> [ByteString] -> ByteString
forall a b. (a -> b) -> a -> b
$
PhyloModel -> [ByteString]
summarizePM
PhyloModel
phyloModel'
PhyloModel
-> ReaderT (Arguments SimulateArguments) (LoggingT IO) PhyloModel
forall (m :: * -> *) a. Monad m => a -> m a
return PhyloModel
phyloModel'
Just (Int
n, Double
alpha) -> do
$(Int
FilePath
LogLevel
FilePath -> Text
FilePath -> FilePath -> FilePath -> (Int, Int) -> (Int, Int) -> Loc
Text -> Text
Loc -> Text -> LogLevel -> Text -> ELynx SimulateArguments ()
(Text -> ELynx SimulateArguments ())
-> (Text -> Text) -> Text -> ELynx SimulateArguments ()
forall a. a -> a
forall b c a. (b -> c) -> (a -> b) -> a -> c
forall (m :: * -> *) msg.
(MonadLogger m, ToLogStr msg) =>
Loc -> Text -> LogLevel -> msg -> m ()
pack :: FilePath -> Text
monadLoggerLog :: forall (m :: * -> *) msg.
(MonadLogger m, ToLogStr msg) =>
Loc -> Text -> LogLevel -> msg -> m ()
id :: forall a. a -> a
. :: forall b c a. (b -> c) -> (a -> b) -> a -> c
logInfo) (Text -> ELynx SimulateArguments ())
-> Text -> ELynx SimulateArguments ()
forall a b. (a -> b) -> a -> b
$
Text -> Text
LT.toStrict (Text -> Text) -> Text -> Text
forall a b. (a -> b) -> a -> b
$
ByteString -> Text
LT.decodeUtf8 (ByteString -> Text) -> ByteString -> Text
forall a b. (a -> b) -> a -> b
$
ByteString -> [ByteString] -> ByteString
BL.intercalate ByteString
"\n" ([ByteString] -> ByteString) -> [ByteString] -> ByteString
forall a b. (a -> b) -> a -> b
$
PhyloModel -> [ByteString]
summarizePM PhyloModel
phyloModel'
$(Int
FilePath
LogLevel
FilePath -> Text
FilePath -> FilePath -> FilePath -> (Int, Int) -> (Int, Int) -> Loc
Text -> Text
Loc -> Text -> LogLevel -> Text -> ELynx SimulateArguments ()
(Text -> ELynx SimulateArguments ())
-> (Text -> Text) -> Text -> ELynx SimulateArguments ()
forall a. a -> a
forall b c a. (b -> c) -> (a -> b) -> a -> c
forall (m :: * -> *) msg.
(MonadLogger m, ToLogStr msg) =>
Loc -> Text -> LogLevel -> msg -> m ()
pack :: FilePath -> Text
monadLoggerLog :: forall (m :: * -> *) msg.
(MonadLogger m, ToLogStr msg) =>
Loc -> Text -> LogLevel -> msg -> m ()
id :: forall a. a -> a
. :: forall b c a. (b -> c) -> (a -> b) -> a -> c
logInfo) Text
""
$(Int
FilePath
LogLevel
FilePath -> Text
FilePath -> FilePath -> FilePath -> (Int, Int) -> (Int, Int) -> Loc
Text -> Text
Loc -> Text -> LogLevel -> Text -> ELynx SimulateArguments ()
(Text -> ELynx SimulateArguments ())
-> (Text -> Text) -> Text -> ELynx SimulateArguments ()
forall a. a -> a
forall b c a. (b -> c) -> (a -> b) -> a -> c
forall (m :: * -> *) msg.
(MonadLogger m, ToLogStr msg) =>
Loc -> Text -> LogLevel -> msg -> m ()
pack :: FilePath -> Text
monadLoggerLog :: forall (m :: * -> *) msg.
(MonadLogger m, ToLogStr msg) =>
Loc -> Text -> LogLevel -> msg -> m ()
id :: forall a. a -> a
. :: forall b c a. (b -> c) -> (a -> b) -> a -> c
logInfo) (Text -> ELynx SimulateArguments ())
-> Text -> ELynx SimulateArguments ()
forall a b. (a -> b) -> a -> b
$
Text -> Text
LT.toStrict (Text -> Text) -> Text -> Text
forall a b. (a -> b) -> a -> b
$
ByteString -> Text
LT.decodeUtf8 (ByteString -> Text) -> ByteString -> Text
forall a b. (a -> b) -> a -> b
$
ByteString -> [ByteString] -> ByteString
BL.intercalate ByteString
"\n" ([ByteString] -> ByteString) -> [ByteString] -> ByteString
forall a b. (a -> b) -> a -> b
$
Int -> Double -> [ByteString]
summarizeGammaRateHeterogeneity Int
n Double
alpha
PhyloModel
-> ReaderT (Arguments SimulateArguments) (LoggingT IO) PhyloModel
forall (m :: * -> *) a. Monad m => a -> m a
return (PhyloModel
-> ReaderT (Arguments SimulateArguments) (LoggingT IO) PhyloModel)
-> PhyloModel
-> ReaderT (Arguments SimulateArguments) (LoggingT IO) PhyloModel
forall a b. (a -> b) -> a -> b
$ Int -> Double -> PhyloModel -> PhyloModel
expand Int
n Double
alpha PhyloModel
phyloModel'
PhyloModel -> ELynx SimulateArguments ()
reportModel PhyloModel
phyloModel
$(Int
FilePath
LogLevel
FilePath -> Text
FilePath -> FilePath -> FilePath -> (Int, Int) -> (Int, Int) -> Loc
Text -> Text
Loc -> Text -> LogLevel -> Text -> ELynx SimulateArguments ()
(Text -> ELynx SimulateArguments ())
-> (Text -> Text) -> Text -> ELynx SimulateArguments ()
forall a. a -> a
forall b c a. (b -> c) -> (a -> b) -> a -> c
forall (m :: * -> *) msg.
(MonadLogger m, ToLogStr msg) =>
Loc -> Text -> LogLevel -> msg -> m ()
pack :: FilePath -> Text
monadLoggerLog :: forall (m :: * -> *) msg.
(MonadLogger m, ToLogStr msg) =>
Loc -> Text -> LogLevel -> msg -> m ()
id :: forall a. a -> a
. :: forall b c a. (b -> c) -> (a -> b) -> a -> c
logInfo) Text
"Simulate alignment."
let alignmentLength :: Int
alignmentLength = SimulateArguments -> Int
argsLength SimulateArguments
l
$(Int
FilePath
LogLevel
FilePath -> Text
FilePath -> FilePath -> FilePath -> (Int, Int) -> (Int, Int) -> Loc
Text -> Text
Loc -> Text -> LogLevel -> Text -> ELynx SimulateArguments ()
(Text -> ELynx SimulateArguments ())
-> (Text -> Text) -> Text -> ELynx SimulateArguments ()
forall a. a -> a
forall b c a. (b -> c) -> (a -> b) -> a -> c
forall (m :: * -> *) msg.
(MonadLogger m, ToLogStr msg) =>
Loc -> Text -> LogLevel -> msg -> m ()
pack :: FilePath -> Text
monadLoggerLog :: forall (m :: * -> *) msg.
(MonadLogger m, ToLogStr msg) =>
Loc -> Text -> LogLevel -> msg -> m ()
id :: forall a. a -> a
. :: forall b c a. (b -> c) -> (a -> b) -> a -> c
logInfo) (Text -> ELynx SimulateArguments ())
-> Text -> ELynx SimulateArguments ()
forall a b. (a -> b) -> a -> b
$ FilePath -> Text
T.pack (FilePath -> Text) -> FilePath -> Text
forall a b. (a -> b) -> a -> b
$ FilePath
"Length: " FilePath -> FilePath -> FilePath
forall a. Semigroup a => a -> a -> a
<> Int -> FilePath
forall a. Show a => a -> FilePath
show Int
alignmentLength FilePath -> FilePath -> FilePath
forall a. Semigroup a => a -> a -> a
<> FilePath
"."
Gen RealWorld
gen <- case SimulateArguments -> Seed
argsSeed SimulateArguments
l of
Seed
Random -> FilePath
-> ReaderT
(Arguments SimulateArguments) (LoggingT IO) (Gen RealWorld)
forall a. HasCallStack => FilePath -> a
error FilePath
"simulateCmd: seed not available; please contact maintainer."
Fixed Vector Word32
s -> IO (Gen RealWorld)
-> ReaderT
(Arguments SimulateArguments) (LoggingT IO) (Gen RealWorld)
forall (m :: * -> *) a. MonadIO m => IO a -> m a
liftIO (IO (Gen RealWorld)
-> ReaderT
(Arguments SimulateArguments) (LoggingT IO) (Gen RealWorld))
-> IO (Gen RealWorld)
-> ReaderT
(Arguments SimulateArguments) (LoggingT IO) (Gen RealWorld)
forall a b. (a -> b) -> a -> b
$ Vector Word32 -> IO GenIO
forall (m :: * -> *) (v :: * -> *).
(PrimMonad m, Vector v Word32) =>
v Word32 -> m (Gen (PrimState m))
initialize Vector Word32
s
PhyloModel
-> Tree Length Name -> Int -> GenIO -> ELynx SimulateArguments ()
forall e a.
(HasLength e, HasName a) =>
PhyloModel
-> Tree e a -> Int -> GenIO -> ELynx SimulateArguments ()
simulateAlignment PhyloModel
phyloModel Tree Length Name
t' Int
alignmentLength Gen RealWorld
GenIO
gen