{-# LANGUAGE DeriveGeneric #-}
module SLynx.Simulate.Options
( GammaRateHeterogeneityParams,
MixtureModelGlobalNormalization (..),
SimulateArguments (..),
simulateArguments,
simulateFooter,
)
where
import Data.Aeson
import Data.Maybe
( fromMaybe,
maybeToList,
)
import ELynx.Tools.Options
import ELynx.Tools.Reproduction
import GHC.Generics
import Options.Applicative
type GammaRateHeterogeneityParams = (Int, Double)
data MixtureModelGlobalNormalization = GlobalNormalization | LocalNormalization
deriving (Int -> MixtureModelGlobalNormalization -> ShowS
[MixtureModelGlobalNormalization] -> ShowS
MixtureModelGlobalNormalization -> FilePath
forall a.
(Int -> a -> ShowS) -> (a -> FilePath) -> ([a] -> ShowS) -> Show a
showList :: [MixtureModelGlobalNormalization] -> ShowS
$cshowList :: [MixtureModelGlobalNormalization] -> ShowS
show :: MixtureModelGlobalNormalization -> FilePath
$cshow :: MixtureModelGlobalNormalization -> FilePath
showsPrec :: Int -> MixtureModelGlobalNormalization -> ShowS
$cshowsPrec :: Int -> MixtureModelGlobalNormalization -> ShowS
Show, ReadPrec [MixtureModelGlobalNormalization]
ReadPrec MixtureModelGlobalNormalization
Int -> ReadS MixtureModelGlobalNormalization
ReadS [MixtureModelGlobalNormalization]
forall a.
(Int -> ReadS a)
-> ReadS [a] -> ReadPrec a -> ReadPrec [a] -> Read a
readListPrec :: ReadPrec [MixtureModelGlobalNormalization]
$creadListPrec :: ReadPrec [MixtureModelGlobalNormalization]
readPrec :: ReadPrec MixtureModelGlobalNormalization
$creadPrec :: ReadPrec MixtureModelGlobalNormalization
readList :: ReadS [MixtureModelGlobalNormalization]
$creadList :: ReadS [MixtureModelGlobalNormalization]
readsPrec :: Int -> ReadS MixtureModelGlobalNormalization
$creadsPrec :: Int -> ReadS MixtureModelGlobalNormalization
Read, MixtureModelGlobalNormalization
-> MixtureModelGlobalNormalization -> Bool
forall a. (a -> a -> Bool) -> (a -> a -> Bool) -> Eq a
/= :: MixtureModelGlobalNormalization
-> MixtureModelGlobalNormalization -> Bool
$c/= :: MixtureModelGlobalNormalization
-> MixtureModelGlobalNormalization -> Bool
== :: MixtureModelGlobalNormalization
-> MixtureModelGlobalNormalization -> Bool
$c== :: MixtureModelGlobalNormalization
-> MixtureModelGlobalNormalization -> Bool
Eq, forall x.
Rep MixtureModelGlobalNormalization x
-> MixtureModelGlobalNormalization
forall x.
MixtureModelGlobalNormalization
-> Rep MixtureModelGlobalNormalization x
forall a.
(forall x. a -> Rep a x) -> (forall x. Rep a x -> a) -> Generic a
$cto :: forall x.
Rep MixtureModelGlobalNormalization x
-> MixtureModelGlobalNormalization
$cfrom :: forall x.
MixtureModelGlobalNormalization
-> Rep MixtureModelGlobalNormalization x
Generic)
instance FromJSON MixtureModelGlobalNormalization
instance ToJSON MixtureModelGlobalNormalization
data SimulateArguments = SimulateArguments
{ SimulateArguments -> FilePath
argsTreeFile :: FilePath,
SimulateArguments -> Maybe FilePath
argsSubstitutionModelString :: Maybe String,
SimulateArguments -> Maybe FilePath
argsMixtureModelString :: Maybe String,
SimulateArguments -> MixtureModelGlobalNormalization
argsMixtureModelGlobalNormalization :: MixtureModelGlobalNormalization,
SimulateArguments -> Maybe FilePath
argsEDMFile :: Maybe FilePath,
SimulateArguments -> Maybe [FilePath]
argsSiteprofilesFiles :: Maybe [FilePath],
SimulateArguments -> Maybe [Double]
argsMixtureWeights :: Maybe [Double],
SimulateArguments -> Maybe GammaRateHeterogeneityParams
argsGammaParams :: Maybe GammaRateHeterogeneityParams,
SimulateArguments -> Int
argsLength :: Int,
SimulateArguments -> SeedOpt
argsSeed :: SeedOpt
}
deriving (SimulateArguments -> SimulateArguments -> Bool
forall a. (a -> a -> Bool) -> (a -> a -> Bool) -> Eq a
/= :: SimulateArguments -> SimulateArguments -> Bool
$c/= :: SimulateArguments -> SimulateArguments -> Bool
== :: SimulateArguments -> SimulateArguments -> Bool
$c== :: SimulateArguments -> SimulateArguments -> Bool
Eq, Int -> SimulateArguments -> ShowS
[SimulateArguments] -> ShowS
SimulateArguments -> FilePath
forall a.
(Int -> a -> ShowS) -> (a -> FilePath) -> ([a] -> ShowS) -> Show a
showList :: [SimulateArguments] -> ShowS
$cshowList :: [SimulateArguments] -> ShowS
show :: SimulateArguments -> FilePath
$cshow :: SimulateArguments -> FilePath
showsPrec :: Int -> SimulateArguments -> ShowS
$cshowsPrec :: Int -> SimulateArguments -> ShowS
Show, forall x. Rep SimulateArguments x -> SimulateArguments
forall x. SimulateArguments -> Rep SimulateArguments x
forall a.
(forall x. a -> Rep a x) -> (forall x. Rep a x -> a) -> Generic a
$cto :: forall x. Rep SimulateArguments x -> SimulateArguments
$cfrom :: forall x. SimulateArguments -> Rep SimulateArguments x
Generic)
instance Reproducible SimulateArguments where
inFiles :: SimulateArguments -> [FilePath]
inFiles SimulateArguments
a =
SimulateArguments -> FilePath
argsTreeFile SimulateArguments
a
forall a. a -> [a] -> [a]
: (forall a. Maybe a -> [a]
maybeToList (SimulateArguments -> Maybe FilePath
argsEDMFile SimulateArguments
a) forall a. [a] -> [a] -> [a]
++ forall a. a -> Maybe a -> a
fromMaybe [] (SimulateArguments -> Maybe [FilePath]
argsSiteprofilesFiles SimulateArguments
a))
outSuffixes :: SimulateArguments -> [FilePath]
outSuffixes SimulateArguments
_ = [FilePath
".model.gz", FilePath
".fasta"]
getSeed :: SimulateArguments -> Maybe SeedOpt
getSeed = forall a. a -> Maybe a
Just forall b c a. (b -> c) -> (a -> b) -> a -> c
. SimulateArguments -> SeedOpt
argsSeed
setSeed :: SimulateArguments -> SeedOpt -> SimulateArguments
setSeed SimulateArguments
a SeedOpt
s = SimulateArguments
a {argsSeed :: SeedOpt
argsSeed = SeedOpt
s}
parser :: Parser SimulateArguments
parser = Parser SimulateArguments
simulateArguments
cmdName :: FilePath
cmdName = FilePath
"simulate"
cmdDsc :: [FilePath]
cmdDsc = [FilePath
"Simulate multi sequence alignments."]
cmdFtr :: [FilePath]
cmdFtr = [FilePath]
simulateFooter
instance FromJSON SimulateArguments
instance ToJSON SimulateArguments
simulateArguments :: Parser SimulateArguments
simulateArguments :: Parser SimulateArguments
simulateArguments =
FilePath
-> Maybe FilePath
-> Maybe FilePath
-> MixtureModelGlobalNormalization
-> Maybe FilePath
-> Maybe [FilePath]
-> Maybe [Double]
-> Maybe GammaRateHeterogeneityParams
-> Int
-> SeedOpt
-> SimulateArguments
SimulateArguments
forall (f :: * -> *) a b. Functor f => (a -> b) -> f a -> f b
<$> Parser FilePath
treeFileOpt
forall (f :: * -> *) a b. Applicative f => f (a -> b) -> f a -> f b
<*> Parser (Maybe FilePath)
phyloSubstitutionModelOpt
forall (f :: * -> *) a b. Applicative f => f (a -> b) -> f a -> f b
<*> Parser (Maybe FilePath)
phyloMixtureModelOpt
forall (f :: * -> *) a b. Applicative f => f (a -> b) -> f a -> f b
<*> Parser MixtureModelGlobalNormalization
globalNormalizationFlag
forall (f :: * -> *) a b. Applicative f => f (a -> b) -> f a -> f b
<*> Parser (Maybe FilePath)
maybeEDMFileOpt
forall (f :: * -> *) a b. Applicative f => f (a -> b) -> f a -> f b
<*> Parser (Maybe [FilePath])
maybeSiteprofilesFilesOpt
forall (f :: * -> *) a b. Applicative f => f (a -> b) -> f a -> f b
<*> Parser (Maybe [Double])
maybeMixtureWeights
forall (f :: * -> *) a b. Applicative f => f (a -> b) -> f a -> f b
<*> Parser (Maybe GammaRateHeterogeneityParams)
maybeGammaParams
forall (f :: * -> *) a b. Applicative f => f (a -> b) -> f a -> f b
<*> Parser Int
lengthOpt
forall (f :: * -> *) a b. Applicative f => f (a -> b) -> f a -> f b
<*> Parser SeedOpt
seedOpt
treeFileOpt :: Parser FilePath
treeFileOpt :: Parser FilePath
treeFileOpt =
forall s. IsString s => Mod OptionFields s -> Parser s
strOption forall a b. (a -> b) -> a -> b
$
forall (f :: * -> *) a. HasName f => FilePath -> Mod f a
long FilePath
"tree-file"
forall a. Semigroup a => a -> a -> a
<> forall (f :: * -> *) a. HasName f => Char -> Mod f a
short Char
't'
forall a. Semigroup a => a -> a -> a
<> forall (f :: * -> *) a. HasMetavar f => FilePath -> Mod f a
metavar FilePath
"Name"
forall a. Semigroup a => a -> a -> a
<> forall (f :: * -> *) a. FilePath -> Mod f a
help
FilePath
"Read tree from Newick file NAME"
phyloSubstitutionModelOpt :: Parser (Maybe String)
phyloSubstitutionModelOpt :: Parser (Maybe FilePath)
phyloSubstitutionModelOpt =
forall (f :: * -> *) a. Alternative f => f a -> f (Maybe a)
optional forall a b. (a -> b) -> a -> b
$
forall s. IsString s => Mod OptionFields s -> Parser s
strOption forall a b. (a -> b) -> a -> b
$
forall (f :: * -> *) a. HasName f => FilePath -> Mod f a
long FilePath
"substitution-model"
forall a. Semigroup a => a -> a -> a
<> forall (f :: * -> *) a. HasName f => Char -> Mod f a
short Char
's'
forall a. Semigroup a => a -> a -> a
<> forall (f :: * -> *) a. HasMetavar f => FilePath -> Mod f a
metavar FilePath
"MODEL"
forall a. Semigroup a => a -> a -> a
<> forall (f :: * -> *) a. FilePath -> Mod f a
help
FilePath
"Set the phylogenetic substitution model; available models are shown below (mutually exclusive with -m option)"
phyloMixtureModelOpt :: Parser (Maybe String)
phyloMixtureModelOpt :: Parser (Maybe FilePath)
phyloMixtureModelOpt =
forall (f :: * -> *) a. Alternative f => f a -> f (Maybe a)
optional forall a b. (a -> b) -> a -> b
$
forall s. IsString s => Mod OptionFields s -> Parser s
strOption
( forall (f :: * -> *) a. HasName f => FilePath -> Mod f a
long FilePath
"mixture-model"
forall a. Semigroup a => a -> a -> a
<> forall (f :: * -> *) a. HasName f => Char -> Mod f a
short Char
'm'
forall a. Semigroup a => a -> a -> a
<> forall (f :: * -> *) a. HasMetavar f => FilePath -> Mod f a
metavar FilePath
"MODEL"
forall a. Semigroup a => a -> a -> a
<> forall (f :: * -> *) a. FilePath -> Mod f a
help
FilePath
"Set the phylogenetic mixture model; available models are shown below (mutually exclusive with -s option)"
)
globalNormalizationFlag :: Parser MixtureModelGlobalNormalization
globalNormalizationFlag :: Parser MixtureModelGlobalNormalization
globalNormalizationFlag =
forall a. a -> a -> Mod FlagFields a -> Parser a
flag
MixtureModelGlobalNormalization
LocalNormalization
MixtureModelGlobalNormalization
GlobalNormalization
( forall (f :: * -> *) a. HasName f => FilePath -> Mod f a
long FilePath
"global-normalization"
forall a. Semigroup a => a -> a -> a
<> forall (f :: * -> *) a. HasName f => Char -> Mod f a
short Char
'n'
forall a. Semigroup a => a -> a -> a
<> forall (f :: * -> *) a. FilePath -> Mod f a
help FilePath
"Normalize mixture model globally (one normalization constant for all components)"
)
maybeEDMFileOpt :: Parser (Maybe FilePath)
maybeEDMFileOpt :: Parser (Maybe FilePath)
maybeEDMFileOpt =
forall (f :: * -> *) a. Alternative f => f a -> f (Maybe a)
optional forall a b. (a -> b) -> a -> b
$
forall s. IsString s => Mod OptionFields s -> Parser s
strOption
( forall (f :: * -> *) a. HasName f => FilePath -> Mod f a
long FilePath
"edm-file"
forall a. Semigroup a => a -> a -> a
<> forall (f :: * -> *) a. HasName f => Char -> Mod f a
short Char
'e'
forall a. Semigroup a => a -> a -> a
<> forall (f :: * -> *) a. HasMetavar f => FilePath -> Mod f a
metavar FilePath
"NAME"
forall a. Semigroup a => a -> a -> a
<> forall (f :: * -> *) a. FilePath -> Mod f a
help
FilePath
"Empirical distribution model file NAME in Phylobayes format"
)
maybeSiteprofilesFilesOpt :: Parser (Maybe [FilePath])
maybeSiteprofilesFilesOpt :: Parser (Maybe [FilePath])
maybeSiteprofilesFilesOpt =
forall (f :: * -> *) a. Alternative f => f a -> f (Maybe a)
optional forall a b. (a -> b) -> a -> b
$
FilePath -> [FilePath]
words
forall (f :: * -> *) a b. Functor f => (a -> b) -> f a -> f b
<$> forall s. IsString s => Mod OptionFields s -> Parser s
strOption
( forall (f :: * -> *) a. HasName f => FilePath -> Mod f a
long FilePath
"siteprofile-files"
forall a. Semigroup a => a -> a -> a
<> forall (f :: * -> *) a. HasName f => Char -> Mod f a
short Char
'p'
forall a. Semigroup a => a -> a -> a
<> forall (f :: * -> *) a. HasMetavar f => FilePath -> Mod f a
metavar FilePath
"NAMES"
forall a. Semigroup a => a -> a -> a
<> forall (f :: * -> *) a. FilePath -> Mod f a
help
FilePath
"File names of site profiles in Phylobayes format"
)
maybeMixtureWeights :: Parser (Maybe [Double])
maybeMixtureWeights :: Parser (Maybe [Double])
maybeMixtureWeights =
forall (f :: * -> *) a. Alternative f => f a -> f (Maybe a)
optional forall a b. (a -> b) -> a -> b
$
forall a. ReadM a -> Mod OptionFields a -> Parser a
option
forall a. Read a => ReadM a
auto
( forall (f :: * -> *) a. HasName f => FilePath -> Mod f a
long FilePath
"mixture-model-weights"
forall a. Semigroup a => a -> a -> a
<> forall (f :: * -> *) a. HasName f => Char -> Mod f a
short Char
'w'
forall a. Semigroup a => a -> a -> a
<> forall (f :: * -> *) a. HasMetavar f => FilePath -> Mod f a
metavar FilePath
"\"[DOUBLE,DOUBLE,...]\""
forall a. Semigroup a => a -> a -> a
<> forall (f :: * -> *) a. FilePath -> Mod f a
help FilePath
"Weights of mixture model components"
)
maybeGammaParams :: Parser (Maybe GammaRateHeterogeneityParams)
maybeGammaParams :: Parser (Maybe GammaRateHeterogeneityParams)
maybeGammaParams =
forall (f :: * -> *) a. Alternative f => f a -> f (Maybe a)
optional forall a b. (a -> b) -> a -> b
$
forall a. ReadM a -> Mod OptionFields a -> Parser a
option
forall a. Read a => ReadM a
auto
( forall (f :: * -> *) a. HasName f => FilePath -> Mod f a
long FilePath
"gamma-rate-heterogeneity"
forall a. Semigroup a => a -> a -> a
<> forall (f :: * -> *) a. HasName f => Char -> Mod f a
short Char
'g'
forall a. Semigroup a => a -> a -> a
<> forall (f :: * -> *) a. HasMetavar f => FilePath -> Mod f a
metavar FilePath
"\"(NCAT,SHAPE)\""
forall a. Semigroup a => a -> a -> a
<> forall (f :: * -> *) a. FilePath -> Mod f a
help FilePath
"Number of gamma rate categories and shape parameter"
)
lengthOpt :: Parser Int
lengthOpt :: Parser Int
lengthOpt =
forall a. ReadM a -> Mod OptionFields a -> Parser a
option
forall a. Read a => ReadM a
auto
( forall (f :: * -> *) a. HasName f => FilePath -> Mod f a
long FilePath
"length"
forall a. Semigroup a => a -> a -> a
<> forall (f :: * -> *) a. HasName f => Char -> Mod f a
short Char
'l'
forall a. Semigroup a => a -> a -> a
<> forall (f :: * -> *) a. HasMetavar f => FilePath -> Mod f a
metavar FilePath
"NUMBER"
forall a. Semigroup a => a -> a -> a
<> forall (f :: * -> *) a. FilePath -> Mod f a
help
FilePath
"Set alignment length to NUMBER"
)
simulateFooter :: [String]
= [FilePath]
sms forall a. [a] -> [a] -> [a]
++ [FilePath]
mms
where
sms :: [FilePath]
sms =
[ FilePath
"Substitution models:",
FilePath
"-s \"MODEL[PARAMETER,PARAMETER,...]{STATIONARY_DISTRIBUTION}\"",
FilePath
" Supported DNA models: JC, F81, HKY, GTR4.",
FilePath
" For example,",
FilePath
" -s HKY[KAPPA]{DOUBLE,DOUBLE,DOUBLE,DOUBLE}",
FilePath
" -s GTR4[e_AC,e_AG,e_AT,e_CG,e_CT,e_GT]{DOUBLE,DOUBLE,DOUBLE,DOUBLE}",
FilePath
" where the 'e_XY' are the exchangeabilities from nucleotide X to Y.",
FilePath
" Supported Protein models: Poisson, Poisson-Custom, LG, LG-Custom, WAG, WAG-Custom, GTR20.",
FilePath
" MODEL-Custom means that only the exchangeabilities of MODEL are used,",
FilePath
" and a custom stationary distribution is provided.",
FilePath
" For example,",
FilePath
" -s LG",
FilePath
" -s LG-Custom{...}",
FilePath
" -s GTR20[e_AR,e_AN,...]{...}",
FilePath
" the 'e_XY' are the exchangeabilities from amino acid X to Y (alphabetical order).",
FilePath
" Notes: The F81 model for DNA is equivalent to the Poisson-Custom for proteins.",
FilePath
" The GTR4 model for DNA is equivalent to the GTR20 for proteins."
]
mms :: [FilePath]
mms =
[ FilePath
"",
FilePath
"Mixture models:",
FilePath
"-m \"MIXTURE(SUBSTITUTION_MODEL_1,SUBSTITUTION_MODEL_2[PARAMETERS]{STATIONARY_DISTRIBUTION},...)\"",
FilePath
" For example,",
FilePath
" -m \"MIXTURE(JC,HKY[6.0]{0.3,0.2,0.2,0.3})\"",
FilePath
"Mixture weights have to be provided with the -w option.",
FilePath
"",
FilePath
"Special mixture models:",
FilePath
"-m CXX",
FilePath
" where XX is 10, 20, 30, 40, 50, or 60; CXX models, Quang et al., 2008.",
FilePath
"-m \"EDM(EXCHANGEABILITIES)\"",
FilePath
" Arbitrary empirical distribution mixture (EDM) models.",
FilePath
" Stationary distributions have to be provided with the -e or -p option.",
FilePath
" For example,",
FilePath
" LG exchangeabilities with stationary distributions given in FILE.",
FilePath
" -m \"EDM(LG-Custom)\" -e FILE",
FilePath
" LG exchangeabilities with site profiles (Phylobayes) given in FILES.",
FilePath
" -m \"EDM(LG-Custom)\" -p FILES",
FilePath
"For special mixture models, mixture weights are optional."
]