Options.hs

{-# LANGUAGE DeriveGeneric #-}
{-# LANGUAGE OverloadedStrings #-}
{-# LANGUAGE StandaloneDeriving #-}
{-# OPTIONS_GHC -Wno-orphans #-}

-- |
-- Module      :  TLynx.Simulate.Options
-- Description :  Argument parser for seq-ana
-- Copyright   :  (c) Dominik Schrempf 2020
-- License     :  GPL-3.0-or-later
--
-- Maintainer  :  dominik.schrempf@gmail.com
-- Stability   :  unstable
-- Portability :  portable
--
-- Creation date: Fri May  3 11:51:07 2019.
module TLynx.Simulate.Options
  ( Process (..),
    SimulateArguments (..),
    simulateArguments,
    reportSimulateArguments,
  )
where

import Data.List
import Data.Maybe
import ELynx.Tools hiding (Random)
import ELynx.Tree.Simulate.PointProcess (TimeSpec (..))
import Options.Applicative

deriving instance Eq TimeSpec

deriving instance Generic TimeSpec

instance Show TimeSpec where
  show Random = "Random"
  show (Origin o) = "Condition on height of origin: " ++ show o
  show (Mrca m) = "Condition on height of MRCA: " ++ show m

instance FromJSON TimeSpec

instance ToJSON TimeSpec

-- | Process to be used for simulation.
data Process
  = BirthDeath
      { -- | Birth rate.
        bdLambda :: Double,
        -- | Death rate.
        bdMu :: Double,
        -- | Sampling rate.
        bdRho :: Maybe Double,
        -- | Condition on height?
        bdHeight :: TimeSpec
      }
  | Coalescent
  deriving (Eq, Show, Generic)

instance FromJSON Process

instance ToJSON Process

reportProcess :: Process -> String
reportProcess (BirthDeath l m mr ts) =
  intercalate
    "\n"
    [ "Model: Birth and death process",
      "  Birth rate: " ++ show l,
      "  Death rate: " ++ show m,
      "  Sampling probability: " ++ maybe "1.0" show mr,
      "  Height specification: " ++ show ts
    ]
reportProcess Coalescent = "Model: Coalescent process"

-- | Arguments need to simulate phylogenetic trees using birth and death processes.
data SimulateArguments = SimulateArguments
  { -- | Simulated trees.
    argsNTrees :: Int,
    -- | Number of leaves.
    argsNLeaves :: Int,
    -- | Process.
    argsProcess :: Process,
    -- | Perform sub-sampling with given probability.
    argsSubSample :: Maybe Double,
    -- | Only print summary statistics?
    argsSumStat :: Bool,
    -- | Seed of NRG, random if 'Nothing'.
    argsSeed :: Seed
  }
  deriving (Eq, Show, Generic)

instance Reproducible SimulateArguments where
  inFiles _ = []
  outSuffixes _ = [".tree"]
  getSeed = Just . argsSeed
  setSeed a s = a {argsSeed = Fixed s}
  parser = simulateArguments
  cmdName = "simulate"
  cmdDsc = ["Simulate phylogenetic trees using a birth and death or coalescent process."]
  cmdFtr = simulateFooter

instance FromJSON SimulateArguments

instance ToJSON SimulateArguments

-- | Print useful information about the provided arguments.
reportSimulateArguments :: SimulateArguments -> String
reportSimulateArguments a =
  intercalate
    "\n"
    [ "Number of simulated trees: " ++ show (argsNTrees a),
      "Number of leaves per tree: " ++ show (argsNLeaves a),
      reportProcess (argsProcess a),
      "Perform sub-sampling: " ++ ssStr,
      "Summary statistics only: " ++ show (argsSumStat a)
    ]
  where
    ssStr = case argsSubSample a of
      Nothing -> "No"
      Just p -> "Yes, with probability " ++ show p

-- | Command line parser.
simulateArguments :: Parser SimulateArguments
simulateArguments =
  SimulateArguments
    <$> nTreeOpt
    <*> nLeavesOpt
    <*> process
    <*> subSampleOpt
    <*> sumStatOpt
    <*> seedOpt

nTreeOpt :: Parser Int
nTreeOpt =
  option auto $
    long "nTrees"
      <> short 't'
      <> metavar "INT"
      <> help "Number of trees"

nLeavesOpt :: Parser Int
nLeavesOpt =
  option auto $
    long "nLeaves"
      <> short 'n'
      <> metavar "INT"
      <> help "Number of leaves per tree"

lambdaOpt :: Parser Double
lambdaOpt =
  option auto $
    long "lambda"
      <> short 'l'
      <> metavar "DOUBLE"
      <> help "Birth rate lambda"

muOpt :: Parser Double
muOpt =
  option auto $
    long "mu"
      <> short 'm'
      <> metavar "DOUBLE"
      <> help "Death rate mu"

rhoOpt :: Parser Double
rhoOpt =
  option auto $
    long "rho"
      <> short 'r'
      <> metavar "DOUBLE"
      <> help "Sampling probability rho"

mrca :: Parser TimeSpec
mrca =
  Mrca
    <$> option
      auto
      ( long "mrca"
          <> metavar "DOUBLE"
          <> help "Condition on height of most recent common ancestor"
      )

origin :: Parser TimeSpec
origin =
  Origin
    <$> option
      auto
      ( long "origin"
          <> metavar "DOUBLE"
          <> help "Condition on height of origin"
      )

timeSpec :: Parser TimeSpec
timeSpec = fromMaybe Random <$> optional (mrca <|> origin)

birthDeath :: Parser Process
birthDeath = BirthDeath <$> lambdaOpt <*> muOpt <*> optional rhoOpt <*> timeSpec

coalescent :: Parser Process
coalescent = pure Coalescent

process :: Parser Process
process =
  hsubparser $
    ( command
        "birthdeath"
        ( info
            birthDeath
            ( progDesc "Birth and death process"
                <> footer "Height: If no tree height is given, the heights will be randomly drawn from the expected distribution given the number of leaves, the birth and the death rate assuming a uniform prior."
            )
        )
        <> command
          "coalescent"
          (info coalescent (progDesc "Coalescent process"))
    )
      <> metavar "PROCESS"
      <> commandGroup "Available processes:"

subSampleOpt :: Parser (Maybe Double)
subSampleOpt =
  optional $
    option auto $
      long
        "sub-sample"
        <> short 'u'
        <> metavar "DOUBLE"
        <> showDefault
        <> help "Perform sub-sampling; see below."

sumStatOpt :: Parser Bool
sumStatOpt =
  switch $
    long "summary-statistics" <> short 's' <> showDefault
      <> help
        "For each branch, print length and number of children"

-- citation :: String
-- citation =
--   "Gernhard, T. (2008). The conditioned reconstructed process. Journal of Theoretical Biology, 253(4), 769–778. http://doi.org/10.1016/j.jtbi.2008.04.005"

-- | And a footer.
simulateFooter :: [String]
simulateFooter =
  [ "See, for example, 'tlynx simulate birthdeath --help'.",
    "Sub-sample with probability p:\n  1. Simulate one big tree with n'=round(n/p), n'>=n, leaves;\n  2. Randomly sample sub-trees with n leaves.\n  (With p=1.0, the same tree is reported over and over again.)"
  ]