Options.hs

{-# LANGUAGE DeriveGeneric #-}

-- |
-- Module      :  SLynx.SubSample.Options
-- Description :  ELynxSeq argument parsing
-- Copyright   :  (c) Dominik Schrempf 2021
-- License     :  GPL-3.0-or-later
--
-- Maintainer  :  dominik.schrempf@gmail.com
-- Stability   :  unstable
-- Portability :  portable
--
-- Creation date: Sun Oct  7 17:29:45 2018.
module SLynx.SubSample.Options
  ( SubSampleArguments (..),
    subSampleArguments,
    getOutSuffixes,
  )
where

import Data.Aeson
import qualified Data.Text as T
import qualified Data.Text.Lazy as LT
import qualified Data.Text.Lazy.Builder as LT
import qualified Data.Text.Lazy.Builder.Int as LT
import ELynx.Alphabet.Alphabet
import ELynx.Tools.Options
import ELynx.Tools.Reproduction
import GHC.Generics
import Options.Applicative
import SLynx.Tools

-- | Data structure holding the Command line arguments.
data SubSampleArguments = SubSampleArguments
  { ssAlphabet :: Alphabet,
    ssInFile :: FilePath,
    ssNSites :: Int,
    ssNAlignments :: Int,
    ssMbSeed :: SeedOpt
  }
  deriving (Eq, Show, Generic)

-- | Get a given number of output file suffixes.
--
-- > getOutSuffixes 11 "fasta"
--
-- Will result in @.00.fasta@ up to @.10.fasta@.
getOutSuffixes :: Int -> String -> [String]
getOutSuffixes n suffix =
  ["." ++ digitStr i ++ "." ++ suffix | i <- [0 .. n - 1]]
  where
    nDigits = ceiling $ logBase (10 :: Double) (fromIntegral n)
    digitStr i =
      T.unpack $
        T.justifyRight nDigits '0' (LT.toStrict $ LT.toLazyText $ LT.decimal i)

instance Reproducible SubSampleArguments where
  inFiles = pure . ssInFile
  outSuffixes a = getOutSuffixes (ssNAlignments a) "fasta"
  getSeed = Just . ssMbSeed
  setSeed a s = a {ssMbSeed = s}
  parser = subSampleArguments
  cmdName = "sub-sample"
  cmdDsc = ["Sub-sample columns from multi sequence alignments."]
  cmdFtr =
    [ "Create a given number of multi sequence alignments, each of which contains a given number of random sites drawn from the original multi sequence alignment."
    ]

instance FromJSON SubSampleArguments

instance ToJSON SubSampleArguments

-- | Sub command parser.
subSampleArguments :: Parser SubSampleArguments
subSampleArguments =
  SubSampleArguments
    <$> alphabetOpt
    <*> filePathArg
    <*> subSampleNSitesOpt
    <*> subSampleNAlignmentsOpt
    <*> seedOpt

subSampleNSitesOpt :: Parser Int
subSampleNSitesOpt =
  option auto $
    long "number-of-sites" <> short 'n' <> metavar "INT"
      <> help
        "Number of sites randomly drawn with replacement"

subSampleNAlignmentsOpt :: Parser Int
subSampleNAlignmentsOpt =
  option auto $
    long "number-of-alignments"
      <> short 'm'
      <> metavar "INT"
      <> help "Number of multi sequence alignments to be created"

filePathArg :: Parser FilePath
filePathArg =
  strArgument $ metavar "INPUT-FILE" <> help "Read sequences from INPUT-FILE"