Options.hs

{-# LANGUAGE DeriveGeneric #-}

{- |
Module      :  SLynx.Filter.Options
Description :  ELynxSeq argument parsing
Copyright   :  (c) Dominik Schrempf 2018
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.Filter.Options
  ( FilterRowsArguments(..)
  , FilterColsArguments(..)
  , filterRowsArguments
  , filterColsArguments
  )
where

import           Control.Applicative
import           Options.Applicative

import           SLynx.Tools

import           ELynx.Data.Alphabet.Alphabet
import           ELynx.Tools

-- | Arguments needed for filtering sequences.
data FilterRowsArguments = FilterRowsArguments
  { frAlphabet :: Alphabet
  , frInFile   :: FilePath
  , frLonger   :: Maybe Int
  , frShorter  :: Maybe Int
  , frStandard :: Bool }
  deriving (Eq, Show, Generic)

instance Reproducible FilterRowsArguments where
  inFiles = pure . frInFile
  outSuffixes _ = [".fasta"]
  getSeed _ = Nothing
  setSeed = const
  parser  = filterRowsArguments
  cmdName = "filter-rows"
  cmdDsc  = ["Filter rows (or sequences) found in input files."]

instance FromJSON FilterRowsArguments

instance ToJSON FilterRowsArguments

-- | Arguments needed for filtering columns of a multi sequence alignment.
data FilterColsArguments = FilterColsArguments
  { fcAlphabet :: Alphabet
  , fcInFile   :: FilePath
  , fcStandard :: Maybe Double }
  deriving (Eq, Show, Generic)

instance Reproducible FilterColsArguments where
  inFiles = pure . fcInFile
  outSuffixes _ = [".fasta"]
  getSeed _ = Nothing
  setSeed = const
  parser  = filterColsArguments
  cmdName = "filter-columns"
  cmdDsc  = ["Filter columns of multi sequence alignments."]

instance FromJSON FilterColsArguments

instance ToJSON FilterColsArguments

-- | Command line parser.
filterRowsArguments :: Parser FilterRowsArguments
filterRowsArguments =
  FilterRowsArguments
    <$> alphabetOpt
    <*> inFileArg
    <*> filterLongerThanOpt
    <*> filterShorterThanOpt
    <*> filterStandardChars

filterLongerThanOpt :: Parser (Maybe Int)
filterLongerThanOpt =
  optional $ option auto $ long "longer-than" <> metavar "LENGTH" <> help
    "Only keep sequences longer than LENGTH"

filterShorterThanOpt :: Parser (Maybe Int)
filterShorterThanOpt =
  optional $ option auto $ long "shorter-than" <> metavar "LENGTH" <> help
    "Only keep sequences shorter than LENGTH"

filterStandardChars :: Parser Bool
filterStandardChars =
  switch
    $  long "standard-characters"
    <> help
         "Only keep sequences containing at least one standard (i.e., non-IUPAC) character"

-- | Command line parser.
filterColsArguments :: Parser FilterColsArguments
filterColsArguments =
  FilterColsArguments <$> alphabetOpt <*> inFileArg <*> filterStandardOpt

filterStandardOpt :: Parser (Maybe Double)
filterStandardOpt =
  optional
    $  option auto
    $  long "standard-chars"
    <> metavar "DOUBLE"
    <> help
         "Keep columns with a proportion standard (non-IUPAC) characters larger than DOUBLE in [0,1]"

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