Tools.hs

{-# LANGUAGE OverloadedStrings #-}
{-# LANGUAGE TemplateHaskell   #-}

{- |
Module      :  SLynx.Tools
Description :  Common tools for sequence lynx
Copyright   :  (c) Dominik Schrempf 2020
License     :  GPL-3.0-or-later

Maintainer  :  dominik.schrempf@gmail.com
Stability   :  unstable
Portability :  portable

Creation date: Sat Sep  7 06:24:22 2019.

-}

module SLynx.Tools
  ( -- * SLynx.Tools
    readSeqs
    -- * Options
  , alphabetOpt
  )
where

import           Control.Monad.IO.Class
import           Control.Monad.Logger
import qualified Data.Text                     as T
import           Options.Applicative

import           ELynx.Data.Alphabet.Alphabet
import           ELynx.Data.Sequence.Sequence
import           ELynx.Import.Sequence.Fasta
                                         hiding ( Parser )
import           ELynx.Tools

-- -- | Read sequences of given alphabet from file or standard input.
-- readSeqs
--   :: (MonadIO m, MonadLogger m) => Alphabet -> Maybe FilePath -> m [Sequence]
-- readSeqs a mfp = do
--   case mfp of
--     Nothing ->
--       $(logInfo)
--         $  T.pack
--         $  "Read sequences from standard input; alphabet "
--         <> show a
--         <> "."
--     Just fp ->
--       $(logInfo)
--         $  T.pack
--         $  "Read sequences from file "
--         <> fp
--         <> "; alphabet "
--         <> show a
--         <> "."
--   liftIO $ parseFileOrIOWith (fasta a) mfp

-- | Read sequences of given alphabet from file or standard input.
readSeqs :: (MonadIO m, MonadLogger m) => Alphabet -> FilePath -> m [Sequence]
readSeqs a fp = do
  $(logInfo)
    $  T.pack
    $  "Read sequences from file "
    <> fp
    <> "; alphabet "
    <> show a
    <> "."
  liftIO $ parseFileWith (fasta a) fp

-- | Command line option to specify the alphabet. Used by various commands.
alphabetOpt :: Parser Alphabet
alphabetOpt =
  option auto $ long "alphabet" <> short 'a' <> metavar "NAME" <> help
    "Specify alphabet type NAME"