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

-- |
-- Module      :  Analyze.Analyze
-- Description :  Parse sequence file formats and analyze them
-- Copyright   :  (c) Dominik Schrempf 2018
-- License     :  GPL-3.0-or-later
--
-- Maintainer  :  dominik.schrempf@gmail.com
-- Stability   :  unstable
-- Portability :  portable
--
-- Creation date: Fri Oct  5 08:41:05 2018.
module SLynx.Concatenate.Concatenate
  ( concatenateCmd,
  )
where

import Control.Monad.Logger
import Control.Monad.Trans.Reader (ask)
import qualified ELynx.Data.Sequence.Sequence as S
import ELynx.Export.Sequence.Fasta
import ELynx.Tools
import SLynx.Concatenate.Options
import SLynx.Tools

-- | Concatenate sequences.
concatenateCmd :: ELynx ConcatenateArguments ()
concatenateCmd :: ELynx ConcatenateArguments ()
concatenateCmd = do
  (ConcatenateArguments Alphabet
al [FilePath]
fps) <- Arguments ConcatenateArguments -> ConcatenateArguments
forall a. Arguments a -> a
local (Arguments ConcatenateArguments -> ConcatenateArguments)
-> ReaderT
     (Arguments ConcatenateArguments)
     (LoggingT IO)
     (Arguments ConcatenateArguments)
-> ReaderT
     (Arguments ConcatenateArguments) (LoggingT IO) ConcatenateArguments
forall (f :: * -> *) a b. Functor f => (a -> b) -> f a -> f b
<$> ReaderT
  (Arguments ConcatenateArguments)
  (LoggingT IO)
  (Arguments ConcatenateArguments)
forall (m :: * -> *) r. Monad m => ReaderT r m r
ask
  $(Int
FilePath
LogLevel
FilePath -> Text
FilePath -> FilePath -> FilePath -> CharPos -> CharPos -> Loc
Text -> Text
Loc -> Text -> LogLevel -> Text -> ELynx ConcatenateArguments ()
(Text -> ELynx ConcatenateArguments ())
-> (Text -> Text) -> Text -> ELynx ConcatenateArguments ()
forall a. a -> a
forall b c a. (b -> c) -> (a -> b) -> a -> c
forall (m :: * -> *) msg.
(MonadLogger m, ToLogStr msg) =>
Loc -> Text -> LogLevel -> msg -> m ()
pack :: FilePath -> Text
monadLoggerLog :: forall (m :: * -> *) msg.
(MonadLogger m, ToLogStr msg) =>
Loc -> Text -> LogLevel -> msg -> m ()
id :: forall a. a -> a
. :: forall b c a. (b -> c) -> (a -> b) -> a -> c
logInfo) Text
"Command: Concatenate sequences."
  [[Sequence]]
sss <- (FilePath
 -> ReaderT
      (Arguments ConcatenateArguments) (LoggingT IO) [Sequence])
-> [FilePath]
-> ReaderT
     (Arguments ConcatenateArguments) (LoggingT IO) [[Sequence]]
forall (t :: * -> *) (m :: * -> *) a b.
(Traversable t, Monad m) =>
(a -> m b) -> t a -> m (t b)
mapM (Alphabet
-> FilePath
-> ReaderT
     (Arguments ConcatenateArguments) (LoggingT IO) [Sequence]
forall (m :: * -> *).
(MonadIO m, MonadLogger m) =>
Alphabet -> FilePath -> m [Sequence]
readSeqs Alphabet
al) [FilePath]
fps
  let result :: ByteString
result = [Sequence] -> ByteString
sequencesToFasta ([Sequence] -> ByteString) -> [Sequence] -> ByteString
forall a b. (a -> b) -> a -> b
$ [[Sequence]] -> [Sequence]
S.concatSequences [[Sequence]]
sss
  FilePath -> ByteString -> FilePath -> ELynx ConcatenateArguments ()
forall a.
Reproducible a =>
FilePath -> ByteString -> FilePath -> ELynx a ()
out FilePath
"concatenated multi sequence alignment " ByteString
result FilePath
".fasta"