{-# LANGUAGE OverloadedStrings #-}
{-# LANGUAGE TemplateHaskell #-}
module Concatenate.Concatenate
( concatenateCmd
)
where
import Control.Monad.Logger
import Control.Monad.Trans.Class
import Control.Monad.Trans.Reader
import Concatenate.Options
import Tools
import qualified ELynx.Data.Sequence.Sequence as S
import ELynx.Export.Sequence.Fasta
import ELynx.Tools.InputOutput
concatenateCmd :: Maybe FilePath -> Concatenate ()
concatenateCmd outFileBaseName = do
$(logInfo) "Command: Concatenate sequences."
ConcatenateArguments al fps <- lift ask
sss <- mapM (readSeqs al . Just) fps
let result = sequencesToFasta $ S.concatSequences sss
let outFilePath = (++ ".fasta") <$> outFileBaseName
out "concatenated multi sequence alignment " result outFilePath