{-# LANGUAGE OverloadedStrings #-}
{-# LANGUAGE TemplateHaskell #-}
module SLynx.Translate.Translate
( translateCmd,
)
where
import Control.Monad.Logger
import Control.Monad.Trans.Reader (ask)
import qualified Data.Text as T
import ELynx.Data.Character.Codon
import ELynx.Data.Sequence.Sequence
import ELynx.Data.Sequence.Translate
import ELynx.Export.Sequence.Fasta
import ELynx.Tools
import SLynx.Tools
import SLynx.Translate.Options
translateSeqs :: Int -> UniversalCode -> [Sequence] -> [Sequence]
translateSeqs rf uc = map (translateSeq uc rf)
translateCmd :: ELynx TranslateArguments ()
translateCmd = do
(TranslateArguments al inFile rf uc) <- local <$> ask
$(logInfo) "Command: Translate sequences to amino acids."
$(logInfo) $ T.pack $ " Universal code: " <> show uc <> "."
$(logInfo) $ T.pack $ " Reading frame: " <> show rf <> "."
$(logInfo) ""
ss <- readSeqs al inFile
let result = sequencesToFasta $ translateSeqs rf uc ss
out "translated sequences" result "fasta"