{-# LANGUAGE OverloadedStrings #-}
{-# LANGUAGE TemplateHaskell #-}
module SLynx.SubSample.SubSample
( subSampleCmd,
)
where
import Control.Monad
import Control.Monad.IO.Class
import Control.Monad.Logger
import Control.Monad.Trans.Reader (ask)
import qualified Data.Text as T
import qualified ELynx.Data.Sequence.Alignment as M
import ELynx.Export.Sequence.Fasta
import ELynx.Tools
import SLynx.SubSample.Options
import SLynx.Tools
import System.Random.MWC
subSampleCmd :: ELynx SubSampleArguments ()
subSampleCmd = do
(SubSampleArguments al inFile nSites nAlignments (Fixed s)) <- local <$> ask
$(logInfo) "Command: Sub sample from a multi sequence alignment."
$(logInfo) $ T.pack $ " Sample " <> show nSites <> " sites."
$(logInfo) $
T.pack $
" Sample "
<> show nAlignments
<> " multi sequence alignments."
ss <- readSeqs al inFile
gen <- liftIO $ initialize s
let a = either error id (M.fromSequences ss)
samples <- liftIO $ replicateM nAlignments $ M.randomSubSample nSites a gen
let results = map (sequencesToFasta . M.toSequences) samples
sfxs = getOutSuffixes nAlignments "fasta"
zipWithM_ (out "sub sampled multi sequence alignments") results sfxs