#!/usr/bin/env stack

-- stack script --resolver lts-14.1 --package turtle

{-# LANGUAGE OverloadedStrings #-}

import Control.Applicative (optional)

import Prelude hiding (FilePath)

import Turtle

data Options = Options {

optGeno :: FilePath,

optSnp :: FilePath,

optInd :: FilePath,

optOutPrefix :: FilePath,

optLSQproject :: Bool,

optPopList :: Maybe FilePath

}

main = do

args <- options "Eigensoft smartpca wrapper" parser

runManaged $ do

paramFile <- mktempfile "." "smartpca_wrapper"

let content = [(format ("genotypename:\t"%fp) (optGeno args)),

(format ("snpname:\t"%fp) (optSnp args)),

(format ("indivname:\t"%fp) (optInd args)),

(format ("evecoutname:\t"%fp%".evec.txt") (optOutPrefix args)),

(format ("evaloutname:\t"%fp%".eval.txt") (optOutPrefix args))]

lsqProjectLine = if (optLSQproject args) then return "lsqproject:\tYES" else empty

popListLine = case optPopList args of

Just popList -> return . unsafeTextToLine $ format ("poplistname:\t"%fp) popList

Nothing -> empty

output paramFile $ select (map unsafeTextToLine content) <|> lsqProjectLine <|> popListLine

ec <- proc "smartpca" ["-p", format fp paramFile] empty

case ec of

ExitSuccess -> return ()

ExitFailure n -> err . unsafeTextToLine $ format ("mergeit failed with exit code "%d) n

parser :: Parser Options

parser = Options <$> optPath "geno" 'g' "Genotype File"

<*> optPath "snp" 's' "Snp File"

<*> optPath "ind" 'i' "Ind File"

<*> optPath "outPrefix" 'o' "Output prefix for *.evec.txt and *.eval.txt output \

\files"

<*> switch "lsqProject" 'l' "set lsqproject option to YES"

<*> optional (optPath "popList" 'p' "give poplist file to restrict PCA to \

\populations listed.")