#!/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,

optFormat :: FilePath,

optPoplist :: Maybe FilePath,

optOutGeno :: FilePath,

optOutSnp :: FilePath,

optOutInd :: FilePath

}

main = do

args <- options "Eigensoft convertf wrapper" parser

runManaged $ do

paramFile <- mktempfile "." "convert_wrapper"

let popListRow = case optPoplist args of

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

Nothing -> empty

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

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

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

(format ("outputformat:\t"%fp) (optFormat args)),

(format ("genotypeoutname:\t"%fp) (optOutGeno args)),

(format ("snpoutname:\t"%fp) (optOutSnp args)),

(format ("indivoutname:\t"%fp) (optOutInd args))]

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

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

case ec of

ExitSuccess -> return ()

ExitFailure n -> err . unsafeTextToLine $ format ("convertf 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 "outFormat" 'f' "output format"

<*> optional (optPath "popList" 'p' "population list")

<*> optPath "outGeno" 'G' "Output Genotype File"

<*> optPath "outSnp" 'S' "Output Snp File"

<*> optPath "outInd" 'I' "Output Ind File"