PlinkSpec.hs

{-# LANGUAGE OverloadedStrings #-}
module SequenceFormats.PlinkSpec (spec) where

import           SequenceFormats.Eigenstrat (EigenstratIndEntry (..),
                                             EigenstratSnpEntry (..), Sex (..), GenoLine, GenoEntry(..))
import           SequenceFormats.Plink      (readBimFile, readFamFile, readPlinkBedFile)
import           SequenceFormats.Utils      (Chrom (..))

import           Control.Foldl              (list, purely)
import           Data.Vector                (fromList)
import qualified Pipes.Prelude              as P
import           Pipes.Safe                 (runSafeT)
import           Test.Hspec

spec :: Spec
spec = do
    testReadBimFile
    testReadFamFile
    testReadBedFile

mockDatEigenstratSnp :: [EigenstratSnpEntry]
mockDatEigenstratSnp = [
    EigenstratSnpEntry (Chrom "11") 0      0.000000 "rs0000" 'A' 'C',
    EigenstratSnpEntry (Chrom "11") 100000 0.001000 "rs1111" 'A' 'G',
    EigenstratSnpEntry (Chrom "11") 200000 0.002000 "rs2222" 'A' 'T',
    EigenstratSnpEntry (Chrom "11") 300000 0.003000 "rs3333" 'C' 'A',
    EigenstratSnpEntry (Chrom "11") 400000 0.004000 "rs4444" 'G' 'A',
    EigenstratSnpEntry (Chrom "11") 500000 0.005000 "rs5555" 'T' 'A',
    EigenstratSnpEntry (Chrom "11") 600000 0.006000 "rs6666" 'G' 'T']

mockDatEigenstratInd :: [EigenstratIndEntry]
mockDatEigenstratInd = [
    EigenstratIndEntry "SAMPLE0" Female "1",
    EigenstratIndEntry "SAMPLE1" Male "2",
    EigenstratIndEntry "SAMPLE2" Female "3",
    EigenstratIndEntry "SAMPLE3" Male "4",
    EigenstratIndEntry "SAMPLE4" Female "5"]

mockDatPlinkBed :: [GenoLine]
mockDatPlinkBed = [
    fromList [Het,    Het,    Het,    HomAlt, HomAlt],
    fromList [HomAlt, Het,    HomRef, Het,    HomRef],
    fromList [HomRef, Het,    Het,    HomAlt, Het],
    fromList [HomAlt, HomAlt, Het,    HomRef, HomRef],
    fromList [HomRef, Het,    Het,    HomAlt, HomAlt],
    fromList [HomAlt, HomAlt, Het,    Het,    Het],
    fromList [HomRef, HomRef, Het,    Het,    HomAlt]]

testReadBimFile :: Spec
testReadBimFile = describe "readBimFile" $
    it "should read a BIM file correctly" $ do
        let esSnpProd = readBimFile "testDat/example.bim"
        (runSafeT $ purely P.fold list esSnpProd) `shouldReturn` mockDatEigenstratSnp

testReadFamFile :: Spec
testReadFamFile = describe "readFamFile" $
    it "should read a FAM file correctly" $ do
        readFamFile "testDat/example.fam" `shouldReturn` mockDatEigenstratInd

testReadBedFile :: Spec
testReadBedFile = describe "readBedFile" $
    it "should read genotypes correctly" $ do
        let fn = "testDat/example.plink.bed"
        bedDat <- runSafeT $ do
            bedProd <- readPlinkBedFile fn 5
            purely P.fold list bedProd
        bedDat `shouldBe` mockDatPlinkBed