sequence-formats 1.4.1 → 1.5.0
raw patch · 5 files changed
+296/−148 lines, 5 filesdep ~attoparsecdep ~basedep ~bytestring
Dependency ranges changed: attoparsec, base, bytestring, containers, errors, exceptions, foldl, hspec, lens-family, pipes, pipes-attoparsec, pipes-bytestring, pipes-safe, tasty, tasty-hunit, transformers, vector
Files
- sequence-formats.cabal +51/−75
- src/SequenceFormats/Eigenstrat.hs +50/−65
- src/SequenceFormats/Plink.hs +127/−0
- test/SequenceFormats/EigenstratSpec.hs +1/−8
- test/SequenceFormats/PlinkSpec.hs +67/−0
sequence-formats.cabal view
@@ -1,78 +1,54 @@-cabal-version: >=1.10-name: sequence-formats-version: 1.4.1-license: GPL-3-license-file: LICENSE-maintainer: stephan.schiffels@mac.com-author: Stephan Schiffels-synopsis: A package with basic parsing utilities for several Bioinformatic data formats.-description:- Contains utilities to parse and write Eigenstrat, Fasta, FreqSum, VCF and other file formats used in population genetics analyses.-category: Bioinformatics-build-type: Simple-extra-source-files:- README.md- Changelog.md- testDat/example.bim- testDat/example.eigenstratgeno- testDat/example.fasta- testDat/example.freqsum- testDat/example.histogram.txt- testDat/example.ind- testDat/example.snp- testDat/example.vcf- testDat/example.pileup+name: sequence-formats+version: 1.5.0+synopsis: A package with basic parsing utilities for several Bioinformatic data formats.+description: Contains utilities to parse and write Eigenstrat, Fasta, FreqSum, VCF, Plink and other file formats used in population genetics analyses.+license: GPL-3+license-file: LICENSE+author: Stephan Schiffels+maintainer: stephan.schiffels@mac.com+category: Bioinformatics+build-type: Simple+cabal-version: >=1.10+extra-source-files: README.md,+ Changelog.md,+ testDat/example.bim,+ testDat/example.eigenstratgeno,+ testDat/example.fasta,+ testDat/example.freqsum,+ testDat/example.histogram.txt,+ testDat/example.ind,+ testDat/example.snp,+ testDat/example.vcf,+ testDat/example.pileup library- exposed-modules:- SequenceFormats.RareAlleleHistogram- SequenceFormats.FreqSum- SequenceFormats.Fasta- SequenceFormats.VCF- SequenceFormats.Eigenstrat- SequenceFormats.Utils- SequenceFormats.Pileup- hs-source-dirs: src- default-language: Haskell2010- build-depends:- base >=4.7 && <5,- containers >=0.6.0.1,- errors >=2.3.0,- attoparsec >=0.13.2.2,- pipes >=4.3.11,- transformers >=0.5.6.2,- bytestring >=0.10.8.2,- lens-family >=1.2.3,- pipes-bytestring >=2.1.6,- foldl >=1.4.5,- exceptions >=0.10.2,- pipes-safe >=2.3.1,- pipes-attoparsec >=0.5.1.5,- vector >=0.12.0.3+ exposed-modules: SequenceFormats.RareAlleleHistogram,+ SequenceFormats.FreqSum,+ SequenceFormats.Fasta,+ SequenceFormats.VCF,+ SequenceFormats.Eigenstrat,+ SequenceFormats.Plink,+ SequenceFormats.Utils,+ SequenceFormats.Pileup+ hs-source-dirs: src+ build-depends: base >= 4.7 && < 5, containers, errors, attoparsec, pipes,+ transformers, bytestring, lens-family,+ pipes-bytestring, foldl, exceptions, pipes-safe,+ pipes-attoparsec, vector+ default-language: Haskell2010 -test-suite sequenceFormatTests- type: exitcode-stdio-1.0- main-is: Spec.hs- hs-source-dirs: test- other-modules:- SequenceFormats.EigenstratSpec- SequenceFormats.FastaSpec- SequenceFormats.FreqSumSpec- SequenceFormats.RareAlleleHistogramSpec- SequenceFormats.UtilsSpec- SequenceFormats.VCFSpec- SequenceFormats.PileupSpec- default-language: Haskell2010- build-depends:- base >=4.12.0.0,- sequence-formats -any,- foldl >=1.4.5,- pipes >=4.3.11,- pipes-safe >=2.3.1,- tasty >=1.2.3,- vector >=0.12.0.3,- transformers >=0.5.6.2,- tasty-hunit >=0.10.0.2,- bytestring >=0.10.8.2,- containers >=0.6.0.1,- hspec >=2.7.1+Test-Suite sequenceFormatTests+ type: exitcode-stdio-1.0+ main-is: Spec.hs+ hs-source-dirs: test+ build-depends: base, sequence-formats, foldl, pipes, pipes-safe, tasty, vector,+ transformers, tasty-hunit, bytestring, containers, hspec+ other-modules: SequenceFormats.EigenstratSpec,+ SequenceFormats.FastaSpec,+ SequenceFormats.FreqSumSpec,+ SequenceFormats.RareAlleleHistogramSpec,+ SequenceFormats.UtilsSpec,+ SequenceFormats.PlinkSpec,+ SequenceFormats.VCFSpec,+ SequenceFormats.PileupSpec+ default-language: Haskell2010
src/SequenceFormats/Eigenstrat.hs view
@@ -4,50 +4,63 @@ -} -module SequenceFormats.Eigenstrat (EigenstratSnpEntry(..), EigenstratIndEntry(..), - readEigenstratInd, GenoEntry(..), GenoLine, Sex(..), - readEigenstratSnpStdIn, readEigenstratSnpFile, readBimStdIn, readBimFile,- readEigenstrat, writeEigenstrat, writeEigenstratIndFile, writeEigenstratSnp, writeBim, +module SequenceFormats.Eigenstrat (EigenstratSnpEntry(..), EigenstratIndEntry(..),+ readEigenstratInd, GenoEntry(..), GenoLine, Sex(..),+ readEigenstratSnpStdIn, readEigenstratSnpFile,+ readEigenstrat, writeEigenstrat, writeEigenstratIndFile, writeEigenstratSnp, writeEigenstratGeno) where -import SequenceFormats.Utils (consumeProducer, SeqFormatException(..),- Chrom(..), readFileProd, word)+import SequenceFormats.Utils (Chrom (..),+ SeqFormatException (..),+ consumeProducer,+ readFileProd, word) -import Control.Applicative ((<|>))-import Control.Exception (throw)-import Control.Monad (void, forM_)-import Control.Monad.Catch (MonadThrow)-import Control.Monad.IO.Class (MonadIO, liftIO)+import Control.Applicative ((<|>))+import Control.Exception (throw)+import Control.Monad (forM_, void)+import Control.Monad.Catch (MonadThrow)+import Control.Monad.IO.Class (MonadIO, liftIO) import qualified Data.Attoparsec.ByteString.Char8 as A-import Data.Vector (Vector, fromList, toList)-import qualified Data.ByteString.Char8 as B-import Pipes (Producer, Pipe, (>->), for, cat, yield, Consumer)-import Pipes.Safe (MonadSafe)-import qualified Pipes.Safe.Prelude as PS-import qualified Pipes.Prelude as P-import qualified Pipes.ByteString as PB-import System.IO (withFile, IOMode(..), Handle, hPutStrLn)+import qualified Data.ByteString.Char8 as B+import Data.Vector (Vector, fromList, toList)+import Pipes (Consumer, Pipe, Producer,+ cat, for, yield, (>->))+import qualified Pipes.ByteString as PB+import qualified Pipes.Prelude as P+import Pipes.Safe (MonadSafe)+import qualified Pipes.Safe.Prelude as PS+import System.IO (Handle, IOMode (..),+ hPutStrLn, withFile) -- |A datatype to represent a single genomic SNP. The constructor arguments are: -- Chromosome, Position, Reference Allele, Alternative Allele.-data EigenstratSnpEntry = EigenstratSnpEntry {- snpChrom :: Chrom,- snpPos :: Int,- snpGeneticPos :: Double,- snpId :: B.ByteString,- snpRef :: Char,- snpAlt :: Char- } deriving (Eq, Show)+data EigenstratSnpEntry = EigenstratSnpEntry+ { snpChrom :: Chrom+ , snpPos :: Int+ , snpGeneticPos :: Double+ , snpId :: B.ByteString+ , snpRef :: Char+ , snpAlt :: Char+ }+ deriving (Eq, Show) -- |A datatype to represent a single individual. The constructor arguments are: -- Name, Sex and Population Name-data EigenstratIndEntry = EigenstratIndEntry String Sex String deriving (Eq, Show)+data EigenstratIndEntry = EigenstratIndEntry String Sex String+ deriving (Eq, Show) -- |A datatype to represent Sex in an Eigenstrat Individual file-data Sex = Male | Female | Unknown deriving (Eq, Show)+data Sex = Male+ | Female+ | Unknown+ deriving (Eq, Show) -- |A datatype to represent the genotype of an individual at a SNP.-data GenoEntry = HomRef | Het | HomAlt | Missing deriving (Eq, Show)+data GenoEntry = HomRef+ | Het+ | HomAlt+ | Missing+ deriving (Eq, Show) -- |Vector of the genotypes of all individuals at a single SNP. type GenoLine = Vector GenoEntry@@ -63,17 +76,6 @@ void A.endOfLine return $ EigenstratSnpEntry (Chrom chrom) pos geneticPos snpId_ ref alt -bimParser :: A.Parser EigenstratSnpEntry-bimParser = do- chrom <- word- snpId_ <- A.skipMany1 A.space >> word- geneticPos <- A.skipMany1 A.space >> A.double- pos <- A.skipMany1 A.space >> A.decimal- ref <- A.skipMany1 A.space >> A.satisfy (A.inClass "ACTGN")- alt <- A.skipMany1 A.space >> A.satisfy (A.inClass "ACTGX")- void A.endOfLine- return $ EigenstratSnpEntry (Chrom chrom) pos geneticPos snpId_ ref alt- eigenstratIndParser :: A.Parser EigenstratIndEntry eigenstratIndParser = do A.skipMany A.space@@ -109,7 +111,7 @@ '1' -> return Het '2' -> return HomRef '9' -> return Missing- _ -> error "this should never happen"+ _ -> error "this should never happen" where isValidNum c = c == '0' || c == '1' || c == '2' || c == '9' @@ -121,14 +123,6 @@ readEigenstratSnpFile :: (MonadSafe m) => FilePath -> Producer EigenstratSnpEntry m () readEigenstratSnpFile = consumeProducer eigenstratSnpParser . readFileProd --- |Function to read a Bim File from StdIn. Returns a Pipes-Producer over the EigenstratSnpEntries.-readBimStdIn :: (MonadThrow m, MonadIO m) => Producer EigenstratSnpEntry m ()-readBimStdIn = consumeProducer bimParser PB.stdin---- |Function to read a Bim File from a file. Returns a Pipes-Producer over the EigenstratSnpEntries.-readBimFile :: (MonadSafe m) => FilePath -> Producer EigenstratSnpEntry m ()-readBimFile = consumeProducer bimParser . readFileProd- -- |Function to read a full Eigenstrat database from files. Returns a pair of the Eigenstrat Individual Entries, and a joint Producer over the snp entries and the genotypes. readEigenstrat :: (MonadSafe m) => FilePath -- ^The Genotype file -> FilePath -- ^The Snp File@@ -137,7 +131,7 @@ readEigenstrat genoFile snpFile indFile = do indEntries <- readEigenstratInd indFile let snpProd = readEigenstratSnpFile snpFile- genoProd = consumeProducer eigenstratGenoParser (readFileProd genoFile) >-> + genoProd = consumeProducer eigenstratGenoParser (readFileProd genoFile) >-> validateEigenstratEntries (length indEntries) return (indEntries, P.zip snpProd genoProd) @@ -159,8 +153,8 @@ hPutStrLn h $ name <> "\t" <> sexToStr sex <> "\t" <> popName where sexToStr sex = case sex of- Male -> "M"- Female -> "F"+ Male -> "M"+ Female -> "F" Unknown -> "U" -- |Function to write an Eigenstrat Snp File. Returns a consumer expecting EigenstratSnpEntries.@@ -174,15 +168,6 @@ in snpLine <> "\n") in toTextPipe >-> snpOutTextConsumer --- |Function to write a Bim file. Returns a consumer expecting EigenstratSnpEntries.-writeBim :: (MonadIO m) => Handle -- ^The Eigenstrat Snp File handle.- -> Consumer EigenstratSnpEntry m () -- ^A consumer to read EigenstratSnpEntries-writeBim snpFileH =- let snpOutTextConsumer = PB.toHandle snpFileH- toTextPipe = P.map (\(EigenstratSnpEntry chrom pos gpos gid ref alt) ->- B.intercalate "\t" [unChrom chrom, gid, B.pack (show gpos), B.pack (show pos), B.singleton ref, B.singleton alt])- in toTextPipe >-> snpOutTextConsumer- -- |Function to write an Eigentrat Geno File. Returns a consumer expecting Eigenstrat Genolines. writeEigenstratGeno :: (MonadIO m) => Handle -- ^The Genotype file handle -> Consumer GenoLine m () -- ^A consumer to read Genotype entries.@@ -194,9 +179,9 @@ in toTextPipe >-> genoOutTextConsumer where toEigenStratNum c = case c of- HomRef -> 2 :: Int- Het -> 1- HomAlt -> 0+ HomRef -> 2 :: Int+ Het -> 1+ HomAlt -> 0 Missing -> 9 -- |Function to write an Eigenstrat Database. Returns a consumer expecting joint Snp- and Genotype lines.
+ src/SequenceFormats/Plink.hs view
@@ -0,0 +1,127 @@+{-# LANGUAGE BinaryLiterals #-}+{-# LANGUAGE OverloadedStrings #-}+module SequenceFormats.Plink (readBimStdIn, readBimFile, writeBim, readFamFile, readPlinkBedFile) where++import SequenceFormats.Eigenstrat (EigenstratIndEntry (..),+ EigenstratSnpEntry (..),+ GenoEntry (..), GenoLine,+ Sex (..))+import SequenceFormats.Utils (Chrom (..), consumeProducer,+ readFileProd, word)++import Control.Applicative ((<|>))+import Control.Monad (void)+import Control.Monad.Catch (MonadThrow, throwM)+import Control.Monad.IO.Class (MonadIO, liftIO)+import Control.Monad.Trans.State.Strict (runStateT)+import qualified Data.Attoparsec.ByteString as AB+import qualified Data.Attoparsec.ByteString.Char8 as A+import Data.Bits (shiftR, (.&.))+import qualified Data.ByteString as BB+import qualified Data.ByteString.Char8 as B+import Data.Vector (fromList)+import Pipes (Consumer, Producer, (>->))+import Pipes.Attoparsec (ParsingError (..), parse)+import qualified Pipes.ByteString as PB+import qualified Pipes.Prelude as P+import Pipes.Safe (MonadSafe, runSafeT)+import qualified Pipes.Safe.Prelude+import System.IO (Handle, IOMode (..),+ withFile)+++bimParser :: A.Parser EigenstratSnpEntry+bimParser = do+ chrom <- word+ snpId_ <- A.skipMany1 A.space >> word+ geneticPos <- A.skipMany1 A.space >> A.double+ pos <- A.skipMany1 A.space >> A.decimal+ ref <- A.skipMany1 A.space >> A.satisfy (A.inClass "ACTGN")+ alt <- A.skipMany1 A.space >> A.satisfy (A.inClass "ACTGX")+ void A.endOfLine+ return $ EigenstratSnpEntry (Chrom chrom) pos geneticPos snpId_ ref alt++famParser :: A.Parser EigenstratIndEntry+famParser = do+ A.skipMany A.space+ pop <- word+ ind <- A.skipMany1 A.space >> word+ _ <- A.skipMany1 A.space >> A.decimal+ _ <- A.skipMany1 A.space >> A.decimal+ sex <- A.skipMany1 A.space >> parseSex+ _ <- A.skipMany1 A.space >> word+ void A.endOfLine+ return $ EigenstratIndEntry (B.unpack ind) sex (B.unpack pop)+ where+ parseSex = parseMale <|> parseFemale <|> parseUnknown+ parseMale = A.char '1' >> return Male+ parseFemale = A.char '2' >> return Female+ parseUnknown = A.anyChar >> return Unknown++bedHeaderParser :: AB.Parser ()+bedHeaderParser = do+ void $ AB.word8 0b01101100 -- magic number I for BED files+ void $ AB.word8 0b00011011 -- magic number II for BED files+ void $ AB.word8 0b00000001 -- we can only parse SNP-major order++bedGenotypeParser :: Int -> AB.Parser GenoLine+bedGenotypeParser nrInds = do+ let nrBytes = if nrInds `rem` 4 == 0 then nrInds `quot` 4 else (nrInds `quot` 4) + 1+ bytes <- BB.unpack <$> AB.take nrBytes+ let indBitPairs = concatMap getBitPairs bytes+ return . fromList . take nrInds . map bitPairToGenotype $ indBitPairs+ where+ getBitPairs byte = map (0b00000011 .&.) [byte, shiftR byte 2, shiftR byte 4, shiftR byte 6]+ bitPairToGenotype 0b00000000 = HomRef+ bitPairToGenotype 0b00000010 = Het+ bitPairToGenotype 0b00000011 = HomAlt+ bitPairToGenotype 0b00000001 = Missing+ bitPairToGenotype _ = error "This should never happen"++readPlinkBedProd :: (MonadThrow m) => Int -> Producer B.ByteString m () -> m (Producer GenoLine m ())+readPlinkBedProd nrInds prod = do+ (res, rest) <- runStateT (parse bedHeaderParser) prod+ _ <- case res of+ Nothing -> throwM $ ParsingError [] "Bed file exhausted prematurely"+ Just (Left e) -> throwM e+ Just (Right h) -> return h+ return $ consumeProducer (bedGenotypeParser nrInds) rest++-- |A function to read a bed file from a file. Returns a Producer over all lines.+readPlinkBedFile :: (MonadSafe m) => FilePath -> Int -> m (Producer GenoLine m ())+readPlinkBedFile file nrInds = readPlinkBedProd nrInds (Pipes.Safe.Prelude.withFile file ReadMode PB.fromHandle)++-- |Function to read a Bim File from StdIn. Returns a Pipes-Producer over the EigenstratSnpEntries.+readBimStdIn :: (MonadThrow m, MonadIO m) => Producer EigenstratSnpEntry m ()+readBimStdIn = consumeProducer bimParser PB.stdin++-- |Function to read a Bim File from a file. Returns a Pipes-Producer over the EigenstratSnpEntries.+readBimFile :: (MonadSafe m) => FilePath -> Producer EigenstratSnpEntry m ()+readBimFile = consumeProducer bimParser . readFileProd++-- |Function to read a Plink fam file. Returns the Eigenstrat Individual Entries as list.+readFamFile :: (MonadIO m) => FilePath -> m [EigenstratIndEntry]+readFamFile fn =+ liftIO . withFile fn ReadMode $ \handle ->+ P.toListM $ consumeProducer famParser (PB.fromHandle handle)++-- |Function to read a full Plink dataset from files. Returns a pair of the Plink Individual Entries, and a joint Producer over the snp entries and the genotypes.+readPlink :: (MonadSafe m) => FilePath -- ^The Bed file+ -> FilePath -- ^The Bim File+ -> FilePath -- ^The Fam file+ -> m ([EigenstratIndEntry], Producer (EigenstratSnpEntry, GenoLine) m ()) -- The return pair of individual entries and a joint Snp/Geno Producer.+readPlink bedFile bimFile famFile = do+ indEntries <- readFamFile famFile+ let nrInds = length indEntries+ snpProd = readBimFile bimFile+ genoProd <- readPlinkBedFile bedFile nrInds+ return (indEntries, P.zip snpProd genoProd)++-- |Function to write a Bim file. Returns a consumer expecting EigenstratSnpEntries.+writeBim :: (MonadIO m) => Handle -- ^The Eigenstrat Snp File handle.+ -> Consumer EigenstratSnpEntry m () -- ^A consumer to read EigenstratSnpEntries+writeBim snpFileH =+ let snpOutTextConsumer = PB.toHandle snpFileH+ toTextPipe = P.map (\(EigenstratSnpEntry chrom pos gpos gid ref alt) ->+ B.intercalate "\t" [unChrom chrom, gid, B.pack (show gpos), B.pack (show pos), B.singleton ref, B.singleton alt])+ in toTextPipe >-> snpOutTextConsumer
test/SequenceFormats/EigenstratSpec.hs view
@@ -7,14 +7,13 @@ import Pipes (each, runEffect, (>->)) import qualified Pipes.Prelude as P import Pipes.Safe (runSafeT)-import SequenceFormats.Eigenstrat (readEigenstrat, writeEigenstrat, readBimFile,+import SequenceFormats.Eigenstrat (readEigenstrat, writeEigenstrat, EigenstratSnpEntry(..), EigenstratIndEntry(..), GenoLine, Sex(..), GenoEntry(..)) import SequenceFormats.Utils (Chrom(..)) import Test.Hspec spec :: Spec spec = do- testReadBimFile testReadEigenstrat testWriteEigenstrat @@ -27,12 +26,6 @@ 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']--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 mockDatEigenstratInd :: [EigenstratIndEntry] mockDatEigenstratInd = [
+ test/SequenceFormats/PlinkSpec.hs view
@@ -0,0 +1,67 @@+{-# 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