diff --git a/Changelog.md b/Changelog.md new file mode 100644 --- /dev/null +++ b/Changelog.md @@ -0,0 +1,1 @@ +V 1.1.4.1: First entry in the Changelog. Added Haddock documentation to all modules and prepare for releasing on Hackage. diff --git a/LICENSE b/LICENSE new file mode 100644 --- /dev/null +++ b/LICENSE @@ -0,0 +1,674 @@ + GNU GENERAL PUBLIC LICENSE + Version 3, 29 June 2007 + + Copyright (C) 2007 Free Software Foundation, Inc. + Everyone is permitted to copy and distribute verbatim copies + of this license document, but changing it is not allowed. + + Preamble + + The GNU General Public License is a free, copyleft license for +software and other kinds of works. + + The licenses for most software and other practical works are designed +to take away your freedom to share and change the works. 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But first, please read +. diff --git a/README.md b/README.md new file mode 100644 --- /dev/null +++ b/README.md @@ -0,0 +1,3 @@ +Sequence-Formats is a Haskell package to provide file parsers and writers for some commonly, and less commonly used file formats in Bioinformatics, speficially population genetics. + +The library makes heavy use of the [pipes library](http://hackage.haskell.org/package/pipes) to provide Producers and Consumers for reading and writing files. diff --git a/sequence-formats.cabal b/sequence-formats.cabal new file mode 100644 --- /dev/null +++ b/sequence-formats.cabal @@ -0,0 +1,48 @@ +cabal-version: >=1.10 +name: sequence-formats +version: 1.1.4.1 +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 + +library + exposed-modules: + SequenceFormats.RareAlleleHistogram + SequenceFormats.FreqSum + SequenceFormats.Fasta + SequenceFormats.VCF + SequenceFormats.Eigenstrat + SequenceFormats.Utils + hs-source-dirs: src + default-language: Haskell2010 + build-depends: + base >=4.7 && <5, + containers >=0.5.10.2 && <0.6, + errors >=2.2.2 && <2.3, + text >=1.2.2.2 && <1.3, + attoparsec >=0.13.2.2 && <0.14, + pipes >=4.3.7 && <4.4, + pipes-text >=0.0.2.5 && <0.1, + transformers >=0.5.2.0 && <0.6, + turtle >=1.4.5 && <1.5, + bytestring >=0.10.8.2 && <0.11, + lens-family >=1.2.2 && <1.3, + pipes-bytestring >=2.1.6 && <2.2, + foldl >=1.3.7 && <1.4, + exceptions >=0.8.3 && <0.9, + pipes-safe >=2.2.6 && <2.3, + pipes-attoparsec >=0.5.1.5 && <0.6, + vector >=0.12.0.1 && <0.13, + data-memocombinators >=0.5.1 && <0.6, + split >=0.2.3.3 && <0.3, + MissingH >=1.4.0.1 && <1.5, + hslogger >=1.2.10 && <1.3 diff --git a/src/SequenceFormats/Eigenstrat.hs b/src/SequenceFormats/Eigenstrat.hs new file mode 100644 --- /dev/null +++ b/src/SequenceFormats/Eigenstrat.hs @@ -0,0 +1,168 @@ +{-# LANGUAGE OverloadedStrings #-} + +{-|Module to read and parse Eigenstrat-formatted genotype data. The Eigenstrat format is defined at . + +-} + +module SequenceFormats.Eigenstrat (EigenstratSnpEntry(..), EigenstratIndEntry(..), + readEigenstratInd, GenoEntry(..), GenoLine, Sex(..), + readEigenstratSnpStdIn, readEigenstratSnpFile, readEigenstrat, writeEigenstrat) where + +import SequenceFormats.Utils (consumeProducer, FormatException(..), Chrom(..)) + +import Control.Applicative ((<|>)) +import Control.Monad (void, forM_) +import Control.Monad.Catch (MonadThrow, throwM) +import Control.Monad.IO.Class (MonadIO, liftIO) +import qualified Data.Attoparsec.Text as A +import Data.Char (isSpace) +import Data.Vector (Vector, fromList, toList) +import qualified Data.Text as T +import qualified Data.Text.IO as T +import Pipes (Producer, Pipe, (>->), for, cat, yield, Consumer) +import Pipes.Safe (MonadSafe) +import qualified Pipes.Prelude as P +import qualified Pipes.Text.IO as PT +import System.IO (withFile, IOMode(..)) +import Turtle (format, w, d, (%), s) + +-- |A datatype to represent a single genomic SNP. The constructor arguments are: +-- Chromosome, Position, Reference Allele, Alternative Allele. +data EigenstratSnpEntry = EigenstratSnpEntry Chrom Int Char Char deriving (Eq, Show) + +-- |A datatype to represent a single individual. The constructor arguments are: +-- Name, Sex and Population Name +data EigenstratIndEntry = EigenstratIndEntry T.Text Sex T.Text deriving (Show) + +-- |A datatype to represent Sex in an Eigenstrat Individual file +data Sex = Male | Female | Unknown deriving (Show) + +-- |A datatype to represent the genotype of an individual at a SNP. +data GenoEntry = HomRef | Het | HomAlt | Missing deriving (Eq, Show) + +-- |Vector of the genotypes of all individuals at a single SNP. +type GenoLine = Vector GenoEntry + +eigenstratSnpParser :: A.Parser EigenstratSnpEntry +eigenstratSnpParser = do + A.skipMany A.space + void word + A.skipMany1 A.space + chrom <- word + A.skipMany1 A.space + void word + A.skipMany1 A.space + pos <- A.decimal + A.skipMany1 A.space + ref <- A.satisfy (A.inClass "ACTGN") + A.skipMany1 A.space + alt <- A.satisfy (A.inClass "ACTGX") + void A.endOfLine + return $ EigenstratSnpEntry (Chrom chrom) pos ref alt + +word :: A.Parser T.Text +word = A.takeTill isSpace + +eigenstratIndParser :: A.Parser EigenstratIndEntry +eigenstratIndParser = do + A.skipMany A.space + name <- word + A.skipMany1 A.space + sex <- parseSex + A.skipMany1 A.space + popName <- word + void A.endOfLine + return $ EigenstratIndEntry name sex popName + +parseSex :: A.Parser Sex +parseSex = parseMale <|> parseFemale <|> parseUnknown + where + parseMale = A.char 'M' >> return Male + parseFemale = A.char 'F' >> return Female + parseUnknown = A.char 'U' >> return Unknown + +-- |Function to read an Eigenstrat individual file. Returns the Eigenstrat Individual Entries as list. +readEigenstratInd :: (MonadIO m) => FilePath -> m [EigenstratIndEntry] +readEigenstratInd fn = do + liftIO . withFile fn ReadMode $ \handle -> do + P.toListM $ consumeProducer eigenstratIndParser (PT.fromHandle handle) + +eigenstratGenoParser :: A.Parser GenoLine +eigenstratGenoParser = do + line <- A.takeWhile1 isValidNum + void A.endOfLine + return . fromList $ do + l <- T.unpack line + case l of + '0' -> return HomAlt + '1' -> return Het + '2' -> return HomRef + '9' -> return Missing + _ -> error "this should never happen" + where + isValidNum c = c == '0' || c == '1' || c == '2' || c == '9' + +-- |Function to read a Snp File from StdIn. Returns a Pipes-Producer over the EigenstratSnpEntries. +readEigenstratSnpStdIn :: (MonadThrow m, MonadIO m) => Producer EigenstratSnpEntry m () +readEigenstratSnpStdIn = consumeProducer eigenstratSnpParser PT.stdin + +-- |Function to read a Snp File from a file. Returns a Pipes-Producer over the EigenstratSnpEntries. +readEigenstratSnpFile :: (MonadSafe m) => FilePath -> Producer EigenstratSnpEntry m () +readEigenstratSnpFile = consumeProducer eigenstratSnpParser . PT.readFile + +-- |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 + -> FilePath -- ^The Ind file + -> m ([EigenstratIndEntry], Producer (EigenstratSnpEntry, GenoLine) m ()) -- The return pair of individual entries and a joint Snp/Geno Producer. +readEigenstrat genoFile snpFile indFile = do + indEntries <- readEigenstratInd indFile + let snpProd = readEigenstratSnpFile snpFile + genoProd = consumeProducer eigenstratGenoParser (PT.readFile genoFile) >-> + validateEigenstratEntries (length indEntries) + return (indEntries, P.zip snpProd genoProd) + +validateEigenstratEntries :: (MonadThrow m) => Int -> Pipe GenoLine GenoLine m () +validateEigenstratEntries nr = for cat $ \line -> do + if length line /= nr + then do + let msg = format ("inconsistent nr of genotypes ("%d%", but should be "%d%") in \ + \genotype line "%w) (length line) nr line + throwM $ FormatException msg + else + yield line + +-- |Function to write an Eigenstrat Database. Returns a consumer expecting joint Snp- and Genotype lines. +writeEigenstrat :: (MonadSafe m) => FilePath -- ^The Genotype file + -> FilePath -- ^The Snp File + -> FilePath -- ^The Ind file + -> [EigenstratIndEntry] -- ^The list of individual entries + -> Consumer (EigenstratSnpEntry, GenoLine) m () -- ^A consumer to read joint Snp/Genotype entries. +writeEigenstrat genoFile snpFile indFile indEntries = do + liftIO $ writeEigenstratIndFile indFile indEntries + let snpOutTextConsumer = PT.writeFile snpFile + genoOutTextConsumer = PT.writeFile genoFile + toTextPipe = P.map (\(EigenstratSnpEntry chrom pos ref alt, genoLine) -> + let n = format (s%"_"%d) (unChrom chrom) pos + snpLine = format (s%"\t"%s%"\t0\t"%d%"\t"%s%"\t"%s%"\n") n (unChrom chrom) pos + (T.singleton ref) (T.singleton alt) + genoLineStr = T.concat . map (format d . toEigenStratNum) . toList $ genoLine + in (snpLine, format (s%"\n") genoLineStr)) + toTextPipe >-> P.tee (P.map fst >-> snpOutTextConsumer) >-> P.map snd >-> genoOutTextConsumer + where + toEigenStratNum c = case c of + HomRef -> 2 :: Int + Het -> 1 + HomAlt -> 0 + Missing -> 9 + +writeEigenstratIndFile :: (MonadIO m) => FilePath -> [EigenstratIndEntry] -> m () +writeEigenstratIndFile f indEntries = do + liftIO . withFile f WriteMode $ \h -> do + forM_ indEntries $ \(EigenstratIndEntry name sex popName) -> do + liftIO . T.hPutStrLn h $ format (s%"\t"%s%"\t"%s) name (sexToStr sex) popName + where + sexToStr sex = case sex of + Male -> "M" + Female -> "F" + Unknown -> "U" diff --git a/src/SequenceFormats/Fasta.hs b/src/SequenceFormats/Fasta.hs new file mode 100644 --- /dev/null +++ b/src/SequenceFormats/Fasta.hs @@ -0,0 +1,67 @@ +{-# LANGUAGE OverloadedStrings #-} + +{-| Module to read and parse through a Fasta file. The Fasta format is defined here: + +-} +module SequenceFormats.Fasta (readNextFastaEntry, loadFastaChrom) where + +import SequenceFormats.Utils (Chrom(..)) + +import Control.Exception.Base (throwIO, AssertionFailed(..)) +import Control.Monad (void) +import Control.Monad.IO.Class (liftIO, MonadIO) +import Control.Monad.Trans.State.Strict (runStateT) +import qualified Data.Attoparsec.ByteString.Char8 as A +import qualified Data.ByteString.Char8 as B +import Data.Char (isAlphaNum) +import qualified Data.Text as T +import Lens.Family2 (view) +import Pipes (Producer, next, (>->), runEffect) +import Pipes.Attoparsec (parse) +import qualified Pipes.ByteString as P +import Pipes.Prelude (drain) +import System.IO (Handle) +import Turtle.Format (format, (%), s) +import Turtle.Prelude (err) +import Turtle.Line (unsafeTextToLine) + +-- |A function to select out a specific chromosome from a Fasta File. Expects a file handle to the +-- file and a chromosome. Note that by Chromosome I simply denote a fasta header line, as is the +-- case for example for the human reference genome. Returns a Bytestring-Producer over the single sequence followed the specified header (the chromosome). +loadFastaChrom :: Handle -> Chrom -> IO (Producer B.ByteString IO ()) +loadFastaChrom refFileHandle chrom = do + let prod = P.fromHandle refFileHandle + go prod + where + go prod = do + (chrom_, prod') <- readNextFastaEntry prod + err . unsafeTextToLine $ format ("found chromosome "%s) (unChrom chrom_) + if chrom_ == chrom + then return (void prod') + else do + newProd <- runEffect $ prod' >-> drain + go newProd + +-- |This function takes a Bytestring-Producer over a Fasta-file, reads in the first header and then returns a produer over its sequence. The return of that producer is the Bytestring-Producer of the rest of the fasta file. +readNextFastaEntry :: (MonadIO m) => Producer B.ByteString m () -> + m (Chrom, Producer B.ByteString m (Producer B.ByteString m ())) +readNextFastaEntry prod = do + (res, rest) <- runStateT (parse fastaHeaderLineParser) prod + header <- case res of + Nothing -> liftIO . throwIO $ AssertionFailed "Could not find chromosome. Fasta file exhausted." + Just (Left e_) -> do + Right (chunk, _) <- next rest + let msg = show e_ ++ B.unpack chunk + liftIO . throwIO $ AssertionFailed ("Fasta header parsing error: " ++ msg) + Just (Right h) -> return h + return (header, view (P.break (==62)) rest >-> P.filter (\c -> c /= 10 && c /= 13)) +-- '>' == 62, '\n' == 10, \r == 13 + +fastaHeaderLineParser :: A.Parser Chrom +fastaHeaderLineParser = do + _ <- A.char '>' + chrom <- A.takeWhile isAlphaNum + A.skipSpace + A.skipWhile (\c -> c /= '\n' && c /= '\r') + A.endOfLine + return . Chrom . T.pack . B.unpack $ chrom diff --git a/src/SequenceFormats/FreqSum.hs b/src/SequenceFormats/FreqSum.hs new file mode 100644 --- /dev/null +++ b/src/SequenceFormats/FreqSum.hs @@ -0,0 +1,109 @@ +{-# LANGUAGE OverloadedStrings #-} + +{-| Module to parse and write freqSum files. The freqsum format is defined here: + +-} + +module SequenceFormats.FreqSum (readFreqSumStdIn, readFreqSumFile, FreqSumEntry(..), + FreqSumHeader(..), printFreqSumStdOut, printFreqSumFile, freqSumEntryToText) where + +import SequenceFormats.Utils (consumeProducer, Chrom(..)) + +import Control.Applicative ((<|>)) +import Control.Monad.Catch (MonadThrow, throwM) +import Control.Monad.IO.Class (MonadIO, liftIO) +import Control.Monad.Trans.State.Strict (runStateT) +import qualified Data.Attoparsec.Text as A +import Data.Char (isAlphaNum, isSpace) +import Data.Text (Text, intercalate, singleton) +import Data.Text.IO (putStr, hPutStr) +import Pipes (Producer, (>->), Consumer) +import Pipes.Attoparsec (parse, ParsingError(..)) +import qualified Pipes.Prelude as P +import Pipes.Safe (MonadSafe) +import Pipes.Safe.Prelude (withFile) +import qualified Pipes.Text.IO as PT +import Prelude hiding (putStr) +import System.IO (IOMode(..)) +import Turtle (format, s, d, (%)) + +-- |A Datatype representing the Header +data FreqSumHeader = FreqSumHeader { + fshNames :: [Text], -- ^A list of individual or group names + fshCounts :: [Int] -- ^A list of haplotype counts per individual/group. +} deriving (Eq) + +freqSumHeaderToText :: FreqSumHeader -> Text +freqSumHeaderToText (FreqSumHeader names nCounts) = + format ("#CHROM\tPOS\tREF\tALT\t"%s%"\n") (intercalate "\t" tuples) + where + tuples = zipWith (\n c -> format (s%"("%d%")") n c) names nCounts + +-- |A Datatype to denote a single freqSum line +data FreqSumEntry = FreqSumEntry { + fsChrom :: Chrom, -- ^The chromosome of the site + fsPos :: Int, -- ^The position of the site + fsRef :: Char, -- ^The reference allele + fsAlt :: Char, -- ^The alternative allele + fsCounts :: [Maybe Int] -- ^A list of allele counts in each group. Nothing denotes missing data. +} + +-- |This function converts a single freqSum entry to a printable freqSum line. +freqSumEntryToText :: FreqSumEntry -> Text +freqSumEntryToText (FreqSumEntry chrom pos ref alt maybeCounts) = + format (s%"\t"%d%"\t"%s%"\t"%s%"\t"%s%"\n") (unChrom chrom) pos (singleton ref) (singleton alt) + countStr + where + countStr = intercalate "\t" . map (format d . convertToNum) $ maybeCounts + convertToNum Nothing = -1 + convertToNum (Just a) = a + +readFreqSumProd :: (MonadThrow m) => + Producer Text m () -> m (FreqSumHeader, Producer FreqSumEntry m ()) +readFreqSumProd prod = do + (res, rest) <- runStateT (parse parseFreqSumHeader) prod + header <- case res of + Nothing -> throwM $ ParsingError [] "freqSum file exhausted" + Just (Left e) -> throwM e + Just (Right h) -> return h + return (header, consumeProducer parseFreqSumEntry rest) + +-- |A function to read a freqsum file from StdIn. Returns a pair of a freqSum Header and a Producer over all lines. +readFreqSumStdIn :: (MonadIO m, MonadThrow m) => m (FreqSumHeader, Producer FreqSumEntry m ()) +readFreqSumStdIn = readFreqSumProd PT.stdin + +-- |A function to read a freqsum file from a file. Returns a pair of a freqSum Header and a Producer over all lines. +readFreqSumFile :: (MonadSafe m) => FilePath -> m (FreqSumHeader, Producer FreqSumEntry m ()) +readFreqSumFile = readFreqSumProd . PT.readFile + +parseFreqSumHeader :: A.Parser FreqSumHeader +parseFreqSumHeader = do + tuples <- A.string "#CHROM\tPOS\tREF\tALT\t" >> A.sepBy' tuple A.space <* A.endOfLine + let names = map fst tuples + counts = map snd tuples + return $ FreqSumHeader names counts + where + tuple = (,) <$> A.takeWhile (\c -> isAlphaNum c || c == '_' || c == '-') <* A.char '(' <*> A.decimal <* A.char ')' + +parseFreqSumEntry :: A.Parser FreqSumEntry +parseFreqSumEntry = FreqSumEntry <$> (Chrom <$> A.takeTill isSpace) <* A.skipSpace <*> A.decimal <* + A.skipSpace <*> base <* A.skipSpace <*> baseOrDot <* A.skipSpace <*> counts <* A.endOfLine + where + counts = (parseMissing <|> parseCount) `A.sepBy` A.char '\t' + parseMissing = A.string "-1" *> pure Nothing + parseCount = Just <$> A.decimal + base = A.satisfy (A.inClass "ACTGN") + baseOrDot = A.satisfy (A.inClass "ACTG.") + +-- |A function to write freqSum data to StdOut. Expects the freqSum header as argument, and then returns a Consumer that accepts freqSum entries. +printFreqSumStdOut :: (MonadIO m) => FreqSumHeader -> Consumer FreqSumEntry m () +printFreqSumStdOut fsh = do + liftIO . putStr . freqSumHeaderToText $ fsh + P.map freqSumEntryToText >-> PT.stdout + +-- |A function that writes a freqSum file. Expects the FilePath and the freqSum header as arguments, and then returns a Consumer that accepts freqSum entries. +printFreqSumFile :: (MonadSafe m) => FilePath -> FreqSumHeader -> Consumer FreqSumEntry m () +printFreqSumFile outFile fsh = do + outFileH <- withFile outFile WriteMode return + liftIO . hPutStr outFileH . freqSumHeaderToText $ fsh + P.map freqSumEntryToText >-> PT.toHandle outFileH diff --git a/src/SequenceFormats/RareAlleleHistogram.hs b/src/SequenceFormats/RareAlleleHistogram.hs new file mode 100644 --- /dev/null +++ b/src/SequenceFormats/RareAlleleHistogram.hs @@ -0,0 +1,116 @@ +{-# LANGUAGE OverloadedStrings #-} + +{-| A module to read and write allele sharing histograms, as defined here: + +-} + +module SequenceFormats.RareAlleleHistogram (RareAlleleHistogram(..), readHistogramFromHandle, + SitePattern, readHistogram, showHistogram, showSitePattern) where + +import Control.Applicative (optional) +import Control.Error (Script, scriptIO, assertErr, throwE) +import Control.Monad.Trans.State.Strict (evalStateT) +import qualified Data.Attoparsec.Text as A +import Data.Char (isAlphaNum) +import Data.Int (Int64) +import Data.List (intercalate, sortBy) +import qualified Data.Map.Strict as Map +import qualified Data.Text as T +import Pipes.Attoparsec (parse) +import qualified Pipes.Text.IO as PT +import System.IO (Handle, openFile, IOMode(..), hClose) +import Turtle.Format ((%), w, format) + +-- |A datatype to represent an Allele Sharing Histogram: +data RareAlleleHistogram = RareAlleleHistogram { + raNames :: [T.Text], -- ^A list of branch names + raNVec :: [Int], -- ^A list of haploid sample sizes. + raMinAf :: Int, -- ^The minimum allele count + raMaxAf :: Int, -- ^The maximum allele count + raConditionOn :: [Int], -- ^A list of branch indices that were used to condition the allele + --sharing pattern + raExcludePatterns :: [SitePattern], -- ^A list of patterns that are excluded. + raTotalNrSites :: Int64, -- ^The total number of non-missing sites in the genome. + raCounts :: Map.Map SitePattern Int64, -- ^The actual data, a dictionary from allele sharing patterns to observed numbers. + raJackknifeEstimates :: Maybe (Map.Map SitePattern (Double, Double)) -- ^An optional dictionary that contains Jackknife estimates and standard deviations for each pattern frequency. +} + +-- |A simple type synonym for the SitePattern, represented as a list of Integers that represents +-- each pattern across the branches. +type SitePattern = [Int] + +-- |A simple function to convert a pattern into a String. +showSitePattern :: SitePattern -> String +showSitePattern nVec = intercalate "," . map show $ nVec + +-- |Function to convert a Rare Allele Histogram to text. Returns an error if attempting to print a +-- histogram with non-standard settings. Many settings, such as minAf>1, are only meant for +-- in-memory representations, but are not compatible with the file format itself. +showHistogram :: RareAlleleHistogram -> Either T.Text T.Text +showHistogram hist = do + assertErr "can only print histogram with minAf=1 due to format-legacy" $ raMinAf hist == 1 + assertErr "can only print histogram with no conditioning due to format-legacy" $ + null (raConditionOn hist) + assertErr "can only print histogram with no exclude pattern due to format-legacy" $ + null (raExcludePatterns hist) + let head0 = T.concat ["NAMES=", T.intercalate "," . raNames $ hist] + head1 = T.concat ["N=", T.pack . intercalate "," . map show . raNVec $ hist] + head2 = T.concat ["MAX_M=", T.pack . show . raMaxAf $ hist] + head3 = T.concat ["TOTAL_SITES=", T.pack . show . raTotalNrSites $ hist] + body = do + (k, v) <- sorted + case raJackknifeEstimates hist of + Nothing -> [T.intercalate " " [T.pack . showSitePattern $ k, T.pack . show $ v]] + Just jkHist -> do + let Just (jkMean, jkSE) = k `Map.lookup` jkHist + return $ T.intercalate " " [T.pack . showSitePattern $ k, T.pack . show $ v, + T.pack . show $ jkMean, T.pack . show $ jkSE] + return $ T.unlines (head0:head1:head2:head3:body) + where + sorted = sortBy (\(_, v1) (_, v2) -> compare v2 v1) $ Map.toList (raCounts hist) + +-- |Read a histogram from a FilePath +readHistogram :: FilePath -> Script RareAlleleHistogram +readHistogram path = do + h <- scriptIO $ openFile path ReadMode + hist <- readHistogramFromHandle h + scriptIO $ hClose h + return hist + +-- |Read a histogram from a File Handle. +readHistogramFromHandle :: Handle -> Script RareAlleleHistogram +readHistogramFromHandle handle = do + res <- evalStateT (parse parseHistogram) . PT.fromHandle $ handle + case res of + Nothing -> throwE "histogram file exhausted too early" + Just (Left err) -> throwE $ format ("Histogram parsing error: "%w) err + Just (Right hist) -> return hist + +parseHistogram :: A.Parser RareAlleleHistogram +parseHistogram = do + names <- parseNames + nVec <- parseNVec + maxM <- parseMaxM + totalNrSites <- parseTotalNrSites + body <- parseBody + let countHist = Map.fromList $ [(k, c) | (k, c, _) <- body] + jkHist = case head body of + (_, _, Just _) -> Just . Map.fromList $ [(k, (jkMean, jkSE)) | + (k, _, Just (jkMean, jkSE)) <- body] + _ -> Nothing + return $ RareAlleleHistogram names nVec 1 maxM [][] totalNrSites countHist jkHist + where + parseNames = A.string "NAMES=" *> name `A.sepBy1` A.char ',' <* A.endOfLine + name = A.takeWhile1 (\c -> isAlphaNum c || c == '_' || c == '-') + parseNVec = A.string "N=" *> A.decimal `A.sepBy1` A.char ',' <* A.endOfLine + parseMaxM = A.string "MAX_M=" *> A.decimal <* A.endOfLine + parseTotalNrSites = A.string "TOTAL_SITES=" *> A.decimal <* A.endOfLine + +parseBody :: A.Parser [(SitePattern, Int64, Maybe (Double, Double))] +parseBody = A.many1 patternLine + where + patternLine = (,,) <$> parsePattern <* A.space <*> parseLargeInt <*> optional parseJackknife <* + A.endOfLine + parsePattern = A.decimal `A.sepBy1` A.char ',' + parseLargeInt = read <$> A.many1 A.digit + parseJackknife = (,) <$> (A.space *> A.double) <* A.space <*> A.double diff --git a/src/SequenceFormats/Utils.hs b/src/SequenceFormats/Utils.hs new file mode 100644 --- /dev/null +++ b/src/SequenceFormats/Utils.hs @@ -0,0 +1,53 @@ +{-# LANGUAGE OverloadedStrings #-} + +-- |This module contains helper functions for file parsing. + +module SequenceFormats.Utils (liftParsingErrors, + consumeProducer, + FormatException(..), + Chrom(..)) where + +import Control.Exception (Exception) +import Control.Monad.Catch (MonadThrow, throwM) +import Control.Monad.Trans.Class (lift) +import qualified Data.Text as T +import qualified Data.Attoparsec.Text as A +import Pipes (Producer, next) +import Pipes.Attoparsec (ParsingError(..), parsed) + +-- |A wrapper datatype for Chromosome names. +newtype Chrom = Chrom {unChrom :: T.Text} deriving (Eq) + +-- |Show instance for Chrom +instance Show Chrom where + show (Chrom c) = show c + +-- |Ord instance for Chrom +instance Ord Chrom where + compare (Chrom c1) (Chrom c2) = + let c1' = if T.take 3 c1 == "chr" then T.drop 3 c1 else c1 + c2' = if T.take 3 c2 == "chr" then T.drop 3 c2 else c2 + cn1 = read . T.unpack $ c1' :: Int + cn2 = read . T.unpack $ c2' :: Int + in cn1 `compare` cn2 + +-- |An exception type for parsing BioInformatic file formats. +data FormatException = FormatException T.Text + deriving Show + +instance Exception FormatException + +-- |A function to help with reporting parsing errors to stderr. Returns a clean Producer over the +-- parsed datatype. +liftParsingErrors :: (MonadThrow m) => + Either (ParsingError, Producer T.Text m r) () -> Producer a m () +liftParsingErrors res = case res of + Left (ParsingError cont msg, restProd) -> do + Right (chunk, _) <- lift $ next restProd + let msg' = msg ++ " Error occurred while trying to parse this chunk: " ++ show chunk + throwM (ParsingError cont msg') + Right () -> return () + +-- |A helper function to parse a text producer, properly reporting all errors to stderr. +consumeProducer :: (MonadThrow m) => A.Parser a -> Producer T.Text m () -> Producer a m () +consumeProducer parser prod = parsed parser prod >>= liftParsingErrors diff --git a/src/SequenceFormats/VCF.hs b/src/SequenceFormats/VCF.hs new file mode 100644 --- /dev/null +++ b/src/SequenceFormats/VCF.hs @@ -0,0 +1,157 @@ +{-# LANGUAGE OverloadedStrings #-} + +{-| A module to help with parsing VCF files. The VCF format is defined here: + +-} + +module SequenceFormats.VCF (VCFheader(..), + VCFentry(..), + readVCFfromStdIn, + readVCFfromFile, + getGenotypes, + getDosages, + isTransversionSnp, + vcfToFreqSumEntry, + isBiallelicSnp) where + +import SequenceFormats.Utils (consumeProducer, Chrom(..)) +import SequenceFormats.FreqSum (FreqSumEntry(..)) + +import Control.Applicative ((<|>), empty) +import Control.Error (headErr, assertErr) +import Control.Monad (void) +import Control.Monad.Catch (MonadThrow, throwM) +import Control.Monad.Trans.State.Strict (runStateT) +import Control.Monad.IO.Class (MonadIO) +import qualified Data.Attoparsec.Text as A +import Data.Char (isSpace) +import qualified Data.Text as T +import Pipes (Producer) +import Pipes.Attoparsec (parse, ParsingError(..)) +import Pipes.Safe (MonadSafe) +import qualified Pipes.Text.IO as PT + +-- |A datatype to represent the VCF Header. Most comments are simply parsed as entire lines, but the very last comment line, containing the sample names, is separated out +data VCFheader = VCFheader { + vcfHeaderComments :: [T.Text], -- ^A list of containing all comments starting with a single '#' + vcfSampleNames :: [T.Text] -- ^The list of sample names parsed from the last comment line + -- starting with '##' +} deriving (Show) + +-- |A Datatype representing a single VCF entry. +data VCFentry = VCFentry { + vcfChrom :: Chrom, -- ^The chromosome + vcfPos :: Int, -- ^The position + vcfId :: Maybe T.Text, -- ^The SNP ID if non-missing + vcfRef :: T.Text, -- ^ The reference allele (supports also multi-character alleles for Indels) + vcfAlt :: [T.Text], -- ^The alternative alleles, each one possible of multiple characters + vcfQual :: Double, -- ^The quality value + vcfFilter :: Maybe T.Text, -- ^The Filter value, if non-missing. + vcfInfo :: [T.Text], -- ^A list of Info fields + vcfFormatString :: [T.Text], -- ^A list of format tags + vcfGenotypeInfo :: [[T.Text]] -- ^A list of format fields for each sapmle. +} deriving (Show) + +readVCFfromProd :: (MonadThrow m) => + Producer T.Text m () -> m (VCFheader, Producer VCFentry m ()) +readVCFfromProd prod = do + (res, rest) <- runStateT (parse vcfHeaderParser) prod + header <- case res of + Nothing -> throwM $ ParsingError [] "freqSum file exhausted" + Just (Left e) -> throwM e + Just (Right h) -> return h + return (header, consumeProducer vcfEntryParser rest) + +-- |Reading a VCF from StdIn. Returns a VCFHeader and a Producer over VCFentries. +readVCFfromStdIn :: (MonadIO m, MonadThrow m) => m (VCFheader, Producer VCFentry m ()) +readVCFfromStdIn = readVCFfromProd PT.stdin + +-- |Reading a VCF from a file. Returns a VCFHeader and a Producer over VCFentries. +readVCFfromFile :: (MonadSafe m) => FilePath -> m (VCFheader, Producer VCFentry m ()) +readVCFfromFile = readVCFfromProd . PT.readFile + +vcfHeaderParser :: A.Parser VCFheader +vcfHeaderParser = VCFheader <$> A.many1' doubleCommentLine <*> singleCommentLine + where + doubleCommentLine = do + c1 <- A.string "##" + s_ <- A.takeWhile1 (not . A.isEndOfLine) + A.endOfLine + return $ T.append c1 s_ + singleCommentLine = do + void $ A.char '#' + s_ <- A.takeWhile1 (not . A.isEndOfLine) + A.endOfLine + let fields = T.splitOn "\t" s_ + return . drop 9 $ fields + +vcfEntryParser :: A.Parser VCFentry +vcfEntryParser = VCFentry <$> (Chrom <$> word) <* sp <*> A.decimal <* sp <*> parseId <* sp <*> + word <* sp <*> parseAlternativeAlleles <* sp <*> A.double <* sp <*> parseFilter <* sp <*> + parseInfoFields <* sp <*> parseFormatStrings <* sp <*> parseGenotypeInfos <* A.endOfLine + where + word = A.takeTill A.isHorizontalSpace + sp = A.satisfy A.isHorizontalSpace + parseId = parseDot <|> (Just <$> word) + parseDot = A.char '.' *> empty + parseAlternativeAlleles = parseDot <|> (parseAllele `A.sepBy1` A.char ',') + parseAllele = A.takeTill (\c -> c == ',' || A.isHorizontalSpace c) + parseFilter = parseDot <|> (Just <$> word) + parseInfoFields = parseDot <|> (parseInfoField `A.sepBy1` A.char ';') + parseInfoField = A.takeTill (\c -> c == ';' || A.isHorizontalSpace c) + parseFormatStrings = A.takeTill (\c -> c == ':' || A.isHorizontalSpace c) `A.sepBy1` A.char ':' + parseGenotypeInfos = parseGenotype `A.sepBy1` (A.satisfy A.isHorizontalSpace) + parseGenotype = parseGenoField `A.sepBy1` (A.char ':') + parseGenoField = A.takeTill (\c -> c == ':' || isSpace c) + +-- |returns True if the SNP is biallelic. +isBiallelicSnp :: T.Text -> [T.Text] -> Bool +isBiallelicSnp ref alt = validRef && validAlt + where + validRef = (ref `elem` ["A", "C", "G", "T"]) + validAlt = case alt of + [alt'] -> alt' `elem` ["A", "C", "G", "T"] + _ -> False + +-- |returns True if the SNp is a biallelic Transversion SNP (i.e. one of G/T, G/C, A/T, A/C) +isTransversionSnp :: T.Text -> [T.Text] -> Bool +isTransversionSnp ref alt = + case alt of + [alt'] -> isBiallelicSnp ref alt && (not $ isTransition ref alt') + _ -> False + where + isTransition r a = ((r == "A") && (a == "G")) || ((r == "G") && (a == "A")) || + ((r == "C") && (a == "T")) || ((r == "T") && (a == "C")) + +-- |Extracts the genotype fields (for each sapmle) from a VCF entry +getGenotypes :: VCFentry -> Either String [T.Text] +getGenotypes vcfEntry = do + gtIndex <- fmap fst . headErr "GT format field not found" . filter ((=="GT") . snd) . + zip [0..] . vcfFormatString $ vcfEntry + return $ map (!!gtIndex) (vcfGenotypeInfo vcfEntry) + +-- |Extracts the dosages (the sum of non-reference alleles) per sample (returns a Left Error if it fails.) +getDosages :: VCFentry -> Either String [Maybe Int] +getDosages vcfEntry = do + genotypes <- getGenotypes vcfEntry + let dosages = do + gen <- genotypes + if '.' `elem` (T.unpack gen) then + return Nothing + else + return . Just $ T.count "1" gen + return dosages + +-- |Converts a VCFentry to the simpler FreqSum format (returns a Left Error if it fails.) +vcfToFreqSumEntry :: VCFentry -> Either String FreqSumEntry +vcfToFreqSumEntry vcfEntry = do + dosages <- getDosages vcfEntry + assertErr "multi-site reference allele" $ T.length (vcfRef vcfEntry) == 1 + assertErr "need exactly one alternative allele" $ length (vcfAlt vcfEntry) == 1 + assertErr "multi-site alternative allele" $ T.length (head . vcfAlt $ vcfEntry) == 1 + let ref = T.head (vcfRef vcfEntry) + let alt = T.head . head . vcfAlt $ vcfEntry + assertErr "Invalid Reference Allele" $ ref `elem` ['A', 'C', 'T', 'G', 'N'] + assertErr "Invalid Alternative Allele" $ alt `elem` ['A', 'C', 'T', 'G', '.'] + return $ FreqSumEntry (vcfChrom vcfEntry) (vcfPos vcfEntry) ref alt dosages +