Safe Haskell	Safe-Inferred
Language	Haskell2010

Poseidon.GenotypeData

Synopsis

data GenoDataSource
- = PacBaseDir {
  - getPacBaseDir :: FilePath
  }
- | GenoDirect {
  - getGenoDirect :: GenotypeDataSpec
  }
data GenotypeDataSpec = GenotypeDataSpec {
- genotypeFileSpec :: GenotypeFileSpec
- genotypeSnpSet :: Maybe SNPSetSpec
}
data GenotypeFileSpec
- = GenotypeEigenstrat {
  - _esGenoFile :: FilePath
  - _esGenoFileChkSum :: Maybe String
  - _esSnpFile :: FilePath
  - _esSnpFileChkSum :: Maybe String
  - _esIndFile :: FilePath
  - _esIndFileChkSum :: Maybe String
  }
- | GenotypePlink {
  - _plGenoFile :: FilePath
  - _plGenoFileChkSum :: Maybe String
  - _plSnpFile :: FilePath
  - _plSnpFileChkSum :: Maybe String
  - _plIndFile :: FilePath
  - _plIndFileChkSum :: Maybe String
  }
- | GenotypeVCF {
  - _vcfGenoFile :: FilePath
  - _vcfGenoFileChkSum :: Maybe String
  }
data GenotypeOutFormatSpec
- = GenotypeOutFormatPlink
- | GenotypeOutFormatEigenstrat
- | GenotypeOutFormatVCF
data SNPSetSpec
- = SNPSet1240K
- | SNPSetHumanOrigins
- | SNPSetOther
snpSetMergeList :: [SNPSetSpec] -> Bool -> SNPSetSpec
snpSetMerge :: SNPSetSpec -> SNPSetSpec -> Bool -> SNPSetSpec
reduceGenotypeFilepaths :: MonadThrow m => GenotypeDataSpec -> m (FilePath, GenotypeDataSpec)
loadIndividuals :: FilePath -> GenotypeDataSpec -> PoseidonIO [EigenstratIndEntry]
findGroupNamesInVCFheader :: [ByteString] -> Maybe [ByteString]
findGeneticSexInVCFheader :: [ByteString] -> Maybe (Either String [Sex])
loadGenotypeData :: MonadSafe m => FilePath -> GenotypeDataSpec -> m (Producer (EigenstratSnpEntry, GenoLine) m ())
vcf2eigenstratPipe :: MonadThrow m => Pipe VCFentry (EigenstratSnpEntry, GenoLine) m r
joinEntries :: MonadIO m => LogA -> [Int] -> [String] -> [Maybe (EigenstratSnpEntry, GenoLine)] -> m (EigenstratSnpEntry, GenoLine)
getConsensusSnpEntry :: MonadIO m => LogA -> [EigenstratSnpEntry] -> m EigenstratSnpEntry
recodeAlleles :: EigenstratSnpEntry -> EigenstratSnpEntry -> GenoLine -> Either String GenoLine
printSNPCopyProgress :: MonadIO m => LogA -> UTCTime -> Pipe a a m ()
selectIndices :: [Int] -> (EigenstratSnpEntry, GenoLine) -> (EigenstratSnpEntry, GenoLine)
writeVCF :: MonadSafe m => LogA -> [JannoRow] -> FilePath -> Consumer (EigenstratSnpEntry, GenoLine) m ()
createVCFentry :: MonadIO m => LogA -> [JannoRow] -> (EigenstratSnpEntry, GenoLine) -> m VCFentry

Documentation

data GenoDataSource Source #

Constructors

PacBaseDir
Fields getPacBaseDir :: FilePath
GenoDirect
Fields getGenoDirect :: GenotypeDataSpec

Instances

Instances details

Show GenoDataSource Source #
Instance details Defined in Poseidon.GenotypeData Methods showsPrec :: Int -> GenoDataSource -> ShowS # show :: GenoDataSource -> String # showList :: [GenoDataSource] -> ShowS #

data GenotypeDataSpec Source #

Constructors

GenotypeDataSpec
Fields genotypeFileSpec :: GenotypeFileSpec genotypeSnpSet :: Maybe SNPSetSpec

Instances

Instances details

FromJSON GenotypeDataSpec Source #	To facilitate automatic parsing of GenotypeDataSpec from JSON files
Instance details Defined in Poseidon.GenotypeData Methods parseJSON :: Value -> Parser GenotypeDataSpec parseJSONList :: Value -> Parser [GenotypeDataSpec]
ToJSON GenotypeDataSpec Source #
Instance details Defined in Poseidon.GenotypeData Methods toJSON :: GenotypeDataSpec -> Value toEncoding :: GenotypeDataSpec -> Encoding toJSONList :: [GenotypeDataSpec] -> Value toEncodingList :: [GenotypeDataSpec] -> Encoding
Show GenotypeDataSpec Source #
Instance details Defined in Poseidon.GenotypeData Methods showsPrec :: Int -> GenotypeDataSpec -> ShowS # show :: GenotypeDataSpec -> String # showList :: [GenotypeDataSpec] -> ShowS #
Eq GenotypeDataSpec Source #
Instance details Defined in Poseidon.GenotypeData Methods (==) :: GenotypeDataSpec -> GenotypeDataSpec -> Bool # (/=) :: GenotypeDataSpec -> GenotypeDataSpec -> Bool #

data GenotypeFileSpec Source #

Constructors

GenotypeEigenstrat
Fields _esGenoFile :: FilePath _esGenoFileChkSum :: Maybe String _esSnpFile :: FilePath _esSnpFileChkSum :: Maybe String _esIndFile :: FilePath _esIndFileChkSum :: Maybe String
GenotypePlink
Fields _plGenoFile :: FilePath _plGenoFileChkSum :: Maybe String _plSnpFile :: FilePath _plSnpFileChkSum :: Maybe String _plIndFile :: FilePath _plIndFileChkSum :: Maybe String
GenotypeVCF
Fields _vcfGenoFile :: FilePath _vcfGenoFileChkSum :: Maybe String

Instances

Instances details

Show GenotypeFileSpec Source #
Instance details Defined in Poseidon.GenotypeData Methods showsPrec :: Int -> GenotypeFileSpec -> ShowS # show :: GenotypeFileSpec -> String # showList :: [GenotypeFileSpec] -> ShowS #
Eq GenotypeFileSpec Source #
Instance details Defined in Poseidon.GenotypeData Methods (==) :: GenotypeFileSpec -> GenotypeFileSpec -> Bool # (/=) :: GenotypeFileSpec -> GenotypeFileSpec -> Bool #

data GenotypeOutFormatSpec Source #

Constructors

GenotypeOutFormatPlink
GenotypeOutFormatEigenstrat
GenotypeOutFormatVCF

Instances

Instances details

Read GenotypeOutFormatSpec Source #
Instance details Defined in Poseidon.GenotypeData Methods readsPrec :: Int -> ReadS GenotypeOutFormatSpec # readList :: ReadS [GenotypeOutFormatSpec] # readPrec :: ReadPrec GenotypeOutFormatSpec # readListPrec :: ReadPrec [GenotypeOutFormatSpec] #
Show GenotypeOutFormatSpec Source #
Instance details Defined in Poseidon.GenotypeData Methods showsPrec :: Int -> GenotypeOutFormatSpec -> ShowS # show :: GenotypeOutFormatSpec -> String # showList :: [GenotypeOutFormatSpec] -> ShowS #

data SNPSetSpec Source #

Constructors

SNPSet1240K
SNPSetHumanOrigins
SNPSetOther

Instances

Instances details

FromJSON SNPSetSpec Source #
Instance details Defined in Poseidon.GenotypeData Methods parseJSON :: Value -> Parser SNPSetSpec parseJSONList :: Value -> Parser [SNPSetSpec]
ToJSON SNPSetSpec Source #
Instance details Defined in Poseidon.GenotypeData Methods toJSON :: SNPSetSpec -> Value toEncoding :: SNPSetSpec -> Encoding toJSONList :: [SNPSetSpec] -> Value toEncodingList :: [SNPSetSpec] -> Encoding
Show SNPSetSpec Source #
Instance details Defined in Poseidon.GenotypeData Methods showsPrec :: Int -> SNPSetSpec -> ShowS # show :: SNPSetSpec -> String # showList :: [SNPSetSpec] -> ShowS #
Eq SNPSetSpec Source #
Instance details Defined in Poseidon.GenotypeData Methods (==) :: SNPSetSpec -> SNPSetSpec -> Bool # (/=) :: SNPSetSpec -> SNPSetSpec -> Bool #

snpSetMergeList :: [SNPSetSpec] -> Bool -> SNPSetSpec Source #

snpSetMerge :: SNPSetSpec -> SNPSetSpec -> Bool -> SNPSetSpec Source #

reduceGenotypeFilepaths :: MonadThrow m => GenotypeDataSpec -> m (FilePath, GenotypeDataSpec) Source #

removes directories of all filenames and returns a tuple of the basename and a modified GenotypeDataSpec with pure filenames In case basedirectories do not match, this function will throw an exception

loadIndividuals Source #

Arguments

:: FilePath	the base directory
-> GenotypeDataSpec	the Genotype spec
-> PoseidonIO [EigenstratIndEntry]	the returned list of EigenstratIndEntries.

A function to return a list of all individuals in the genotype files of a package.

findGroupNamesInVCFheader :: [ByteString] -> Maybe [ByteString] Source #

findGeneticSexInVCFheader :: [ByteString] -> Maybe (Either String [Sex]) Source #

loadGenotypeData Source #

Arguments

:: MonadSafe m
=> FilePath	the base path
-> GenotypeDataSpec	the genotype spec
-> m (Producer (EigenstratSnpEntry, GenoLine) m ())	a Producer over the Snp position values and the genotype line.

A function to read the genotype data of a package

vcf2eigenstratPipe :: MonadThrow m => Pipe VCFentry (EigenstratSnpEntry, GenoLine) m r Source #

joinEntries :: MonadIO m => LogA -> [Int] -> [String] -> [Maybe (EigenstratSnpEntry, GenoLine)] -> m (EigenstratSnpEntry, GenoLine) Source #

getConsensusSnpEntry :: MonadIO m => LogA -> [EigenstratSnpEntry] -> m EigenstratSnpEntry Source #

recodeAlleles :: EigenstratSnpEntry -> EigenstratSnpEntry -> GenoLine -> Either String GenoLine Source #

printSNPCopyProgress :: MonadIO m => LogA -> UTCTime -> Pipe a a m () Source #

selectIndices :: [Int] -> (EigenstratSnpEntry, GenoLine) -> (EigenstratSnpEntry, GenoLine) Source #

writeVCF :: MonadSafe m => LogA -> [JannoRow] -> FilePath -> Consumer (EigenstratSnpEntry, GenoLine) m () Source #

createVCFentry :: MonadIO m => LogA -> [JannoRow] -> (EigenstratSnpEntry, GenoLine) -> m VCFentry Source #