Safe Haskell	None
Language	Haskell2010

SequenceFormats.Eigenstrat

Description

Module to read and parse Eigenstrat-formatted genotype data. The Eigenstrat format is defined at https://github.com/argriffing/eigensoft/blob/master/CONVERTF/README.

Synopsis

data EigenstratSnpEntry = EigenstratSnpEntry {
- snpChrom :: Chrom
- snpPos :: Int
- snpGeneticPos :: Double
- snpId :: ByteString
- snpRef :: Char
- snpAlt :: Char
}
data EigenstratIndEntry = EigenstratIndEntry String Sex String
readEigenstratInd :: MonadIO m => FilePath -> m [EigenstratIndEntry]
data GenoEntry
- = HomRef
- | Het
- | HomAlt
- | Missing
type GenoLine = Vector GenoEntry
data Sex
- = Male
- | Female
- | Unknown
readEigenstratSnpStdIn :: (MonadThrow m, MonadIO m) => Producer EigenstratSnpEntry m ()
readEigenstratSnpFile :: MonadSafe m => FilePath -> Producer EigenstratSnpEntry m ()
readEigenstrat :: MonadSafe m => FilePath -> FilePath -> FilePath -> m ([EigenstratIndEntry], Producer (EigenstratSnpEntry, GenoLine) m ())
writeEigenstrat :: MonadSafe m => FilePath -> FilePath -> FilePath -> [EigenstratIndEntry] -> Consumer (EigenstratSnpEntry, GenoLine) m ()
writeEigenstratIndFile :: MonadIO m => FilePath -> [EigenstratIndEntry] -> m ()
writeEigenstratSnp :: MonadIO m => Handle -> Consumer EigenstratSnpEntry m ()
writeEigenstratGeno :: MonadIO m => Handle -> Consumer GenoLine m ()

Documentation

data EigenstratSnpEntry Source #

A datatype to represent a single genomic SNP. The constructor arguments are: Chromosome, Position, Reference Allele, Alternative Allele.

Constructors

EigenstratSnpEntry
Fields snpChrom :: Chrom snpPos :: Int snpGeneticPos :: Double snpId :: ByteString snpRef :: Char snpAlt :: Char

Instances

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

data EigenstratIndEntry Source #

A datatype to represent a single individual. The constructor arguments are: Name, Sex and Population Name

Constructors

EigenstratIndEntry String Sex String

Instances

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

readEigenstratInd :: MonadIO m => FilePath -> m [EigenstratIndEntry] Source #

Function to read an Eigenstrat individual file. Returns the Eigenstrat Individual Entries as list.

data GenoEntry Source #

A datatype to represent the genotype of an individual at a SNP.

Constructors

HomRef
Het
HomAlt
Missing

Instances

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

type GenoLine = Vector GenoEntry Source #

Vector of the genotypes of all individuals at a single SNP.

data Sex Source #

A datatype to represent Sex in an Eigenstrat Individual file

Constructors

Male
Female
Unknown

Instances

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

readEigenstratSnpStdIn :: (MonadThrow m, MonadIO m) => Producer EigenstratSnpEntry m () Source #

Function to read a Snp File from StdIn. Returns a Pipes-Producer over the EigenstratSnpEntries.

readEigenstratSnpFile :: MonadSafe m => FilePath -> Producer EigenstratSnpEntry m () Source #

Function to read a Snp File from a file. Returns a Pipes-Producer over the EigenstratSnpEntries.

readEigenstrat Source #

Arguments

:: MonadSafe m
=> FilePath	The Genotype file
-> FilePath	The Snp File
-> FilePath	The Ind file
-> m ([EigenstratIndEntry], Producer (EigenstratSnpEntry, GenoLine) m ())

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.

writeEigenstrat Source #

Arguments

:: 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.

Function to write an Eigenstrat Database. Returns a consumer expecting joint Snp- and Genotype lines.

writeEigenstratIndFile :: MonadIO m => FilePath -> [EigenstratIndEntry] -> m () Source #

Function to write an Eigenstrat Ind file.

writeEigenstratSnp Source #

Arguments

:: MonadIO m
=> Handle	The Eigenstrat Snp File Handle.
-> Consumer EigenstratSnpEntry m ()	A consumer to read EigenstratSnpEntries

Function to write an Eigenstrat Snp File. Returns a consumer expecting EigenstratSnpEntries.

writeEigenstratGeno Source #

Arguments

:: MonadIO m
=> Handle	The Genotype file handle
-> Consumer GenoLine m ()	A consumer to read Genotype entries.

Function to write an Eigentrat Geno File. Returns a consumer expecting Eigenstrat Genolines.