SequenceFormats.Plink

Documentation

readBimStdIn :: (MonadThrow m, MonadIO m) => Producer EigenstratSnpEntry m ()

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

readBimFile :: MonadSafe m => FilePath -> Producer EigenstratSnpEntry m ()

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

writeBim

Arguments

:: MonadIO m

=> Handle

The Eigenstrat Snp File handle.

-> Consumer EigenstratSnpEntry m ()

A consumer to read EigenstratSnpEntries

Function to write a Bim file. Returns a consumer expecting EigenstratSnpEntries.

readFamFile :: MonadIO m => FilePath -> m [EigenstratIndEntry]

Function to read a Plink fam file. Returns the Eigenstrat Individual Entries as list.

readPlinkBedFile :: MonadSafe m => FilePath -> Int -> m (Producer GenoLine m ())

A function to read a bed file from a file. Returns a Producer over all lines.

readPlink

Arguments

:: MonadSafe m

=> FilePath

The Bed file

-> FilePath

The Bim File

-> FilePath

The Fam file

-> m ([EigenstratIndEntry], Producer (EigenstratSnpEntry, GenoLine) m ())

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.

writePlink

Arguments

:: MonadSafe m

=> FilePath

The Bed file

-> FilePath

The Bim File

-> FilePath

The Fam file

-> [EigenstratIndEntry]

The list of individual entries

-> Consumer (EigenstratSnpEntry, GenoLine) m ()

A consumer to read joint Snp/Genotype entries.

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