Safe Haskell | Safe-Inferred |
---|---|
Language | Haskell2010 |
Synopsis
- readBimStdIn :: (MonadThrow m, MonadIO m) => Producer EigenstratSnpEntry m ()
- readBimFile :: MonadSafe m => FilePath -> Producer EigenstratSnpEntry m ()
- writeBim :: MonadIO m => Handle -> Consumer EigenstratSnpEntry m ()
- readFamFile :: MonadIO m => FilePath -> m [PlinkFamEntry]
- readPlinkBedFile :: MonadSafe m => FilePath -> Int -> m (Producer GenoLine m ())
- readPlink :: MonadSafe m => FilePath -> FilePath -> FilePath -> m ([PlinkFamEntry], Producer (EigenstratSnpEntry, GenoLine) m ())
- writePlink :: MonadSafe m => FilePath -> FilePath -> FilePath -> [PlinkFamEntry] -> Consumer (EigenstratSnpEntry, GenoLine) m ()
- data PlinkFamEntry = PlinkFamEntry {}
- plinkFam2EigenstratInd :: PlinkPopNameMode -> PlinkFamEntry -> EigenstratIndEntry
- eigenstratInd2PlinkFam :: PlinkPopNameMode -> EigenstratIndEntry -> PlinkFamEntry
- data PlinkPopNameMode
Documentation
readBimStdIn :: (MonadThrow m, MonadIO m) => Producer EigenstratSnpEntry m () Source #
Function to read a Bim File from StdIn. Returns a Pipes-Producer over the EigenstratSnpEntries.
readBimFile :: MonadSafe m => FilePath -> Producer EigenstratSnpEntry m () Source #
Function to read a Bim File from a file. Returns a Pipes-Producer over the EigenstratSnpEntries.
:: 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 [PlinkFamEntry] Source #
Function to read a Plink fam file. Returns the Eigenstrat Individual Entries as list.
readPlinkBedFile :: MonadSafe m => FilePath -> Int -> m (Producer GenoLine m ()) Source #
A function to read a bed file from a file. Returns a Producer over all lines.
:: MonadSafe m | |
=> FilePath | The Bed file |
-> FilePath | The Bim File |
-> FilePath | The Fam file |
-> m ([PlinkFamEntry], 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.
:: MonadSafe m | |
=> FilePath | The Bed file |
-> FilePath | The Bim File |
-> FilePath | The Fam file |
-> [PlinkFamEntry] | 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.
data PlinkFamEntry Source #
PlinkFamEntry | |
|
Instances
Show PlinkFamEntry Source # | |
Defined in SequenceFormats.Plink showsPrec :: Int -> PlinkFamEntry -> ShowS # show :: PlinkFamEntry -> String # showList :: [PlinkFamEntry] -> ShowS # | |
Eq PlinkFamEntry Source # | |
Defined in SequenceFormats.Plink (==) :: PlinkFamEntry -> PlinkFamEntry -> Bool # (/=) :: PlinkFamEntry -> PlinkFamEntry -> Bool # |
data PlinkPopNameMode Source #
Instances
Show PlinkPopNameMode Source # | |
Defined in SequenceFormats.Plink showsPrec :: Int -> PlinkPopNameMode -> ShowS # show :: PlinkPopNameMode -> String # showList :: [PlinkPopNameMode] -> ShowS # | |
Eq PlinkPopNameMode Source # | |
Defined in SequenceFormats.Plink (==) :: PlinkPopNameMode -> PlinkPopNameMode -> Bool # (/=) :: PlinkPopNameMode -> PlinkPopNameMode -> Bool # |