Re-export the most import parts.
- data TabularHit = TabularHit {
- thModel :: ByteString
- thTarget :: ByteString
- thScaffoldStart :: Int
- thScaffoldStop :: Int
- thQueryStart :: Int
- thQueryStop :: Int
- thBitScore :: Double
- thEvalue :: Double
- thGCpercent :: Int
- thFromFile :: FilePath -> IO [TabularHit]
- eneeTabularHit :: (Functor m, Monad m) => Enumeratee ByteString [TabularHit] m a
- data VerboseHit = VerboseHit {
- vhTarget :: !(Int, Int)
- vhQuery :: !(Int, Int)
- vhCM :: !ByteString
- vhStrand :: !Strand
- vhScore :: !Double
- vhEvalue :: !Double
- vhPvalue :: !Double
- vhGC :: !Int
- vhScaffold :: !ByteString
- vhWuss :: !ByteString
- vhConsensus :: !ByteString
- vhScoring :: !ByteString
- vhSequence :: !ByteString
- vhAnnotation :: ![ByteString]
- vhFromFile :: FilePath -> IO [VerboseHit]
- eneeVerboseHit :: (Functor m, Monad m) => Enumeratee ByteString [VerboseHit] m a
- vhEneeByteString :: Monad m => Enumeratee [VerboseHit] ByteString m a
- vhEneeByteStrings :: Monad m => Enumeratee [VerboseHit] [ByteString] m a
- data Species = Species {
- name :: ByteString
- classification :: [ByteString]
- taxid :: Int
- tFromFile :: FilePath -> IO (Map ByteString Species, Map Int Species)
- data Clan = Clan {
- accession :: ByteString
- identifier :: ByteString
- members :: [ByteString]
- strings :: [ByteString]
- cFromFile :: FilePath -> IO [Clan]
Documentation
data TabularHit Source
TabularHit | |
|
thFromFile :: FilePath -> IO [TabularHit]Source
eneeTabularHit :: (Functor m, Monad m) => Enumeratee ByteString [TabularHit] m aSource
Transform a stream into tabular hits.
data VerboseHit Source
Captures a complete alignment
VerboseHit | |
|
vhFromFile :: FilePath -> IO [VerboseHit]Source
eneeVerboseHit :: (Functor m, Monad m) => Enumeratee ByteString [VerboseHit] m aSource
Transforms a stream into verbose hits. We need to keep a state in the accumulator to keep track of the current CM, scaffold and strand.
vhEneeByteString :: Monad m => Enumeratee [VerboseHit] ByteString m aSource
vhEneeByteStrings :: Monad m => Enumeratee [VerboseHit] [ByteString] m aSource
For each species, we store the name and a classification list from most general (head) to most specific (last). The database comes with the NCBI taxon identifier (taxid).
Species | |
|
Simple RfamClan data wrapper. Could Easily be just a list of bytestrings, which it is using strings
Clan | |
|