BiobaseInfernal- Infernal data structures and tools



Re-export the most import parts.



eneeTabularHit :: (Functor m, Monad m) => Enumeratee ByteString [TabularHit] m aSource

Transform a stream into tabular hits.

data VerboseHit Source

Captures a complete alignment




vhTarget :: (Int, Int)

part of target sequence (start counting at 1)

vhQuery :: (Int, Int)

which part of the CM/stk do we align to

vhCM :: ByteString

the CM for this alignment

vhStrand :: Strand

should be either + or -

vhScore :: Double

bit score

vhEvalue :: Double

number of hits we expect to find with score or higher for targetSequence length

vhPvalue :: Double


vhGC :: Int


vhScaffold :: ByteString

scaffold, chromosome, ... (the name of the sequence, not the sequence data!)

vhWuss :: ByteString

fancy secondary structure annotation using wuss notation

vhConsensus :: ByteString

query consensus (upper: highly, lower: weak/no)

vhScoring :: ByteString

represents where positive and negative scores come from

vhSequence :: ByteString

the target sequence which aligns to the model

vhAnnotation :: [ByteString]

any annotations that could be associated (# lines)

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.

data Species Source

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).




data Clan Source

Simple RfamClan data wrapper. Could Easily be just a list of bytestrings, which it is using strings