Documentation

Constructors

TabularHit
Fields thModel :: ByteString thTarget :: ByteString thScaffoldStart :: Int thScaffoldStop :: Int thQueryStart :: Int thQueryStop :: Int thBitScore :: Double thEvalue :: Double thGCpercent :: Int

Instances

Read TabularHit
Show 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

Constructors

VerboseHit

Fields

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

Instances

Read VerboseHit
Show 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

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).

Constructors

Species
Fields name :: ByteString classification :: [ByteString] taxid :: Int

Instances

Show Species