Biobase.Infernal
Description
Re-export the most import parts.
- data TabularHit = TabularHit {
- thModel :: !ModelIdentification
- thTarget :: !Scaffold
- thTargetStart :: !Int
- thTargetStop :: !Int
- thModelStart :: !Int
- thModelStop :: !Int
- thBitScore :: !BitScore
- thEvalue :: !Double
- thGCpercent :: !Int
- thFromFile :: FilePath -> IO [TabularHit]
- eneeTabularHit :: (Functor m, Monad m) => Enumeratee ByteString [TabularHit] m a
- data VerboseHit = VerboseHit {
- vhTargetStart :: !Int
- vhTargetStop :: !Int
- vhModelStart :: !Int
- vhModelStop :: !Int
- vhModel :: !ModelIdentification
- vhStrand :: !Strand
- vhBitScore :: !BitScore
- vhEvalue :: !Double
- vhPvalue :: !Double
- vhGCpercent :: !Int
- vhTarget :: !Scaffold
- 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 SpeciesTaxonomy = SpeciesTaxonomy {}
- tFromFile :: FilePath -> IO (Map SpeciesName SpeciesTaxonomy, Map SpeciesAccession SpeciesTaxonomy)
- data Clan = Clan {
- cAccession :: !ClanAccession
- cIdentifier :: !ClanIdentification
- cMembers :: ![ModelAccession]
- cStrings :: ![ByteString]
- cFromFile :: FilePath -> IO [Clan]
Documentation
data TabularHit Source
Tabular Infernal hits. See Biobase.Infernal.Hit for description of the individual fields.
Constructors
| TabularHit | |
Fields
| |
Instances
| Read TabularHit | |
| Show TabularHit | |
| Hit TabularHit | Generalized accessors. |
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
| |
Instances
| Read VerboseHit | |
| Show VerboseHit | |
| Hit VerboseHit | Generalized accessors. |
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
data SpeciesTaxonomy 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
| SpeciesTaxonomy | |
Fields
| |
Instances
tFromFile :: FilePath -> IO (Map SpeciesName SpeciesTaxonomy, Map SpeciesAccession SpeciesTaxonomy)Source
Simple Rfam clan data.
Constructors
| Clan | |
Fields
| |