Biobase.Infernal.RfamFasta.Import
Contents
Description
Imports an Rfam Fasta file and provides simultaneous export to four different data structures for lookups.
- eneeRfamFasta :: Monad m => Enumeratee ByteString [RfamFasta] m a
- iModelAC2ID :: Monad m => Iteratee [RfamFasta] m ModelAC2ID
- iModelID2AC :: Monad m => Iteratee [RfamFasta] m ModelID2AC
- iACAC2RfamFasta :: Monad m => Iteratee [RfamFasta] m ACAC2RfamFasta
- iIDAC2RfamFasta :: Monad m => Iteratee [RfamFasta] m IDAC2RfamFasta
- fromFileZip :: FilePath -> IO (ModelAC2ID, ModelID2AC, ACAC2RfamFasta, IDAC2RfamFasta)
- fromFile :: FilePath -> IO (ModelAC2ID, ModelID2AC, ACAC2RfamFasta, IDAC2RfamFasta)
Documentation
eneeRfamFasta :: Monad m => Enumeratee ByteString [RfamFasta] m aSource
Enumeratee for RfamFasta entries from a ByteString.
In-memory lookup
iModelAC2ID :: Monad m => Iteratee [RfamFasta] m ModelAC2IDSource
Create a mapping between rfam family accession numbers and rfam family names.
iModelID2AC :: Monad m => Iteratee [RfamFasta] m ModelID2ACSource
Create a mapping between rfam family names and rfam family accession numbers.
iACAC2RfamFasta :: Monad m => Iteratee [RfamFasta] m ACAC2RfamFastaSource
Provides a mapping between (Rfam accession, sequence accession) and the
complete RfamFasta.
iIDAC2RfamFasta :: Monad m => Iteratee [RfamFasta] m IDAC2RfamFastaSource
Provides a mapping between (Rfam name, sequence accession) and the complete
RfamFasta.
File reading.
fromFileZip :: FilePath -> IO (ModelAC2ID, ModelID2AC, ACAC2RfamFasta, IDAC2RfamFasta)Source
Convenience function creating all maps.
fromFile :: FilePath -> IO (ModelAC2ID, ModelID2AC, ACAC2RfamFasta, IDAC2RfamFasta)Source
Convenience function creating all maps.