| Safe Haskell | None |
|---|---|
| Language | Haskell98 |
Data.Fasta.ByteString.Lazy.Parse
Description
Collection of functions for the parsing of a fasta file. Uses the lazy - ByteString type.
- parsecFasta :: ByteString -> [FastaSequence]
- parsecCLIPFasta :: ByteString -> CloneMap
- attoFasta :: ByteString -> [FastaSequence]
- attoCLIPFasta :: ByteString -> [(Germline, [FastaSequence])]
- pipesFasta :: MonadIO m => Producer ByteString m () -> Producer FastaSequence m ()
- pipesCLIPFasta :: MonadIO m => Producer ByteString m () -> Producer (Germline, [FastaSequence]) m (Either (ParsingError, Producer ByteString m ()) ())
- removeNs :: [FastaSequence] -> [FastaSequence]
- removeN :: FastaSequence -> FastaSequence
- removeCLIPNs :: CloneMap -> CloneMap
Documentation
parsecFasta :: ByteString -> [FastaSequence] #
Parse a standard fasta file into
parsecCLIPFasta :: ByteString -> CloneMap #
Parse a CLIP fasta file into
attoFasta :: ByteString -> [FastaSequence] #
Parse a standard fasta file
attoCLIPFasta :: ByteString -> [(Germline, [FastaSequence])] #
Parse a CLIP fasta file into text sequences
pipesFasta :: MonadIO m => Producer ByteString m () -> Producer FastaSequence m () #
Parse a standard fasta file into a pipe
pipesCLIPFasta :: MonadIO m => Producer ByteString m () -> Producer (Germline, [FastaSequence]) m (Either (ParsingError, Producer ByteString m ()) ()) #
Parse a CLIP fasta file into strict text sequences for pipes.
removeNs :: [FastaSequence] -> [FastaSequence] #
Remove Ns from a collection of sequences
removeN :: FastaSequence -> FastaSequence #
Remove Ns from a sequence
removeCLIPNs :: CloneMap -> CloneMap #
Remove Ns from a collection of CLIP fasta sequences