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