Data.Fasta.Text.Parse

Collection of functions for the parsing of a fasta file. Uses the Text type.

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