Data.Fasta.ByteString.Parse

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

Documentation

parsecFasta :: ByteString -> [FastaSequence]

Parse a standard fasta file into text sequences

parsecCLIPFasta :: ByteString -> CloneMap

Parse a CLIP fasta file into text sequences

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 strict text sequences for pipes. This is the highly recommeded way of parsing, as it is computationally fast and uses memory based on line length

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