Data.Fasta.String.Parse

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

Documentation

parseFasta :: String -> [FastaSequence]

Parse a standard fasta file into string sequences

parseCLIPFasta :: String -> CloneMap

Parse a CLIP fasta file into string sequences

pipesFasta :: MonadIO m => Handle -> Pipe String FastaSequence m ()

Parse a standard fasta file into string sequences for pipes. This is the highly recommeded way of parsing, as it is computationally fast and uses constant file memory

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