fasta-0.6.1.1: A simple, mindless parser for fasta files.

Safe HaskellSafe-Inferred
LanguageHaskell98

Data.Fasta.String.Parse

Description

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

Synopsis

Documentation

parseFasta :: String -> [FastaSequence] Source

Parse a standard fasta file into string sequences

parseCLIPFasta :: String -> CloneMap Source

Parse a CLIP fasta file into string sequences

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

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] Source

Remove Ns from a collection of sequences

removeN :: FastaSequence -> FastaSequence Source

Remove Ns from a sequence

removeCLIPNs :: CloneMap -> CloneMap Source

Remove Ns from a collection of CLIP fasta sequences