fasta-0.10.4.2: A simple, mindless parser for fasta files.

Safe HaskellNone
LanguageHaskell98

Data.Fasta.Text.Parse

Description

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

Synopsis

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