Safe Haskell	None
Language	Haskell2010

Bio.Parse.Sequence.Fasta

Synopsis

Documentation

data FastaSequence #

Constructors

FastaSequence
Fields _header :: [ByteString] _sequence :: ByteString

Instances

Eq FastaSequence #
Methods (==) :: FastaSequence -> FastaSequence -> Bool # (/=) :: FastaSequence -> FastaSequence -> Bool #
Ord FastaSequence #
Methods compare :: FastaSequence -> FastaSequence -> Ordering # (<) :: FastaSequence -> FastaSequence -> Bool # (<=) :: FastaSequence -> FastaSequence -> Bool # (>) :: FastaSequence -> FastaSequence -> Bool # (>=) :: FastaSequence -> FastaSequence -> Bool # max :: FastaSequence -> FastaSequence -> FastaSequence # min :: FastaSequence -> FastaSequence -> FastaSequence #
Show FastaSequence #
Methods showsPrec :: Int -> FastaSequence -> ShowS # show :: FastaSequence -> String # showList :: [FastaSequence] -> ShowS #
SequenceParser FastaSequence #
Methods parseSequence :: ParseConstraint m => m FastaSequence # parseSequences :: ParseConstraint m => m [FastaSequence] #

sequence :: Lens' FastaSequence ByteString #

header :: Lens' FastaSequence [ByteString] #

parseHeader :: ParseConstraint m => m [ByteString] #

Parses the header of a FASTA file.

The header starts with a > character and gets separated by | (pipe) characters. When making use of BioSeq, the first word of the header is used as the seqid.

parseSequenceLine :: ParseConstraint m => m ByteString #

Parses an individual line of the sequence.

parseSequence' :: ParseConstraint m => m FastaSequence #

Parses an entire sequence including its header.

parseSequences' :: ParseConstraint m => m [FastaSequence] #

Parses many sequences.