Bio.Sequence.Fasta

This module incorporates functionality for reading and writing sequence data in the Fasta format. Each sequence consists of a header (with a > prefix) and a set of lines containing the sequence data.

As Fasta is used for both amino acids and nucleotides, the resulting Sequences are type-tagged with Unknown. If you know the type of sequence you are reading, use castToAmino or castToNuc.

Documentation

data Sequence

Constructors

Seq SeqLabel SeqData (Maybe QualData)

Instances

Eq Sequence

Show Sequence

BioSeq Sequence

Reading and writing plain FASTA files

readFasta :: FilePath -> IO [Sequence]

Lazily read sequences from a FASTA-formatted file

writeFasta :: FilePath -> [Sequence] -> IO ()

Write sequences to a FASTA-formatted file. Line length is 60.

hReadFasta :: Handle -> IO [Sequence]

Lazily read sequence from handle

hWriteFasta :: Handle -> [Sequence] -> IO ()

Write sequences in FASTA format to a handle.

Counting sequences in a FASTA file

countSeqs :: FilePath -> IO Int

Helper function for reading your own sequences

mkSeqs :: [ByteString] -> [Sequence]

Convert a list of FASTA-formatted lines into a list of sequences. Blank lines are ignored. Comment lines start with are allowed between sequences (and ignored). Lines starting with > initiate a new sequence.