| Safe Haskell | None |
|---|---|
| Language | Haskell98 |
Bio.Sequence.Fasta
Contents
Description
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..
- data Sequence = Seq SeqLabel SeqData (Maybe QualData)
- readFasta :: FilePath -> IO [Sequence]
- writeFasta :: FilePath -> [Sequence] -> IO ()
- hReadFasta :: Handle -> IO [Sequence]
- hWriteFasta :: Handle -> [Sequence] -> IO ()
- countSeqs :: FilePath -> IO Int
- mkSeqs :: [ByteString] -> [Sequence]
- toStr :: SeqData -> String
- seqid :: BioSeq s => s -> SeqLabel
- seqheader :: BioSeq s => s -> SeqLabel
- seqdata :: BioSeq s => s -> SeqData
- seqlength :: BioSeq s => s -> Offset
Documentation
Reading and writing plain FASTA files
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
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.