bio-0.4.6: A bioinformatics librarySource codeContentsIndex
Bio.Sequence.FastQ
Contents
Reading FastQ
Writing FastQ
Description

Support the FastQ format that combines sequence and quality. See:

Of course, this is yet another vaguely defined pseudo-standard with conflicting definitions. Of course Solexa had to go and invent a different, but indistinguishably so, way to do it:

Currently, we only support the non-Solexa FastQ, adding/subtracting 33 for the quality values.

As far as I know, FastQ is only used for nucleotide sequences, never amino acid.

Synopsis
readFastQ :: FilePath -> IO [Sequence Nuc]
hReadFastQ :: Handle -> IO [Sequence Nuc]
parse :: [ByteString] -> Maybe (Either String (Sequence Nuc), [ByteString])
writeFastQ :: FilePath -> [Sequence a] -> IO ()
hWriteFastQ :: Handle -> [Sequence a] -> IO ()
unparse :: Sequence a -> ByteString
Reading FastQ
readFastQ :: FilePath -> IO [Sequence Nuc]Source
hReadFastQ :: Handle -> IO [Sequence Nuc]Source
parse :: [ByteString] -> Maybe (Either String (Sequence Nuc), [ByteString])Source
Parse one FastQ entry, suitable for using in unfoldr over lines from a file
Writing FastQ
writeFastQ :: FilePath -> [Sequence a] -> IO ()Source
hWriteFastQ :: Handle -> [Sequence a] -> IO ()Source
unparse :: Sequence a -> ByteStringSource
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