| bio-0.4.6: A bioinformatics library | Source code | Contents | Index
Bio.Sequence.FastQ
Contents
Reading FastQ Writing FastQ
Description
Support the FastQ format that combines sequence and quality. See: http://www.bioperl.org/wiki/FASTQ_sequence_format 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: http://www.bcgsc.ca/pipermail/ssrformat/2007-March/000137.html http://maq.sourceforge.net/fastq.shtml 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 -> ByteString | Source
Produced by Haddock version 2.4.2