| bio-0.4: 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