Safe Haskell	None
Language	Haskell98

Bio.Sequence.FastQ

Contents

Reading FastQ
Writing FastQ
use Sanger-style quality information
use Illumina (>v1.3)-style quality information

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 not one, but two different, and indistinguishably so, ways to do it:

Sanger-style FastQ-format is supported with the (h)read/writeSangerQ functions, and the new IlluminaSolexa-style with (h)readwriteIllumina.

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

Synopsis

Reading FastQ

readFastQ :: FilePath -> IO [Sequence] #

Deprecated: FastQ assumes Sanger-style quality info use {read,write}SangerQ or -Illumina instead

hReadFastQ :: Handle -> IO [Sequence] #

Deprecated: FastQ assumes Sanger-style quality info use {read,write}SangerQ or -Illumina instead

parse :: [ByteString] -> Maybe (Either String Sequence, [ByteString]) #

Parse one FastQ entry, suitable for using in unfoldr over lines from a file

Writing FastQ

writeFastQ :: FilePath -> [Sequence] -> IO () #

Deprecated: FastQ assumes Sanger-style quality info use {read,write}SangerQ or -Illumina instead

hWriteFastQ :: Handle -> [Sequence] -> IO () #

Deprecated: FastQ assumes Sanger-style quality info use {read,write}SangerQ or -Illumina instead

use Sanger-style quality information

readSangerQ :: FilePath -> IO [Sequence] #

hReadSangerQ :: Handle -> IO [Sequence] #

writeSangerQ :: FilePath -> [Sequence] -> IO () #

hWriteSangerQ :: Handle -> [Sequence] -> IO () #

use Illumina (>v1.3)-style quality information

readIllumina :: FilePath -> IO [Sequence] #

hReadIllumina :: Handle -> IO [Sequence] #

writeIllumina :: FilePath -> [Sequence] -> IO () #

hWriteIllumina :: Handle -> [Sequence] -> IO () #