Package Bio :: Package SeqIO :: Module QualityIO :: Class FastqIlluminaWriter
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Class FastqIlluminaWriter

source code

                     object --+        
                              |        
      Interfaces.SequenceWriter --+    
                                  |    
Interfaces.SequentialSequenceWriter --+
                                      |
                                     FastqIlluminaWriter

Write Illumina 1.3+ FASTQ format files (with PHRED quality scores).

This outputs FASTQ files like those from the Solexa/Illumina 1.3+ pipeline, using PHRED scores and an ASCII offset of 64. Note these files are NOT compatible with the standard Sanger style PHRED FASTQ files which use an ASCII offset of 32.

Although you can use this class directly, you are strongly encouraged to use the Bio.SeqIO.write() function with format name "fastq-illumina" instead. This code is also called if you use the .format("fastq-illumina") method of a SeqRecord. For example,

>>> from Bio import SeqIO
>>> record = SeqIO.read(open("Quality/sanger_faked.fastq"), "fastq-sanger")
>>> print(record.format("fastq-illumina"))
@Test PHRED qualities from 40 to 0 inclusive
ACGTACGTACGTACGTACGTACGTACGTACGTACGTACGTN
+
hgfedcba`_^]\[ZYXWVUTSRQPONMLKJIHGFEDCBA@
<BLANKLINE>

Note that Illumina FASTQ files have an upper limit of PHRED quality 62, which is encoded as ASCII 126, the tilde. If your quality scores are truncated to fit, a warning is issued.

Instance Methods [hide private]
 
write_record(self, record)
Write a single FASTQ record to the file.
source code

Inherited from Interfaces.SequentialSequenceWriter: __init__, write_file, write_footer, write_header, write_records

Inherited from Interfaces.SequenceWriter: clean

Inherited from Interfaces.SequenceWriter (private): _get_seq_string

Inherited from object: __delattr__, __format__, __getattribute__, __hash__, __new__, __reduce__, __reduce_ex__, __repr__, __setattr__, __sizeof__, __str__, __subclasshook__

Properties [hide private]

Inherited from object: __class__

Method Details [hide private]

write_record(self, record)

source code 

Write a single FASTQ record to the file.

Overrides: Interfaces.SequentialSequenceWriter.write_record