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.
|
|
Inherited from Interfaces.SequentialSequenceWriter :
__init__ ,
write_file ,
write_footer ,
write_header ,
write_records
Inherited from Interfaces.SequenceWriter :
clean
Inherited from object :
__delattr__ ,
__format__ ,
__getattribute__ ,
__hash__ ,
__new__ ,
__reduce__ ,
__reduce_ex__ ,
__repr__ ,
__setattr__ ,
__sizeof__ ,
__str__ ,
__subclasshook__
|
Inherited from object :
__class__
|