Class FastqSolexaWriter
source code
Interfaces.SequenceWriter --+
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Interfaces.SequentialSequenceWriter --+
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FastqSolexaWriter
Class to write FASTQ format files (using Solexa quality scores).
Although you can use this class directly, you are strongly encouraged
to use the Bio.SeqIO.write() function instead. For example, this code
reads in a FASTQ file and re-saves it as another FASTQ file:
>>> from Bio import SeqIO
>>> record_iterator = SeqIO.parse(open("Quality/solexa.fastq"), "fastq-solexa")
>>> out_handle = open("Quality/temp.fastq", "w")
>>> SeqIO.write(record_iterator, out_handle, "fastq-solexa")
1
>>> out_handle.close()
You might want to do this if the original file included extra line
breaks, which (while valid) may not be supported by all tools. The
output file from Biopython will have each sequence on a single line, and
each quality string on a single line (which is considered desirable for
maximum compatibility).
This code is also called if you use the
.format("fastq-solexa") method of a SeqRecord.
P.S. Don't forget to delete the temp file if you don't need it
anymore:
>>> import os
>>> os.remove("Quality/temp.fastq")