lightweight, easy to use fastq parser/writer for Python
How to use:
fastq = FastqParser("/path/to/my_fastq.fastq.gz")
for read in fastq:
# set its first two bases to GG
read.sequence = 'GG' + read.sequence[2:]
# write it to stdout if it passed filter
if read.header.filter != 'Y':
sys.stdout.write(str(read))
If you don't care about parsing the read headers, you can improve performance by initializing the parser like this:
fastq = FastqParser("/path/to/my_fastq.fastq.gz", parse_headers=False)