How to use the cutadapt.seqio.FastqReader function in cutadapt

def test_fastq_wrongformat(self):
		with FastqReader("tests/data/withplus.fastq") as f:
			reads = list(f)

def test_fastqreader_dos(self):
		with FastqReader("tests/data/dos.fastq") as f:
			dos_reads = list(f)
		with FastqReader("tests/data/small.fastq") as f:
			unix_reads = list(f)
		assert dos_reads == unix_reads

def test_fastq_incomplete(self):
		fastq = StringIO("@name\nACGT+\n")
		with FastqReader(fastq) as fq:
			list(fq)

def test_fastqreader(self):
		with FastqReader("tests/data/simple.fastq") as f:
			reads = list(f)
		assert reads == simple_fastq

def test_fastqreader_dos(self):
		with FastqReader("tests/data/dos.fastq") as f:
			dos_reads = list(f)
		with FastqReader("tests/data/small.fastq") as f:
			unix_reads = list(f)
		assert dos_reads == unix_reads

def test_context_manager(self):
		filename = "tests/data/simple.fastq"
		with open(filename) as f:
			assert not f.closed
			reads = list(openseq(f))
			assert not f.closed
		assert f.closed

		with FastqReader(filename) as sr:
			tmp_sr = sr
			assert not sr._file.closed
			reads = list(sr)
			assert not sr._file.closed
		assert tmp_sr._file is None

def trim_file(infile, adapter, outfile, threads=1, phred=33):
	read_queue = Queue()
	result_queue = Queue()
	trimmed_queue = Queue()
	workers = []
	def start_workers():
		for i in xrange(threads):
			worker = Worker(queue=read_queue, results=result_queue, phred64=phred==64, adapter=adapter)
			workers.append(worker)
			worker.start()
	writer = Writer(queue=result_queue, trimmed=trimmed_queue, outfile=outfile)
	writer.start()
	batch = []
	for index, read in enumerate(FastqReader(infile)):
		batch.append(read)
		if index < 1000 and phred == 33:
			if any([i for i in read.qualities if ord(i) > 74]):
				phred = 64
		if index % 10000 == 0:
			if not workers:
				start_workers()
			read_queue.put(batch)
			batch = []
	if not workers:
		start_workers()
	read_queue.put(batch)
	processed = index+1
	# poison pill to stop workers
	for i in xrange(threads):
		read_queue.put(None)