How to use the mappy.fastx_read function in mappy

global read_mappings
	global reference_names
	global matched_counts
	global unmatched_counts

	path = query_path.split("/")
	query_file = path[-1]

	print("Mapping query file: " + query_file)

	i = 0
	unmatched = 0

	# barcode = default_barcode

	for name, seq, qual, comment in mp.fastx_read(query_path, read_comment=True): # read one sequence
		read_time = re.search(r'start_time=([^\s]+)', comment).group(1)
		# if default_barcode is None:
		barcode = re.search(r'barcode=([^\s]+)', comment).group(1)
		try:
			barcode_index = barcodes.index(barcode)
		except ValueError:
			generic = re.match("^barcode(\d\d)$", barcode)
			if generic:
				barcode_index = int(generic[1])-1
			else:
				raise ValueError('unknown barcode "' + barcode + '"... skipping')

		time_stamp = datetime.strptime(read_time, "%Y-%m-%dT%H:%M:%SZ")

		try:
			count += 1

sys.exit(1)

	preset = min_cnt = min_sc = k = w = bw = None
	out_cs = False
	for opt, arg in opts:
		if opt == '-x': preset = arg
		elif opt == '-n': min_cnt = int(arg)
		elif opt == '-m': min_chain_score = int(arg)
		elif opt == '-r': bw = int(arg)
		elif opt == '-k': k = int(arg)
		elif opt == '-w': w = int(arg)
		elif opt == '-c': out_cs = True

	a = mp.Aligner(args[0], preset=preset, min_cnt=min_cnt, min_chain_score=min_sc, k=k, w=w, bw=bw)
	if not a: raise Exception("ERROR: failed to load/build index file '{}'".format(args[0]))
	for name, seq, qual in mp.fastx_read(args[1]): # read one sequence
		for h in a.map(seq, cs=out_cs): # traverse hits
			print('{}\t{}\t{}'.format(name, len(seq), h))

print("  -w INT      minimizer window length")
		print("  -r INT      band width")
		sys.exit(1)

	preset, min_cnt, min_sc, k, w, bw = None, None, None, None, None, None
	for opt, arg in opts:
		if opt == '-x': preset = arg
		elif opt == '-n': min_cnt = int(arg)
		elif opt == '-m': min_chain_score = int(arg)
		elif opt == '-r': bw = int(arg)
		elif opt == '-k': k = int(arg)
		elif opt == '-w': w = int(arg)

	a = mp.Aligner(args[0], preset=preset, min_cnt=min_cnt, min_chain_score=min_sc, k=k, w=w, bw=bw)
	if not a: raise Exception("ERROR: failed to load/build index file '{}'".format(args[0]))
	for name, seq, qual in mp.fastx_read(args[1]): # read one sequence
		for h in a.map(seq): # traverse hits
			print('{}\t{}\t{}'.format(name, len(seq), h))

def create_index(reference_file):
	aligner = mp.Aligner(reference_file, best_n = 1)

	for name, seq, qual in mp.fastx_read(reference_file, read_comment=False):
		reference_names.append(name)
		reference_lengths[name] = len(seq)

	if not aligner:
		raise Exception("ERROR: failed to load/build index file '{}'".format(reference_file))

	return aligner

def get_fasta_names(path):
    fasta_names = []
    for name, seq, qual in mp.fastx_read(path, read_comment=False):
        fasta_names.append(name)
    return fasta_names

def _method_mappy(self, *args, **kwargs):
        with open(self.outfile, "w") as fasta:
            for (name, seq, _) in fastx_read(self.infile):
                fasta.write(">{}\n{}\n".format(name, seq))

def create_coordinate_index(coordinate_reference):
    """Initialise minimap2 for 2 different reference FASTAs"""
    ## Parse the (single) reference sequence used to find co-ordinates:
    coordinate_aligner = mp.Aligner(coordinate_reference, best_n=1)
    name, seq, qual = next(mp.fastx_read(coordinate_reference, read_comment=False))
    coordinate_reference_length = len(seq)
    if not coordinate_aligner:
        raise Exception("ERROR: failed to load/build index file '{}'".format(coordinate_reference))

    return (coordinate_aligner, coordinate_reference_length)