def __init__(self, handle, in_read=False, fmt=None, start=None, end=None):
"""Configure a barcode extractor.
:arg stream handle: Handle to an NGS data file.
:arg bool in_read: Inspect the read instead of the header.
:arg str fmt: Header format.
:arg int start: Start of the barcode.
:arg int end: End of the barcode.
"""
self._start = start
self._end = end
if self._start:
self._start -= 1
if not fmt:
if not in_read:
self._get_barcode = _get_barcode[guess_header_format(handle)]
else:
self._get_barcode = _get_barcode['unknown']
else:
self._get_barcode = _get_barcode[fmt]
def test_guess_header_x(self):
assert guess_header_format(self._input_x) == 'x'
def test_guess_header_unknown(self):
assert guess_header_format(make_fake_file(
'', '@name description\n')) == 'unknown'
def test_guess_header_normal(self):
assert guess_header_format(self._input) == 'normal'