def test_io(self):
vac_file = self.__build_vac_file()
self.assertTupleEqual((3, 3), Vac.read_header(vac_file))
self.assertTupleEqual((2000000000, 0, [3, 2, 1, 0]),
Vac.read_snv_record(vac_file))
self.assertTupleEqual((2000000002, 1, [0, 1, 2, 3]),
Vac.read_snv_record(vac_file))
self.assertTupleEqual((2000000004, 2, [1, 1, 1, 1]),
Vac.read_snv_record(vac_file))
self.assertTupleEqual((2000000001, [10, 1], ['A', 'ATCG']),
Vac.read_indel_record(vac_file))
self.assertTupleEqual((2000000003, [10, 1], ['AT', 'ATCGT']),
Vac.read_indel_record(vac_file))
self.assertTupleEqual((2000000005, [10, 10, 0], ['AAAA', 'ATCG', 'A']),
Vac.read_indel_record(vac_file))
self.assertRaises(EOFError, lambda: Vac.read_snv_record(vac_file))
def __init__(self, vac_filename: str, fai: FastaIndex):
"""
:param vac_filename:
:param fai:
does not affect bases listed in VAC file
"""
with open(vac_filename, 'rb') as vac_file:
# read header
self._snv_count, self._indel_count = Vac.read_header(vac_file)
self._snv_file = open(vac_filename, 'rb')
self._snv_file.seek(Vac.HEADER_SIZE)
self._indel_file = open(vac_filename, 'rb')
self._indel_file.seek(Vac.HEADER_SIZE +
self._snv_count * Vac.SNV_RECORD_SIZE)
self._fai = fai
self._counter = 0
# init iteration
self._snv_variant = self._read_snv()
self._indel_variant = self._read_indel()