def test_yield_fast5_reads_set_versus_list_equality(self):
f5_read_gen_by_id_set = yield_fast5_reads(self.fast5_path,
recursive=False,
read_ids=self.read_id_set)
f5_read_gen_by_id_list = yield_fast5_reads(self.fast5_path,
recursive=False,
read_ids=self.read_id_list)
# Consume the generators into sets
ids_by_set = set(rid for rid, _ in f5_read_gen_by_id_set)
ids_by_list = set(rid for rid, _ in f5_read_gen_by_id_list)
self.assertTrue(ids_by_list == ids_by_set,
'Ids differ when using read_id list versus set')
def test_yield_fast5_reads_with_garbage_set(self):
f5_read_gen = yield_fast5_reads(self.fast5_path,
recursive=False,
read_ids={'_g4rbag£_'})
f5_reads = list(f5_read_gen)
self.assertTrue(
len(f5_reads) == 0, "Garbage read_ids returned non-zero reads")
def test_yield_fast5_reads_with_empty_set(self):
f5_read_gen = yield_fast5_reads(self.fast5_path,
recursive=False,
read_ids=set([]))
self.assertTrue(
len(list(f5_read_gen)) != 0,
"Empty read_ids resulted in zero returned reads")
def test_yield_fast5_reads_with_list(self):
f5_read_gen = yield_fast5_reads(self.fast5_path,
recursive=False,
read_ids=self.read_id_set)
f5_reads = list(f5_read_gen)
self.assertTrue(len(f5_reads) == len(self.read_id_list))
for read_id, read_data in f5_reads:
self.assertTrue(read_id in self.read_id_set,
"A read_id is not a member of read_id_list")
self.assertTrue(isinstance(read_data, Fast5Read),
"Return is not Fast5Read instance")
def test_yield_fast5_reads_from_dir(self):
f5_read_gen = yield_fast5_reads(test_data, recursive=False)
read_id, read_data = next(f5_read_gen)
self.assertTrue(read_id is not None, "read_id is None")
self.assertTrue(isinstance(read_data, Fast5Read),
"Return is not Fast5Read instance")
def test_yield_fast5_reads_type_error(self):
with self.assertRaisesRegex(TypeError, 'read_ids'):
f5_read_gen = yield_fast5_reads(self.fast5_path,
recursive=False,
read_ids=int(1))
next(f5_read_gen)