def test_regions_to_process_fails_with_bad_shard_args(self, task, num_shards):
with self.assertRaises(ValueError):
make_examples.regions_to_process(
contigs=_make_contigs([('z', 100), ('a', 100), ('n', 100)]),
partition_size=10,
task_id=task,
num_shards=num_shards)
def test_regions_to_process_fails_with_bad_shard_args(self, task, num_shards):
with self.assertRaises(ValueError):
make_examples.regions_to_process(
contigs=_make_contigs([('z', 100), ('a', 100), ('n', 100)]),
partition_size=10,
task_id=task,
num_shards=num_shards)
def test_regions_to_process_partition(self, max_size, calling_regions,
expected):
contigs = _make_contigs([('1', 100), ('2', 76), ('3', 121)])
self.assertCountEqual(
_from_literals_list(expected),
make_examples.regions_to_process(
contigs, max_size, calling_regions=_from_literals(calling_regions)))
def get_regions(task_id, num_shards):
return make_examples.regions_to_process(contigs=_make_contigs([
('z', 100), ('a', 100), ('n', 100)
]),
partition_size=5,
task_id=task_id,
num_shards=num_shards)
def test_regions_to_process(self, calling_regions, expected):
contigs = _make_contigs([('1', 100), ('2', 200)])
self.assertCountEqual(
_from_literals_list(expected),
make_examples.regions_to_process(
contigs, 1000,
calling_regions=_from_literals(calling_regions)))
def test_regions_to_process_partition(self, max_size, calling_regions,
expected):
contigs = _make_contigs([('1', 100), ('2', 76), ('3', 121)])
self.assertCountEqual(
_from_literals_list(expected),
make_examples.regions_to_process(
contigs, max_size, calling_regions=_from_literals(calling_regions)))
def test_regions_to_process_sorted_contigs(self):
# These contig names are out of order lexicographically.
contigs = _make_contigs([('z', 100), ('a', 100), ('n', 100)])
in_regions = _from_literals(['a:10', 'n:1', 'z:20', 'z:5'])
sorted_regions = _from_literals_list(['z:5', 'z:20', 'a:10', 'n:1'])
actual_regions = list(
make_examples.regions_to_process(
contigs, 100, calling_regions=in_regions))
# The assertEqual here is checking the order is exactly what we expect.
self.assertEqual(sorted_regions, actual_regions)
def test_regions_to_process_sorted_contigs(self):
# These contig names are out of order lexicographically.
contigs = _make_contigs([('z', 100), ('a', 100), ('n', 100)])
in_regions = _from_literals(['a:10', 'n:1', 'z:20', 'z:5'])
sorted_regions = _from_literals_list(['z:5', 'z:20', 'a:10', 'n:1'])
actual_regions = list(
make_examples.regions_to_process(
contigs, 100, calling_regions=in_regions))
# The assertEqual here is checking the order is exactly what we expect.
self.assertEqual(sorted_regions, actual_regions)
def test_regions_to_process_sorted_within_contig(self):
# These regions are out of order but within a single contig.
contigs = _make_contigs([('z', 100)])
in_regions = _from_literals(['z:15', 'z:20', 'z:6', 'z:25-30', 'z:3-4'])
sorted_regions = _from_literals_list(
['z:3-4', 'z:6', 'z:15', 'z:20', 'z:25-30'])
actual_regions = list(
make_examples.regions_to_process(
contigs, 100, calling_regions=in_regions))
# The assertEqual here is checking the order is exactly what we expect.
self.assertEqual(sorted_regions, actual_regions)
def test_regions_to_process_sorted_within_contig(self):
# These regions are out of order but within a single contig.
contigs = _make_contigs([('z', 100)])
in_regions = _from_literals(['z:15', 'z:20', 'z:6', 'z:25-30', 'z:3-4'])
sorted_regions = _from_literals_list(
['z:3-4', 'z:6', 'z:15', 'z:20', 'z:25-30'])
actual_regions = list(
make_examples.regions_to_process(
contigs, 100, calling_regions=in_regions))
# The assertEqual here is checking the order is exactly what we expect.
self.assertEqual(sorted_regions, actual_regions)
def get_regions(task_id, num_shards):
return make_examples.regions_to_process(
contigs=_make_contigs([('z', 100), ('a', 100), ('n', 100)]),
partition_size=5,
task_id=task_id,
num_shards=num_shards)
def test_regions_to_process(self, calling_regions, expected):
contigs = _make_contigs([('1', 100), ('2', 200)])
self.assertCountEqual(
_from_literals_list(expected),
make_examples.regions_to_process(
contigs, 1000, calling_regions=_from_literals(calling_regions)))