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from gffutils.test.synth_test_base import (
TestWithSynthDB,
num_synthetic_features,
num_synthetic_overlap,
)
class TestMerge_all(TestWithSynthDB):
def test_defaults(self):
merged = self.db.merge_all()
dump = self._dump_db()
self.assertEqual(
num_synthetic_features + 1, self.db.count_features_of_type(), dump
)
self.assertEqual(1, len(merged), dump)
self.assertEqual(num_synthetic_overlap, len(merged[0].children), dump)
def test_empty(self):
self.db.delete(self.db.all_features())
dump = self._dump_db()
self.assertEqual(0, self.db.count_features_of_type(), dump)
merged = self.db.merge_all()
dump = self._dump_db()
self.assertEqual(0, self.db.count_features_of_type(), dump)
self.assertEqual(0, len(merged), dump)
def test_one(self):
features = self.db.all_features()
next(features)
self.db.delete(features)
dump = self._dump_db()
self.assertEqual(1, self.db.count_features_of_type(), dump)
merged = self.db.merge_all()
dump = self._dump_db()
self.assertEqual(1, self.db.count_features_of_type(), dump)
self.assertEqual(0, len(merged), dump)
def test_no_overlap(self):
self.db.delete(
f for f in self.db.all_features() if f.id not in ("basic1", "no_overlap1")
)
dump = self._dump_db()
self.assertEqual(2, self.db.count_features_of_type(), dump)
merged = self.db.merge_all()
dump = self._dump_db()
self.assertEqual(2, self.db.count_features_of_type(), dump)
self.assertEqual(0, len(merged), dump)
def test_merge_groups(self):
merged = self.db.merge_all(
featuretypes_groups=({"sequence_feature", "misc_feature"},)
)
dump = self._dump_db()
self.assertEqual(
num_synthetic_features + 1, self.db.count_features_of_type(), dump
)
self.assertEqual(1, len(merged), dump)
self.assertEqual(num_synthetic_overlap, len(merged[0].children), dump)
def test_exclude_components(self):
merged = self.db.merge_all(exclude_components=True)
dump = self._dump_db()
self.assertEqual(6, self.db.count_features_of_type(), dump)
self.assertEqual(1, len(merged), dump)
self.assertEqual(num_synthetic_overlap, len(merged[0].children), dump)
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