def test_input_file_with_no_duplicate_sequences(self):
preprocessfasta = PreProcessFasta(
os.path.join(data_dir, 'preprocessfasta/no_duplicates.aln'))
self.assertEqual(
preprocessfasta.hash_sequences(), {
b"\x840\x89L\xfe\xb5J6%\xf1\x8f\xe2O\xce'.": ['sample1'],
b'\x9c\xe6\x8b\xf7\xae\xe2\x1f\xf5j\xcfu\xf4\xfdO\x8b\xec':
['sample4'],
b'\xc3n`\xf5t\x00\x1e\xf3\xde\nU\x1f\x95\x0b\xdb9':
['sample2'],
b'\xdf\xedM\xdf1\xf2PPO\xc1\xf54T?\xdb\xa2': ['sample3']
})
self.assertEqual(
preprocessfasta.calculate_sequences_missing_data_percentage(), {
'sample1': 0.0,
'sample2': 0.0,
'sample3': 0.0,
'sample4': 0.0
})
self.assertEqual(preprocessfasta.taxa_of_duplicate_sequences(), [])
preprocessfasta.remove_duplicate_sequences_and_sequences_missing_too_much_data(
'output.aln', 1)
self.assertTrue(
filecmp.cmp(
'output.aln',
os.path.join(data_dir, 'preprocessfasta/no_duplicates.aln')))
def test_dont_filter_input_file_with_multiple_duplicate_sequences(self):
preprocessfasta = PreProcessFasta('gubbins/tests/data/preprocessfasta/multiple_duplicates.aln')
self.assertEqual(preprocessfasta.hash_sequences(),
{b"\x840\x89L\xfe\xb5J6%\xf1\x8f\xe2O\xce'.": ['sample1', 'sample3'],
b'\x9c\xe6\x8b\xf7\xae\xe2\x1f\xf5j\xcfu\xf4\xfdO\x8b\xec': ['sample2', 'sample4']})
self.assertEqual(preprocessfasta.taxa_of_duplicate_sequences(),['sample1','sample2'])
preprocessfasta.remove_duplicate_sequences_and_sequences_missing_too_much_data('output.aln',0)
self.assertTrue(filecmp.cmp('output.aln', 'gubbins/tests/data/preprocessfasta/multiple_duplicates.aln'))
def test_input_file_with_multiple_duplicate_sequences(self):
preprocessfasta = PreProcessFasta('gubbins/tests/data/preprocessfasta/multiple_duplicates.aln')
self.assertEqual(preprocessfasta.hash_sequences(),
{b"\x840\x89L\xfe\xb5J6%\xf1\x8f\xe2O\xce'.": ['sample1', 'sample3'],
b'\x9c\xe6\x8b\xf7\xae\xe2\x1f\xf5j\xcfu\xf4\xfdO\x8b\xec': ['sample2', 'sample4']})
self.assertEqual(preprocessfasta.taxa_of_duplicate_sequences(),['sample1','sample2'])
preprocessfasta.remove_duplicate_sequences_and_sequences_missing_too_much_data('output.aln')
self.assertTrue(filecmp.cmp('output.aln', 'gubbins/tests/data/preprocessfasta/expected_multiple_duplicates.aln'))
def test_input_file_with_all_duplicate_sequences(self):
preprocessfasta = PreProcessFasta(
os.path.join(data_dir, 'preprocessfasta/all_same_sequence.aln'))
self.assertEqual(
preprocessfasta.hash_sequences(), {
b"\x840\x89L\xfe\xb5J6%\xf1\x8f\xe2O\xce'.":
['sample1', 'sample2', 'sample3', 'sample4']
})
self.assertEqual(preprocessfasta.taxa_of_duplicate_sequences(),
['sample1', 'sample2', 'sample3'])
def test_input_file_with_one_duplicate_sequences(self):
preprocessfasta = PreProcessFasta('gubbins/tests/data/preprocessfasta/one_duplicate.aln')
self.assertEqual(preprocessfasta.hash_sequences(),
{b"\x840\x89L\xfe\xb5J6%\xf1\x8f\xe2O\xce'.": ['sample1', 'sample3'],
b'\x9c\xe6\x8b\xf7\xae\xe2\x1f\xf5j\xcfu\xf4\xfdO\x8b\xec': ['sample4'],
b'\xc3n`\xf5t\x00\x1e\xf3\xde\nU\x1f\x95\x0b\xdb9': ['sample2']})
self.assertEqual(preprocessfasta.taxa_of_duplicate_sequences(),['sample1'])
preprocessfasta.remove_duplicate_sequences_and_sequences_missing_too_much_data('output.aln',1)
self.assertTrue(filecmp.cmp('output.aln', 'gubbins/tests/data/preprocessfasta/expected_one_duplicate.aln'))
def test_input_file_with_all_duplicate_sequences(self):
preprocessfasta = PreProcessFasta('gubbins/tests/data/preprocessfasta/all_same_sequence.aln')
self.assertEqual(preprocessfasta.hash_sequences(),
{b"\x840\x89L\xfe\xb5J6%\xf1\x8f\xe2O\xce'.": ['sample1',
'sample2',
'sample3',
'sample4']})
self.assertEqual(preprocessfasta.taxa_of_duplicate_sequences(),['sample1',
'sample2',
'sample3'])
def test_input_file_with_no_duplicate_sequences(self):
preprocessfasta = PreProcessFasta('gubbins/tests/data/preprocessfasta/no_duplicates.aln')
self.assertEqual(preprocessfasta.hash_sequences(),
{b"\x840\x89L\xfe\xb5J6%\xf1\x8f\xe2O\xce'.": ['sample1'],
b'\x9c\xe6\x8b\xf7\xae\xe2\x1f\xf5j\xcfu\xf4\xfdO\x8b\xec': ['sample4'],
b'\xc3n`\xf5t\x00\x1e\xf3\xde\nU\x1f\x95\x0b\xdb9': ['sample2'],
b'\xdf\xedM\xdf1\xf2PPO\xc1\xf54T?\xdb\xa2': ['sample3']})
self.assertEqual(preprocessfasta.calculate_sequences_missing_data_percentage(), {'sample1': 0.0,
'sample2': 0.0,
'sample3': 0.0,
'sample4': 0.0})
self.assertEqual(preprocessfasta.taxa_of_duplicate_sequences(),[])
preprocessfasta.remove_duplicate_sequences_and_sequences_missing_too_much_data('output.aln')
self.assertTrue(filecmp.cmp('output.aln', 'gubbins/tests/data/preprocessfasta/no_duplicates.aln'))
