def test_run_snp_sites(self):
builder = SNPFeatureBuilder()
fasta_filename = os.path.join(test_data(), 'file_with_SNPs.aln')
with context_aware_tempdir() as output_directory:
stdout, stderr = builder._run_snp_sites('snp-sites', {},
fasta_filename,
output_directory)
expected_output_filename = os.path.join(output_directory, 'all_snps.vcf')
self.assertTrue(os.path.isfile(expected_output_filename))
def test_add_record_to_features(self):
builder = SNPFeatureBuilder()
record = FakeRecord(1,1,['0', '0', '1'])
builder._add_record_to_features(record)
self.assertItemsEqual(builder.features.keys(), ['sample_0', 'sample_1',
'sample_2'])
self.assertEqual(builder.features['sample_0'], [0])
self.assertEqual(builder.features['sample_1'], [0])
self.assertEqual(builder.features['sample_2'], [1])
self.assertEqual(builder.feature_labels, ['SNP:1:1'])
record = FakeRecord(1,2,['0', '1', '2'])
builder._add_record_to_features(record)
self.assertItemsEqual(builder.features.keys(), ['sample_0', 'sample_1',
'sample_2'])
self.assertEqual(builder.features['sample_0'], [0,0])
self.assertEqual(builder.features['sample_1'], [0,1])
self.assertEqual(builder.features['sample_2'], [1,1])
self.assertEqual(builder.feature_labels, ['SNP:1:1', 'SNP:1:2'])
record = FakeRecord(1,3,['1', '2', '0'])
record.samples[1].data.__delattr__('GT') # One of the samples is missing an 'AB'
builder._add_record_to_features(record)
self.assertItemsEqual(builder.features.keys(), ['sample_0', 'sample_1',
'sample_2'])
self.assertEqual(builder.features['sample_0'], [0,0])
self.assertEqual(builder.features['sample_1'], [0,1])
self.assertEqual(builder.features['sample_2'], [1,1])
self.assertEqual(builder.feature_labels, ['SNP:1:1', 'SNP:1:2'])
def test_create_features(self):
builder = SNPFeatureBuilder()
fake_vcf = []
fake_vcf.append(FakeRecord(1,1,['0', '0', '1']))
fake_vcf.append(FakeRecord(1,2,['0', '1', '2']))
fake_vcf.append(FakeRecord(1,3,['1', '2', '0']))
builder._get_records_from_vcf=MagicMock(return_value=fake_vcf)
builder.create_features()
self.assertItemsEqual(builder.features.keys(), ['sample_0', 'sample_1',
'sample_2'])
self.assertEqual(builder.features['sample_0'], [0,0,1])
self.assertEqual(builder.features['sample_1'], [0,1,1])
self.assertEqual(builder.features['sample_2'], [1,1,0])
self.assertEqual(builder.feature_labels, ['SNP:1:1', 'SNP:1:2', 'SNP:1:3'])
fake_vcf = [FakeRecord(2,1,['1', '0'])]
builder._get_records_from_vcf=MagicMock(return_value=fake_vcf)
builder.create_features()
self.assertItemsEqual(builder.features.keys(), ['sample_0', 'sample_1'])
self.assertEqual(builder.features['sample_0'], [1])
self.assertEqual(builder.features['sample_1'], [0])
self.assertEqual(builder.feature_labels, ['SNP:2:1'])
def test_create_vcf_from_sequences(self, temp_mock, ctx_tempfile_mock,
ctx_tempdir_mock):
builder = SNPFeatureBuilder()
temp_vcf_file = tempfile.NamedTemporaryFile('w', delete=False)
temp_files = []
temp_folders = []
ctx_tempfile_mock.side_effect = create_context_aware_tempfile_mock(temp_files)
ctx_tempdir_mock.side_effect = create_context_aware_tempdir_mock(temp_folders)
temp_mock.NamedTemporaryFile.return_value = temp_vcf_file
fasta_filename = os.path.join(test_data(), 'file_with_SNPs.aln')
fasta_file = open(fasta_filename, 'r')
builder.load_fasta_sequences(fasta_file)
builder.create_vcf_from_sequences()
self.assertEqual(len(temp_files), 1)
self.assertFalse(os.path.isfile(temp_files[0]))
self.assertEqual(len(temp_folders), 1)
self.assertFalse(os.path.isdir(temp_folders[0]))
self.assertTrue(os.path.isfile(temp_vcf_file.name))
builder.vcf_input_file.seek(0)
records = SNPSitesReader(builder.vcf_input_file)
number_of_records = sum((1 for record in records))
self.assertEqual(number_of_records, 5)
fasta_file.close()
temp_vcf_file.close()
os.remove(temp_vcf_file.name)
def test_get_records_from_vcf(self):
builder = SNPFeatureBuilder()
fasta_filename = os.path.join(test_data(), 'file_with_SNPs.aln')
fasta_file = open(fasta_filename, 'r')
builder.load_fasta_sequences(fasta_file)
builder.create_vcf_from_sequences()
records = builder._get_records_from_vcf()
number_of_records = sum((1 for record in records))
self.assertEqual(number_of_records, 5)
records = builder._get_records_from_vcf()
number_of_records = sum((1 for record in records))
self.assertEqual(number_of_records, 5)
def test_create_vcf_from_sequences_does_not_delete_existing(self, os_mock):
builder = SNPFeatureBuilder()
os_mock.remove.side_effect = os.remove
with context_aware_tempfile('w', delete=False) as temp_vcf_file:
builder.vcf_input_file = temp_vcf_file
fasta_filename = os.path.join(test_data(), 'file_with_SNPs.aln')
fasta_file = open(fasta_filename, 'r')
builder.load_fasta_sequences(fasta_file)
builder.create_vcf_from_sequences()
self.assertFalse(temp_vcf_file.name in os_mock.remove.call_args_list)
def test_create_vcf_from_sequences_deletes_when_done(self, os_mock):
builder = SNPFeatureBuilder()
os_mock.remove.side_effect = os.remove
fasta_filename = os.path.join(test_data(), 'file_with_SNPs.aln')
fasta_file = open(fasta_filename, 'r')
builder.load_fasta_sequences(fasta_file)
builder.create_vcf_from_sequences()
temp_vcf_filename = builder.vcf_input_file.name
del(builder)
os_mock.remove.assert_any_call(temp_vcf_filename)
try:
os.remove(temp_vcf_filename)
except OSError:
# Looks like it's already deleted
pass
