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_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_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_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
