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_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)