class TestCheckPrimers(unittest.TestCase): def setUp(self): self.ets = ExcelToSQL('TestCP_COL4A5.xlsx', 'Test.db') df_primers, primer_faults = self.ets.get_primers() self.cp = CheckPrimers(df_primers) def test_check_gene(self): checks = self.cp.check_gene() self.assertEqual(checks, 8) def test_check_exon(self): checks = self.cp.check_exon() self.assertEqual(checks, 4) def test_check_direction(self): checks = self.cp.check_direction() self.assertEqual(checks, 2) def test_check_version(self): checks = self.cp.check_version() self.assertEqual(checks, 1) def test_check_seq(self): checks = self.cp.check_seq() self.assertEqual(checks, 3) def test_check_tag(self): checks = self.cp.check_tag() self.assertEqual(checks, 2) def test_check_batch(self): checks = self.cp.check_batch() self.assertEqual(checks, 3) def test_check_dates(self): checks = self.cp.check_dates() self.assertEqual(checks, 1) def test_check_frag_size(self): checks = self.cp.check_frag_size() self.assertEqual(checks, 2) def test_check_anneal_temp(self): checks = self.cp.check_anneal_temp() self.assertEqual(checks, 1) def test_check_all(self): self.assertEqual(len(self.cp.check_all()), 10)
class TestCheckSNPs(unittest.TestCase): def setUp(self): self.ets = ExcelToSQL("TestCS_COL4A5.xlsx", "Test.db") df_snps, snp_faults = self.ets.get_snps() self.cs = CheckSNPs(df_snps) def test_check_no_snps(self): checks = self.cs.check_no_snps() self.assertEqual(checks, 2) def test_check_rs(self): checks = self.cs.check_rs() self.assertEqual(checks, 3) def test_check_hgvs(self): checks = self.cs.check_hgvs() self.assertEqual(checks, 2) def test_check_all(self): self.assertEqual(len(self.cs.check_all()), 3)
class TestExcelToSQL(unittest.TestCase): def setUp(self): self.ets = ExcelToSQL('TestETS_COL4A5.xlsx', 'Test.db') self.sheet_name = self.ets.get_sheet_name() self.df_primers, self.primer_faults = self.ets.get_primers() self.df_snps, self.snp_faults = self.ets.get_snps() self.curs, self.con = self.ets.get_cursor() def test_get_sheet_name(self): self.assertIsNotNone(self.sheet_name, msg="Sheet_name is empty") # tests sheetname has been obtained self.assertIn('Current primers', self.sheet_name, msg="Selected sheetname does not contain 'Current primers'") def test_get_primers(self): self.assertIsInstance(self.primer_faults, int, msg="No of primer_faults is not an integer") self.assertIsInstance(self.df_primers, pd.DataFrame, msg="df_primers is not a data frame") self.assertEqual(len(self.df_primers), 84, msg="Incorrect number of rows") self.assertEqual(len(self.df_primers.columns), 12, msg="Incorrect number of columns") self.assertEqual(str(self.df_primers.iat[8, 4]), 'GTGCAATGAAGACAATGCTCC', "Entry does not match predicted") def test_get_snps(self): self.assertIsInstance(self.snp_faults, int, msg="No of snp_faults is not an integer") self.assertIsInstance(self.df_snps, pd.DataFrame, msg="df_snps is not a data frame") self.assertEqual(len(self.df_snps), 92, msg="Incorrect number of rows") self.assertEqual(len(self.df_snps.columns), 13, msg="Incorrect number of columns") self.assertEqual(str(self.df_snps.iat[2, 6]), 'c.82-82T>C') def test_to_sql(self): self.ets.to_sql() self.curs.execute("SELECT * FROM 'Primers'") primer_result = self.curs.fetchone() self.assertIsNotNone(primer_result, msg="Primers table is empty") self.curs.execute("SELECT * FROM 'Genes'") gene_result = self.curs.fetchone() self.assertIsNotNone(gene_result, msg="Genes table is empty") self.curs.execute("SELECT * FROM 'SNPs'") snp_result = self.curs.fetchone() self.assertIsNotNone(snp_result, msg="SNPs table is empty")
def setUp(self): self.ets = ExcelToSQL('TestCP_COL4A5.xlsx', 'Test.db') df_primers, primer_faults = self.ets.get_primers() self.cp = CheckPrimers(df_primers)
def setUp(self): self.ets = ExcelToSQL("TestCS_COL4A5.xlsx", "Test.db") df_snps, snp_faults = self.ets.get_snps() self.cs = CheckSNPs(df_snps)
import warnings from exceltosqldev import ExcelToSQL warnings.simplefilter("ignore", UserWarning) excel_file = 'TestETS_COL4A5.xlsx' db = 'Test.db' ets = ExcelToSQL(excel_file, db) ets.to_sql()
def setUp(self): self.ets = ExcelToSQL('TestETS_COL4A5.xlsx', 'Test.db') self.sheet_name = self.ets.get_sheet_name() self.df_primers, self.primer_faults = self.ets.get_primers() self.df_snps, self.snp_faults = self.ets.get_snps() self.curs, self.con = self.ets.get_cursor()