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()
