def test_invalid_header_2(self): """case: without reference genome informaion in header-lines""" try: p = andmeParser(open(os.path.join(self.basedir, "test", "test.23andme.invalid-header.2.txt"), "r")) except andmeParseError as e: self.assertEqual(e.error_code, "Could not determine reference-genome version from header-lines.") else: self.fail("should have thrown andmeParseError")
def test_invalid_header_1(self): """case: without whole header-lines""" try: p = andmeParser(open(os.path.join(self.basedir, "test", "test.23andme.invalid-header.1.txt"), "r")) except andmeParseError as e: self.assertEqual(e.error_code, "Header-lines seem invalid. `# rsid ...` does not exists.") else: self.fail("should have thrown andmeParseError")
def test_success(self): p = andmeParser(open(os.path.join(self.basedir, "test", "test.23andme.txt"), "r")) self.assertEqual(p.ref_genome_version, "b37") record = p.parse_lines().next() self.assertEqual(record["id"], "rs4477212") self.assertEqual(record["rs"], 4477212) self.assertEqual(record["chrom"], "1") self.assertEqual(record["pos"], 82154) self.assertEqual(record["genotype"], "AA")
def test_success(self): p = andmeParser( open(os.path.join(self.basedir, 'test', 'test.23andme.txt'), 'r')) self.assertEqual(p.ref_genome_version, 'b37') record = p.parse_lines().next() self.assertEqual(record['id'], 'rs4477212') self.assertEqual(record['rs'], 4477212) self.assertEqual(record['chrom'], '1') self.assertEqual(record['pos'], 82154) self.assertEqual(record['genotype'], 'AA')
def test_invalid_header_1(self): """case: without whole header-lines""" try: p = andmeParser( open( os.path.join(self.basedir, 'test', 'test.23andme.invalid-header.1.txt'), 'r')) except andmeParseError as e: self.assertEqual( e.error_code, 'Header-lines seem invalid. `# rsid ...` does not exists.') else: self.fail('should have thrown andmeParseError')
def test_invalid_header_2(self): """case: without reference genome informaion in header-lines""" try: p = andmeParser( open( os.path.join(self.basedir, 'test', 'test.23andme.invalid-header.2.txt'), 'r')) except andmeParseError as e: self.assertEqual( e.error_code, 'Could not determine reference-genome version from header-lines.' ) else: self.fail('should have thrown andmeParseError')
def test_invalid_file(self): """case: fin is another file-format""" # py27 # with self.assertRaises(andmeParseError) as cm: # p = andmeParser(open(os.path.join(self.basedir, 'test', 'test.vcf41.vcf'), 'r')) # # self.assertEqual(cm.exception.error_code, 'Header-lines seem invalid. `# rsid ...` does not exists.') # py26 try: p = andmeParser(open(os.path.join(self.basedir, "test", "test.vcf41.vcf"), "r")) except andmeParseError as e: self.assertEqual(e.error_code, "Header-lines seem invalid. `# rsid ...` does not exists.") else: self.fail("should have thrown andmeParseError")
def test_invalid_file(self): """case: fin is another file-format""" # py27 # with self.assertRaises(andmeParseError) as cm: # p = andmeParser(open(os.path.join(self.basedir, 'test', 'test.vcf41.vcf'), 'r')) # # self.assertEqual(cm.exception.error_code, 'Header-lines seem invalid. `# rsid ...` does not exists.') # py26 try: p = andmeParser( open(os.path.join(self.basedir, 'test', 'test.vcf41.vcf'), 'r')) except andmeParseError as e: self.assertEqual( e.error_code, 'Header-lines seem invalid. `# rsid ...` does not exists.') else: self.fail('should have thrown andmeParseError')