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')
