def test_rvd_invalid_input(self):
"""
Don't accept invalid RVD sequences.
"""
with self.assertRaises(ValueError):
pfusx.rvd_to_tal("This is not valid input.")
with self.assertRaises(ValueError):
pfusx.rvd_to_tal("atatatagatataga") # DNA and not RVD
def test_rvd_invalid_input(self):
"""
Don't accept invalid RVD sequences.
"""
with self.assertRaises(ValueError):
pfusx.rvd_to_tal("This is not valid input.")
with self.assertRaises(ValueError):
pfusx.rvd_to_tal("atatatagatataga") # DNA and not RVD
def test_fusx_query(self):
"""
Query FusX database to find the well positions of necessary plasmids.
"""
# Example from the FusX PHP script at <http://talendesign.org>.
rvd = pfusx.rvd_to_tal('NI NG NI HD HD NN NG HD NG NG NI NG NG NG NG')
sequences = pfusx.tal_to_codons(rvd)
result = pfusx.get_fusx_locations(sequences)
expected = [
('pFX1', 'E2'), ('pFX2', 'G3'), ('pFX3', 'H7'), ('pFX4', 'D7'),
('pB2/B3', 'H12')
]
self.assertEqual(result, expected)
def test_rvd_to_tal(self):
"""
Translate RVD2 to TAL2.
"""
# Various input formats.
stripped = 'NIHDNGNNNN'
slashes = 'NI/HD/NG/NN/NN'
spaces = 'NI HD NG NN NN'
dashes = 'NI-HD-NG-NN-NN'
commas = 'NI,HD,NG,NN,NN'
space_commas = 'NI, HD, NG, NN, NN'
# Uniform output.
expected = 'ACTGG'
self.assertEqual(pfusx.rvd_to_tal(stripped), expected)
self.assertEqual(pfusx.rvd_to_tal(slashes), expected)
self.assertEqual(pfusx.rvd_to_tal(spaces), expected)
self.assertEqual(pfusx.rvd_to_tal(dashes), expected)
self.assertEqual(pfusx.rvd_to_tal(commas), expected)
self.assertEqual(pfusx.rvd_to_tal(space_commas), expected)
def test_rvd_to_tal(self):
"""
Translate RVD2 to TAL2.
"""
# Various input formats.
stripped = 'NIHDNGNNNN'
slashes = 'NI/HD/NG/NN/NN'
spaces = 'NI HD NG NN NN'
dashes = 'NI-HD-NG-NN-NN'
commas = 'NI,HD,NG,NN,NN'
space_commas = 'NI, HD, NG, NN, NN'
# Uniform output.
expected = 'ACTGG'
self.assertEqual(pfusx.rvd_to_tal(stripped), expected)
self.assertEqual(pfusx.rvd_to_tal(slashes), expected)
self.assertEqual(pfusx.rvd_to_tal(spaces), expected)
self.assertEqual(pfusx.rvd_to_tal(dashes), expected)
self.assertEqual(pfusx.rvd_to_tal(commas), expected)
self.assertEqual(pfusx.rvd_to_tal(space_commas), expected)
