def test_recode_dense_alignment_to_orig(self):
"""recode_dense_alignment: recode aln to orig returns original aln
"""
# provided with alphabet_id
self.assertEqual(recode_dense_alignment(self.aln, alphabet_id="orig"), self.aln)
# provided with alphabet_def
self.assertEqual(recode_dense_alignment(self.aln, alphabet_def=self.orig), self.aln)
def test_recode_dense_alignment_leaves_original_alignment_intact(self):
"""recode_dense_alignment: leaves input alignment intact
"""
# provided with alphabet_id
actual = recode_dense_alignment(self.aln, alphabet_id='charge_2')
self.assertNotEqual(actual,self.aln)
# provided with alphabet_def
actual = recode_dense_alignment(self.aln, alphabet_def=self.charge_2)
self.assertNotEqual(actual,self.aln)
def test_recode_dense_alignment_to_orig(self):
"""recode_dense_alignment: recode aln to orig returns original aln
"""
# provided with alphabet_id
self.assertEqual(recode_dense_alignment(\
self.aln, alphabet_id='orig'), self.aln)
# provided with alphabet_def
self.assertEqual(recode_dense_alignment(\
self.aln, alphabet_def=self.orig), self.aln)
def test_recode_dense_alignment_leaves_original_alignment_intact(self):
"""recode_dense_alignment: leaves input alignment intact
"""
# provided with alphabet_id
actual = recode_dense_alignment(self.aln, alphabet_id='charge_2')
self.assertNotEqual(actual, self.aln)
# provided with alphabet_def
actual = recode_dense_alignment(self.aln, alphabet_def=self.charge_2)
self.assertNotEqual(actual, self.aln)
def test_recode_dense_alignment_handles_all_ids_and_defs_wo_error(self):
"""recode_dense_alignment: handles pre-defined alphabets w/o error"""
for alphabet_id, alphabet_def in alphabets.items():
try:
recode_dense_alignment(self.aln,alphabet_id=alphabet_id)
except ValueError:
raise AssertionError, "Failed on id: %s" % alphabet_id
try:
recode_dense_alignment(self.aln,alphabet_def=alphabet_def)
except ValueError:
raise AssertionError, "Failed on def: %s" % str(alphabet_def)
def test_recode_dense_alignment_handles_all_ids_and_defs_wo_error(self):
"""recode_dense_alignment: handles pre-defined alphabets w/o error"""
for alphabet_id, alphabet_def in list(alphabets.items()):
try:
recode_dense_alignment(self.aln, alphabet_id=alphabet_id)
except ValueError:
raise AssertionError("Failed on id: %s" % alphabet_id)
try:
recode_dense_alignment(self.aln, alphabet_def=alphabet_def)
except ValueError:
raise AssertionError("Failed on def: %s" % str(alphabet_def))
def test_recode_dense_alignment(self):
"""recode_dense_alignment: recode alignment to charge_2 alpha works
"""
expected_c2 = DenseAlignment(data={"1": "AKKAKAK", "2": "AKK-KAK", "3": "AAAAAA-"})
expected_h3 = DenseAlignment(data={"1": "PRRPRPR", "2": "PRR-RPR", "3": "PPPPYY-"})
expected_aa = DenseAlignment(data={"1": "AAAAAAA", "2": "AAA-AAA", "3": "AAAAAA-"})
# provided with alphabet_id
actual = recode_dense_alignment(self.aln, alphabet_id="charge_2")
self.assertEqual(actual, expected_c2)
# provided with alphabet_def
actual = recode_dense_alignment(self.aln, alphabet_def=self.charge_2)
self.assertEqual(actual, expected_c2)
# different alphabet
actual = recode_dense_alignment(self.aln, alphabet_id="hydropathy_3")
self.assertEqual(actual, expected_h3)
actual = recode_dense_alignment(self.aln, alphabet_def=self.hydropathy_3)
self.assertEqual(actual, expected_h3)
# different alphabet
actual = recode_dense_alignment(self.aln, alphabet_def=self.all_to_a)
self.assertEqual(actual, expected_aa)
# original charactars which aren't remapped are let in original state
actual = recode_dense_alignment(self.aln, alphabet_def=[("a", "b")])
self.assertEqual(actual, self.aln)
# non-alphabetic character mapped same as alphabetic characters
actual = recode_dense_alignment(self.aln, alphabet_def=[(".", "-")])
expected = DenseAlignment(data={"1": "CDDFBXZ", "2": "CDD.BXZ", "3": "AAAASS."})
self.assertEqual(actual, expected)
def test_recode_dense_alignment(self):
"""recode_dense_alignment: recode alignment to charge_2 alpha works
"""
expected_c2 = DenseAlignment(data=\
{'1':'AKKAKAK','2':'AKK-KAK','3':'AAAAAA-'})
expected_h3 = DenseAlignment(data=\
{'1':'PRRPRPR','2':'PRR-RPR','3':'PPPPYY-'})
expected_aa = DenseAlignment(data=\
{'1':'AAAAAAA','2':'AAA-AAA','3':'AAAAAA-'})
# provided with alphabet_id
actual = recode_dense_alignment(self.aln, alphabet_id='charge_2')
self.assertEqual(actual,expected_c2)
# provided with alphabet_def
actual = recode_dense_alignment(self.aln, alphabet_def=self.charge_2)
self.assertEqual(actual,expected_c2)
# different alphabet
actual = recode_dense_alignment(self.aln, alphabet_id='hydropathy_3')
self.assertEqual(actual,expected_h3)
actual = recode_dense_alignment(self.aln,\
alphabet_def=self.hydropathy_3)
self.assertEqual(actual,expected_h3)
# different alphabet
actual = recode_dense_alignment(self.aln, alphabet_def=self.all_to_a)
self.assertEqual(actual,expected_aa)
# original charactars which aren't remapped are let in original state
actual = recode_dense_alignment(self.aln, alphabet_def=[('a','b')])
self.assertEqual(actual,self.aln)
# non-alphabetic character mapped same as alphabetic characters
actual = recode_dense_alignment(self.aln, alphabet_def=[('.','-')])
expected = DenseAlignment(\
data={'1':'CDDFBXZ', '2':'CDD.BXZ', '3':'AAAASS.'})
self.assertEqual(actual,expected)
def test_recode_dense_alignment(self):
"""recode_dense_alignment: recode alignment to charge_2 alpha works
"""
expected_c2 = DenseAlignment(data=\
{'1':'AKKAKAK','2':'AKK-KAK','3':'AAAAAA-'})
expected_h3 = DenseAlignment(data=\
{'1':'PRRPRPR','2':'PRR-RPR','3':'PPPPYY-'})
expected_aa = DenseAlignment(data=\
{'1':'AAAAAAA','2':'AAA-AAA','3':'AAAAAA-'})
# provided with alphabet_id
actual = recode_dense_alignment(self.aln, alphabet_id='charge_2')
self.assertEqual(actual, expected_c2)
# provided with alphabet_def
actual = recode_dense_alignment(self.aln, alphabet_def=self.charge_2)
self.assertEqual(actual, expected_c2)
# different alphabet
actual = recode_dense_alignment(self.aln, alphabet_id='hydropathy_3')
self.assertEqual(actual, expected_h3)
actual = recode_dense_alignment(self.aln,\
alphabet_def=self.hydropathy_3)
self.assertEqual(actual, expected_h3)
# different alphabet
actual = recode_dense_alignment(self.aln, alphabet_def=self.all_to_a)
self.assertEqual(actual, expected_aa)
# original charactars which aren't remapped are let in original state
actual = recode_dense_alignment(self.aln, alphabet_def=[('a', 'b')])
self.assertEqual(actual, self.aln)
# non-alphabetic character mapped same as alphabetic characters
actual = recode_dense_alignment(self.aln, alphabet_def=[('.', '-')])
expected = DenseAlignment(\
data={'1':'CDDFBXZ', '2':'CDD.BXZ', '3':'AAAASS.'})
self.assertEqual(actual, expected)