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 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 = ArrayAlignment(data={
"1": "AKKAKAK",
"2": "AKK-KAK",
"3": "AAAAAA-"
})
expected_h3 = ArrayAlignment(data={
"1": "PRRPRPR",
"2": "PRR-RPR",
"3": "PPPPYY-"
})
expected_aa = ArrayAlignment(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 = ArrayAlignment(data={
"1": "CDDFBXZ",
"2": "CDD.BXZ",
"3": "AAAASS."
})
self.assertEqual(actual, expected)
