def test_works_w_dimer(self):
top2 = md.load(test_filenames.small_dimer).top
seq_1_res_idxs = [6,7,8,9,10,11]
df = sequence.align_tops_or_seqs(top2, top2, seq_1_res_idxs=seq_1_res_idxs)
_np.testing.assert_array_equal(df[df["match"]==True]["idx_0"].to_list(),
seq_1_res_idxs)
_np.testing.assert_array_equal(df[df["match"]==True]["idx_1"].to_list(),
seq_1_res_idxs)
def test_works(self):
df = sequence.align_tops_or_seqs("AABBCC", "AADDCC")
df_re_matched = sequence.re_match_df(df)
assert all(df_re_matched["match"].values)
def test_substitions(self):
top2 = md.load(test_filenames.small_monomer).top
df = sequence.align_tops_or_seqs(top2, top2, substitutions={"E": "G", "X": "Y"})
_np.testing.assert_array_equal("GVWIGKYY", ''.join(df["AA_0"]))
def test_works_w_itself_list(self):
top = md.load(test_filenames.small_monomer).top
df = sequence.align_tops_or_seqs(top, top, return_DF=False)
assert isinstance(df, list)
def test_works_w_itself_strs(self):
top = md.load(test_filenames.small_monomer).top
str1 = sequence.top2seq(top)
df = sequence.align_tops_or_seqs(str1, str1, return_DF=False)
assert isinstance(df, list)
def test_works_w_itself(self):
top = md.load(test_filenames.small_monomer).top
df = sequence.align_tops_or_seqs(top, top)
assert isinstance(df, _DF)
def test_detects_insertion(self):
df_bad = sequence.align_tops_or_seqs("AABBFFFFFCC", "AADDCC")
map1, map2 = sequence.df2maps(df_bad)
self.assertDictEqual(map1, {0: 0, 1: 1, 9: 4, 10: 5})
self.assertDictEqual(map2, {0: 0, 1: 1, 4: 9, 5: 10})
def test_works_only_matches(self):
df_good = sequence.align_tops_or_seqs("AABBCC", "AADDCC")
map1, map2 = sequence.df2maps(df_good, allow_nonmatch=False)
self.assertDictEqual(map1,map2)
self.assertDictEqual(map1,{0:0, 1:1, 4:4, 5:5})
def test_works(self):
df_good = sequence.align_tops_or_seqs("AABBCC", "AADDCC")
map1, map2 = sequence.df2maps(df_good)
self.assertDictEqual(map1,map2)
self.assertDictEqual(map1,{ii:ii for ii in range(len(map1))})
def test_detects_insertion(self):
df = sequence.align_tops_or_seqs("AABBFFFFFCC", "AADDCC")
df_re_matched = sequence.re_match_df(df)
print(df_re_matched)
self.assertListEqual(df_re_matched["match"].values.tolist(),[True,True,False,False,False,False,False,False,False,True,True])
