def test_generate_tree_edges(alb_resources, monkeypatch):
mock_tmp_dir = br.TempDir()
tmp_dir = br.TempDir()
for root, dirs, files in os.walk("%smock_resources%stest_fasttree_inputs" % (RES_PATH, os.path.sep)):
for _file in files:
shutil.copyfile("%s%s%s" % (root, os.path.sep, _file), "%s%s%s" % (mock_tmp_dir.path, os.path.sep, _file))
monkeypatch.setattr(Pb.shutil, "which", lambda *_: True)
monkeypatch.setattr(Pb, "Popen", MockPopen)
monkeypatch.setattr(br, "TempDir", lambda: mock_tmp_dir)
with pytest.raises(RuntimeError) as err:
Pb.generate_tree(alb_resources.get_one("o d n"), 'fasttree', "--nonsense")
assert "fasttree threw an error. Scroll up for more info." in str(err)
with pytest.raises(FileExistsError) as err:
Pb.generate_tree(alb_resources.get_one("o d n"), 'raxml', keep_temp=tmp_dir.path)
assert "Execution of raxml was halted to prevent files in" in str(err)
with pytest.raises(FileNotFoundError) as err:
Pb.generate_tree(alb_resources.get_one("o d n"), 'Foo')
assert 'Foo failed to generate a tree' in str(err)
monkeypatch.setattr(Pb.shutil, "which", lambda *_: None)
with pytest.raises(ProcessLookupError) as err:
Pb.generate_tree(alb_resources.get_one("o d n"), 'Foo')
assert "ProcessLookupError: #### Could not find Foo on your system. ####" in str(err)
monkeypatch.setattr(Pb.Popen, "communicate", lambda *_: ["".encode(), "".encode()])
with pytest.raises(AttributeError) as err:
Pb.generate_tree(alb_resources.get_one("o d n"), 'Foo')
assert "Foo is not a recognized tree inference tool. Please check your spelling (case sensitive)" in str(err)
def test_fasttree_inputs(alb_resources, hf):
temp_dir = br.TempDir()
# Nucleotide
alignbuddy = alb_resources.get_one("o d n")
tester = Pb.generate_tree(Alb.make_copy(alignbuddy), 'FastTree',
'-seed 12345')
assert hf.buddy2hash(tester) in [
'd7f505182dd1a1744b45cc326096f70c', 'da8a67cae6f3f70668f7cf04060b7cd8',
'732c5e9a978cebb1cfce6af6d64950c2'
]
tester = Pb.generate_tree(alignbuddy,
'fasttree',
'-seed 12345',
quiet=True)
assert hf.buddy2hash(tester) in [
'd7f505182dd1a1744b45cc326096f70c', 'da8a67cae6f3f70668f7cf04060b7cd8',
'732c5e9a978cebb1cfce6af6d64950c2'
]
alignbuddy = alb_resources.get_one("o p n")
tester = Pb.generate_tree(alignbuddy,
'fasttree',
'-seed 12345',
keep_temp="%s%snew_dir" %
(temp_dir.path, os.sep))
assert hf.buddy2hash(tester) in [
'57eace9bdd2074297cbd2692c1f4cd38', '82d5a9d4f44fbedf29565686a7cdfcaa',
'682210ef16beedee0e9f43c05edac112'
]
def test_phyml_inputs():
# Nucleotide
tester = Alb.AlignBuddy(resource("Mnemiopsis_cds.nex"))
tester = Pb.generate_tree(tester, 'phyml', '-m GTR --r_seed 12345')
assert phylo_to_hash(tester) == 'd3a4e7601998885f333ddd714ca764db'
# Peptide
tester = Alb.AlignBuddy(resource("Mnemiopsis_pep.nex"))
tester = Pb.generate_tree(tester, 'phyml', '-m Blosum62 --r_seed 12345')
assert phylo_to_hash(tester) == '52c7d028341b250bcc867d57a68c794c'
def test_raxml_inputs():
# Nucleotide
tester = Alb.AlignBuddy(resource("Mnemiopsis_cds.nex"))
tester = Pb.generate_tree(tester, 'raxml')
assert phylo_to_hash(tester) == '706ba436f8657ef3aee7875217dd07c0'
# Peptide
tester = Alb.AlignBuddy(resource("Mnemiopsis_pep.nex"))
tester = Pb.generate_tree(tester, 'raxml')
assert phylo_to_hash(tester) == 'fc35569091eeba49ac4dcec7fc6890bf'
def test_fasttree_inputs():
temp_dir = MyFuncs.TempDir()
# Nucleotide
alignbuddy = Alb.AlignBuddy(resource("Mnemiopsis_cds.nex"))
tester = Pb.generate_tree(alignbuddy, 'fasttree', '-seed 12345')
assert phylo_to_hash(tester) == 'd7f505182dd1a1744b45cc326096f70c'
alignbuddy = Alb.AlignBuddy(resource("Mnemiopsis_pep.nex"))
tester = Pb.generate_tree(alignbuddy, 'fasttree', '-seed 12345', keep_temp="%s/new_dir" % temp_dir.path)
assert phylo_to_hash(tester) == '57eace9bdd2074297cbd2692c1f4cd38'
def test_raxml_multiple_searches(alb_resources, hf):
tester = alb_resources.get_one("o d py")
tester = Pb.generate_tree(tester, 'raxml', '-N 3')
assert hf.buddy2hash(tester) in [
'76356987f7e2368cdf13c42567cb7453', 'ee223e46a9f9753203553e6fd7473ec9',
'b3a8359c62e9d29b952782df53a4782a', '807de55171690b2af1b724d86390cbc7',
'46e0a6d38e3c44b93a04d2b5b7f4aca1'
]
def test_raxml_inputs_quiet(alb_resources, hf):
tester = alb_resources.get_one("o d n")
tester = Pb.generate_tree(tester, 'raxml', quiet=True)
assert hf.buddy2hash(tester) in [
'7569f9f6c7f8079579bfb77291b99616', '4e083fc6d8b4f4342674efd93d5e313c',
'706ba436f8657ef3aee7875217dd07c0', '1cede6c576bb88125e2387d850f813ab',
'3280f0b404d62fbedd2e6090cfd6fedc'
]
def test_phyml_pep(alb_resources, hf):
# Peptide
tester = alb_resources.get_one("o p py")
tester = Pb.generate_tree(tester, 'phyml', '-m Blosum62 --r_seed 12345')
assert hf.buddy2hash(tester) in ['7caa5c641fa83085c2980efca875112a',
'2bf0a204b2de7bc5132aa7073ecfb011',
'981d16e8f02989a8642095016c88af90',
'd8ee3631002b6603d08272c2b44fd21c'], print(tester)
def test_phyml_dna(alb_resources, hf):
# Nucleotide
tester = alb_resources.get_one("o d py")
tester = Pb.generate_tree(tester, 'phyml', '-m GTR --r_seed 12345')
assert hf.buddy2hash(tester) in ['b61e75e4706d35e92f2208d438f52771',
'b0bdb3f5bf1fb2e44bef3c16f80c38f2',
'b9d3f11e332c3589110322e939aa41cc',
'754c38fab99c01c68a68c0a59248d242'], print(tester)
def test_raxml_inputs_pep(alb_resources, hf):
tester = alb_resources.get_one("o p py")
tester = Pb.generate_tree(tester, 'raxml')
assert hf.buddy2hash(tester) in [
'3e6ab2efc088d5547fa8244462f7cc03', '832f3b301a2a320affb9864b4c6a3979',
'41ccd8852002f3b98c032378403c38b0', '6443e4dddb9b64a783bd9e97b369e0d4',
'caff20f9bb5192a799ec18db0faa8569', '31218fd9e1b803df09fce22eee8da62e'
]
def test_raxml_multi_param(alb_resources, hf):
tester = alb_resources.get_one("o d n")
tester = Pb.generate_tree(tester, 'raxml',
'-m GTRCAT -p 112358 -K MK -N 3')
assert hf.buddy2hash(tester) in [
'08fa932a0cbb33d936ef4c8aef3c0095', '53ea2002e19d1d88c684f0ddc02de187',
'02e5ea7b756b68b8622636ba7e28e15b', 'c24b5e9c1899246b9a459a61efe0aad5',
'1999ef930c0d6cadbe5844b7c6355029', 'ead385a55d3cad48ecfdd1ebddb00b8b'
]
def test_raxml_multiple_searches(alb_resources, hf):
tester = alb_resources.get_one("o d py")
tester = Pb.generate_tree(tester, 'raxml', '-N 3')
assert hf.buddy2hash(tester) in [
'76356987f7e2368cdf13c42567cb7453', 'ee223e46a9f9753203553e6fd7473ec9',
'b3a8359c62e9d29b952782df53a4782a', '807de55171690b2af1b724d86390cbc7',
'46e0a6d38e3c44b93a04d2b5b7f4aca1', 'ecf0cabfab48bc2449ca3e43645b3d36',
'ce60f6627ff665994f0c6836d7469632', 'c8f5fe6c50150e55b43d545e44c7c5ce'
]
def test_raxml_inputs_quiet(alb_resources, hf):
tester = alb_resources.get_one("o d n")
tester = Pb.generate_tree(tester, 'raxml', quiet=True)
assert hf.buddy2hash(tester) in [
'7569f9f6c7f8079579bfb77291b99616', '4e083fc6d8b4f4342674efd93d5e313c',
'706ba436f8657ef3aee7875217dd07c0', '1cede6c576bb88125e2387d850f813ab',
'3280f0b404d62fbedd2e6090cfd6fedc', 'b954440b4baa338eb4a63b0a5a7f7942',
'629fa27f6e636c137257abc6a8a40956', '878e1ca74539e9b969c539bd8743c27e'
]
def test_generate_trees_edge_cases(alb_resources):
temp_file = br.TempFile()
tester = alb_resources.get_one("o d n")
with pytest.raises(FileExistsError):
Pb.generate_tree(tester, "raxml", keep_temp=temp_file.path)
with pytest.raises(AttributeError):
Pb.generate_tree(tester, "foo")
with pytest.raises(FileNotFoundError):
Pb.generate_tree(tester, "raxml", "-m BINCATLG")
with pytest.raises(RuntimeError):
Pb.generate_tree(tester, "fasttree", "-s 12345")
# noinspection PyUnresolvedReferences
with mock.patch.dict(os.environ, {"PATH": ""}):
with pytest.raises(ProcessLookupError):
Pb.generate_tree(tester, "raxml")
def test_generate_trees_edge_cases():
temp_file = MyFuncs.TempFile()
tester = Alb.AlignBuddy(resource("Mnemiopsis_cds.nex"))
with pytest.raises(FileExistsError):
Pb.generate_tree(tester, "raxml", keep_temp=temp_file.path)
with pytest.raises(AttributeError):
Pb.generate_tree(tester, "foo")
with pytest.raises(FileNotFoundError):
Pb.generate_tree(tester, "raxml", "-m BINCATLG")
with pytest.raises(RuntimeError):
Pb.generate_tree(tester, "fasttree", "-s 12345")
# noinspection PyUnresolvedReferences
with mock.patch.dict(os.environ, {"PATH": ""}):
with pytest.raises(ProcessLookupError):
Pb.generate_tree(tester, "raxml")
def test_raxml_multi_param(alb_resources, hf):
tester = alb_resources.get_one("o d n")
tester = Pb.generate_tree(tester, 'raxml',
'-m GTRCAT -p 112358 -K MK -N 3')
assert hf.buddy2hash(tester) in [
'08fa932a0cbb33d936ef4c8aef3c0095', '53ea2002e19d1d88c684f0ddc02de187',
'02e5ea7b756b68b8622636ba7e28e15b', 'c24b5e9c1899246b9a459a61efe0aad5',
'1999ef930c0d6cadbe5844b7c6355029', 'ead385a55d3cad48ecfdd1ebddb00b8b',
'ae6e53a6e7c03786928b087a15e0435e', '135f244c3de9ba417fe685715fef6807',
'886a9d841e68c2fd4c6052ad85c4eaf7'
]
def test_phyml_pep(alb_resources, hf):
# Peptide
tester = alb_resources.get_one("o p py")
tester = Pb.generate_tree(tester, 'phyml', '-m Blosum62 --r_seed 12345')
assert hf.buddy2hash(tester) in {
'7caa5c641fa83085c2980efca875112a': "",
'2bf0a204b2de7bc5132aa7073ecfb011': "",
'981d16e8f02989a8642095016c88af90': "",
'd8ee3631002b6603d08272c2b44fd21c': "",
'03acc8e899955f7e838852d7d71049ad': "",
'abe46f3bac533ad2f510bd4657aa9505': "",
'06f5ec5db5e1a27c07e4e8b5f5850685': "3.3.20170530"
}, print(tester)
def test_fasttree(alb_resources, hf, monkeypatch):
mock_tmp_dir = br.TempDir()
tmp_dir = br.TempDir()
for root, dirs, files in os.walk("%smock_resources%stest_fasttree_inputs" %
(RES_PATH, os.path.sep)):
for _file in files:
shutil.copyfile("%s%s%s" % (root, os.path.sep, _file),
"%s%s%s" % (mock_tmp_dir.path, os.path.sep, _file))
monkeypatch.setattr(Pb.shutil, "which", lambda *_: True)
monkeypatch.setattr(Pb, "Popen", MockPopen)
monkeypatch.setattr(Pb, "check_output", mock_check_output)
monkeypatch.setattr(br, "TempDir", lambda: mock_tmp_dir)
# basic
tester = alb_resources.get_one("o d n")
tester.hash_map = HASH_MAP
tester = Pb.generate_tree(tester, 'fasttree')
assert hf.buddy2hash(
tester) == "4b2ab8c39f27b9871f9a370ca7d0c4b3", tester.write("temp.del")
# quiet
tester = alb_resources.get_one("o d n")
tester.hash_map = HASH_MAP
tester = Pb.generate_tree(tester, 'fasttree', quiet=True)
assert hf.buddy2hash(
tester) == "4b2ab8c39f27b9871f9a370ca7d0c4b3", tester.write("temp.del")
# params
tester = alb_resources.get_one("o d n")
tester.hash_map = HASH_MAP
tester = Pb.generate_tree(tester, 'fasttree', "-pseudo", quiet=True)
assert hf.buddy2hash(
tester) == "4b2ab8c39f27b9871f9a370ca7d0c4b3", tester.write("temp.del")
# slight edges
tester = alb_resources.get_one("m p s")
tester.hash_map = HASH_MAP
tester = Pb.generate_tree(tester, 'fasttree-foo', quiet=True)
assert hf.buddy2hash(
tester) == "7692ee7edb8df4f91d2bdca6c3767796", tester.write("temp.del")
# keep
tester = alb_resources.get_one("o d n")
tester.hash_map = HASH_MAP
Pb.generate_tree(tester,
'fasttree',
keep_temp="%s%skeep_files" % (tmp_dir.path, os.path.sep))
root, dirs, files = next(
os.walk("%s%skeep_files" % (tmp_dir.path, os.path.sep)))
kept_output = ""
for file in sorted(files):
with open("%s%s%s" % (root, os.path.sep, file), "r") as ifile:
kept_output += ifile.read()
if os.name == "nt":
assert hf.string2hash(
kept_output) == "bcd034f0db63a7b41f4b3b6661200ef3"
else:
assert hf.string2hash(
kept_output) == "10df99cd1696b002f841aa18b78477ca"
def test_phyml_dna(alb_resources, hf):
# Nucleotide
tester = alb_resources.get_one("o d py")
tester = Pb.generate_tree(tester, 'phyml', '-m GTR --r_seed 12345')
assert hf.buddy2hash(tester) in {
'b61e75e4706d35e92f2208d438f52771': "",
'b0bdb3f5bf1fb2e44bef3c16f80c38f2': "",
'b9d3f11e332c3589110322e939aa41cc': "",
'754c38fab99c01c68a68c0a59248d242': "",
'3ca772c34cdcf0a22c09e1592aba9ebf': "",
'd7ae1badd31d48487276495bad4522e5': "",
'e84fb949f1a6ed0296cda4e5a8422423': "3.3.20170530"
}, print(tester)
def test_phyml(alb_resources, hf, monkeypatch):
mock_tmp_dir = br.TempDir()
tmp_dir = br.TempDir()
for root, dirs, files in os.walk("%smock_resources%stest_phyml_inputs" %
(RES_PATH, os.path.sep)):
for _file in files:
shutil.copyfile("%s%s%s" % (root, os.path.sep, _file),
"%s%s%s" % (mock_tmp_dir.path, os.path.sep, _file))
monkeypatch.setattr(Pb.shutil, "which", lambda *_: True)
monkeypatch.setattr(Pb, "Popen", MockPopen)
monkeypatch.setattr(br, "TempDir", lambda: mock_tmp_dir)
# basic
tester = alb_resources.get_one("o d n")
tester.hash_map = HASH_MAP
tester = Pb.generate_tree(tester, 'phyml')
assert hf.buddy2hash(
tester) == "9fbcfe1d565b9fd23e2c5fca86019f8e", tester.write("temp.del")
# quiet
tester = alb_resources.get_one("o d n")
tester.hash_map = HASH_MAP
tester = Pb.generate_tree(tester, 'phyml', quiet=True)
assert hf.buddy2hash(
tester) == "9fbcfe1d565b9fd23e2c5fca86019f8e", tester.write("temp.del")
# params
tester = alb_resources.get_one("o d n")
tester.hash_map = HASH_MAP
tester = Pb.generate_tree(tester, 'phyml', "--sequential", quiet=True)
assert hf.buddy2hash(
tester) == "9fbcfe1d565b9fd23e2c5fca86019f8e", tester.write("temp.del")
# slight edges
tester = alb_resources.get_one("o p n")
tester.hash_map = HASH_MAP
tester = Pb.generate_tree(tester, 'phyml-foo', tmp_dir.path, quiet=True)
assert hf.buddy2hash(
tester) == "9fbcfe1d565b9fd23e2c5fca86019f8e", tester.write("temp.del")
# keep
tester = alb_resources.get_one("o d n")
tester.hash_map = HASH_MAP
Pb.generate_tree(tester,
'phyml',
keep_temp="%s%skeep_files" % (tmp_dir.path, os.path.sep))
root, dirs, files = next(
os.walk("%s%skeep_files" % (tmp_dir.path, os.path.sep)))
kept_output = ""
for file in sorted(files):
with open("%s%s%s" % (root, os.path.sep, file), "r") as ifile:
kept_output += ifile.read()
if os.name == "nt":
assert hf.string2hash(
kept_output) == "a795da6869c5e3a34962a52ec35006ed"
else:
assert hf.string2hash(
kept_output) == "5a3559c264cb4c4779f15a515aaf2286"
def test_raxml_multi_param():
tester = Alb.AlignBuddy(resource("Mnemiopsis_cds.nex"))
tester = Pb.generate_tree(tester, 'raxml', '-m GTRCAT -p 112358 -K MK -N 2')
assert phylo_to_hash(tester) == '2bce58a9c6756fa68fd828a307850d7d'
def test_raxml_inputs_pep(alb_resources, hf):
tester = alb_resources.get_one("o p py")
tester = Pb.generate_tree(tester, 'raxml')
assert hf.buddy2hash(tester) in ['3e6ab2efc088d5547fa8244462f7cc03', '832f3b301a2a320affb9864b4c6a3979',
'41ccd8852002f3b98c032378403c38b0', '6443e4dddb9b64a783bd9e97b369e0d4']
def test_raxml(alb_resources, hf, monkeypatch):
mock_tmp_dir = br.TempDir()
tmp_dir = br.TempDir()
root, dirs, files = next(os.walk("%smock_resources%stest_raxml_inputs" % (RES_PATH, os.path.sep)))
for _file in files:
shutil.copyfile("%s%s%s" % (root, os.path.sep, _file), "%s%s%s" % (mock_tmp_dir.path, os.path.sep, _file))
monkeypatch.setattr(Pb.shutil, "which", lambda *_: True)
monkeypatch.setattr(Pb, "Popen", MockPopen)
monkeypatch.setattr(br, "TempDir", lambda: mock_tmp_dir)
# basic
tester = alb_resources.get_one("o d n")
tester.hash_map = HASH_MAP
tester = Pb.generate_tree(tester, 'raxml')
assert hf.buddy2hash(tester) == "1cede6c576bb88125e2387d850f813ab", tester.write("temp.del")
# quiet
tester = alb_resources.get_one("o d n")
tester.hash_map = HASH_MAP
tester = Pb.generate_tree(tester, 'raxml', quiet=True)
assert hf.buddy2hash(tester) == "1cede6c576bb88125e2387d850f813ab", tester.write("temp.del")
# params
tester = alb_resources.get_one("o d n")
tester.hash_map = HASH_MAP
tester = Pb.generate_tree(tester, 'raxml', "-w path{0}to{0}nowhere".format(os.path.sep), quiet=True)
assert hf.buddy2hash(tester) == "1cede6c576bb88125e2387d850f813ab", tester.write("temp.del")
# slight edges
tester = alb_resources.get_one("o p n")
tester.hash_map = HASH_MAP
tester = Pb.generate_tree(tester, 'raxml-HPC', tmp_dir.path, quiet=True)
assert hf.buddy2hash(tester) == "1cede6c576bb88125e2387d850f813ab", tester.write("temp.del")
# bootstraps
tester = alb_resources.get_one("o d n")
tester.hash_map = HASH_MAP
tester = Pb.generate_tree(tester, 'raxml', "-b 1234 -N 4", quiet=True)
assert hf.buddy2hash(tester) == "b8a3b6068aa06bd8a70fcc9bda0efad9", tester.write("temp.del")
# keep
tester = alb_resources.get_one("o d n")
tester.hash_map = HASH_MAP
Pb.generate_tree(tester, 'raxml', keep_temp="%s%skeep_files" % (tmp_dir.path, os.path.sep))
root, dirs, files = next(os.walk("%s%skeep_files" % (tmp_dir.path, os.path.sep)))
kept_output = ""
for file in sorted(files):
with open("%s%s%s" % (root, os.path.sep, file), "r") as ifile:
kept_output += ifile.read()
if os.name == "nt":
assert hf.string2hash(kept_output) == "7f2fdfe55dbe805bd994f3f56c79bb1b"
else:
assert hf.string2hash(kept_output) == "393353fb47861460aecaefa69a6ec55c"
# multi-run
os.remove("%s%sRAxML_bestTree.result" % (mock_tmp_dir.path, os.path.sep))
tester = alb_resources.get_one("o d n")
tester.hash_map = HASH_MAP
tester = Pb.generate_tree(tester, 'raxml', "-N 3", quiet=True)
assert hf.buddy2hash(tester) == "e8ce19bba744f0188df2ebb4ffced4d8", tester.write("temp.del")
# bipartitions
shutil.copy("{0}mock_resources{1}test_raxml_inputs{1}bipartitions{1}RAxML_bipartitions.result".format(RES_PATH,
os.path.sep),
"%s%s" % (mock_tmp_dir.path, os.path.sep))
tester = alb_resources.get_one("o d n")
tester.hash_map = HASH_MAP
tester = Pb.generate_tree(tester, 'raxml', "-f b -z {0}{1}RAxML_bootstrap.result "
"-t {0}{1}RAxML_bestTree.result".format(tmp_dir.path, os.path.sep))
assert hf.buddy2hash(tester) == "457533ada8e987fd0c50a41aabe1700b"
def test_fasttree_multi_param():
temp_file = MyFuncs.TempFile()
tester = Alb.AlignBuddy(resource("Alignments_cds.phyr"))
tester = Pb.generate_tree(tester, 'fasttree', '-seed 12345 -wag -fastest -log %s' % temp_file.path)
assert phylo_to_hash(tester) == '28debf1cc6a7ab69f94c69626fbe5db0'
def test_fasttree_multi_param():
temp_file = MyFuncs.TempFile()
tester = Alb.AlignBuddy(resource("Alignments_cds.phyr"))
tester = Pb.generate_tree(tester, 'fasttree', '-seed 12345 -wag -fastest -log %s' % temp_file.path)
assert phylo_to_hash(tester) == '0877f4e8f46c3f77390dbf962d24ff71'
def test_phyml_multi_param():
tester = Alb.AlignBuddy(resource("Mnemiopsis_cds.nex"))
tester = Pb.generate_tree(tester, 'phyml', '-m GTR -o tl -b 2 --r_seed 12345')
assert phylo_to_hash(tester) == '5434f29509eab76dd52dd69d2c0e186f'
