本文整理汇总了Python中PhyloBuddy.generate_tree方法的典型用法代码示例。如果您正苦于以下问题：Python PhyloBuddy.generate_tree方法的具体用法？Python PhyloBuddy.generate_tree怎么用？Python PhyloBuddy.generate_tree使用的例子？那么恭喜您, 这里精选的方法代码示例或许可以为您提供帮助。您也可以进一步了解该方法所在类PhyloBuddy的用法示例。
在下文中一共展示了PhyloBuddy.generate_tree方法的7个代码示例，这些例子默认根据受欢迎程度排序。您可以为喜欢或者感觉有用的代码点赞，您的评价将有助于系统推荐出更棒的Python代码示例。
示例1: test_phyml_inputs
# 需要导入模块: import PhyloBuddy [as 别名]
# 或者: from PhyloBuddy import generate_tree [as 别名]
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'示例2: test_raxml_inputs
# 需要导入模块: import PhyloBuddy [as 别名]
# 或者: from PhyloBuddy import generate_tree [as 别名]
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'示例3: test_fasttree_inputs
# 需要导入模块: import PhyloBuddy [as 别名]
# 或者: from PhyloBuddy import generate_tree [as 别名]
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'示例4: test_generate_trees_edge_cases
# 需要导入模块: import PhyloBuddy [as 别名]
# 或者: from PhyloBuddy import generate_tree [as 别名]
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")示例5: test_fasttree_multi_param
# 需要导入模块: import PhyloBuddy [as 别名]
# 或者: from PhyloBuddy import generate_tree [as 别名]
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'示例6: test_phyml_multi_param
# 需要导入模块: import PhyloBuddy [as 别名]
# 或者: from PhyloBuddy import generate_tree [as 别名]
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'示例7: test_raxml_multi_param
# 需要导入模块: import PhyloBuddy [as 别名]
# 或者: from PhyloBuddy import generate_tree [as 别名]
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'