def test_paraphyletic_genotype6():
tree_source = "((Sample.bar-6b, Ref.byre-6b), (Ref.baz-6c, (Ref.foo-1a, Sample.floop-1a)));"
report = StringIO()
expected_report = ""
check_tree(tree_source, report)
assert expected_report == report.getvalue()
def test_monophyletic():
tree_source = "(Ref.foo-1a, (Sample.bar-2b, Ref.baz-2b));"
report = StringIO()
expected_report = ''
check_tree(tree_source, report)
assert expected_report == report.getvalue()
def test_paraphyletic_genotype6():
tree_source = "((Sample.bar-6b, Ref.byre-6b), (Ref.baz-6c, (Ref.foo-1a, Sample.floop-1a)));"
report = StringIO()
expected_report = ""
check_tree(tree_source, report)
assert expected_report == report.getvalue()
def test_monophyletic():
tree_source = "(Ref.foo-1a, (Sample.bar-2b, Ref.baz-2b));"
report = StringIO()
expected_report = ''
check_tree(tree_source, report)
assert expected_report == report.getvalue()
def test_paraphyletic():
tree_source = "((Sample.bar-2b, Ref.byre-2b), (Ref.baz-2c, (Ref.foo-1a, Sample.floop-1a)));"
report = StringIO()
expected_report = r"""2 paraphyletic Ref.foo-1a, Sample.floop-1a
/-Sample.bar-2b
/-|
| \-Ref.byre-2b
--|
| /-Ref.baz-2c
\-|
| /-Ref.foo-1a
\-|
\-Sample.floop-1a
"""
check_tree(tree_source, report)
assert expected_report == report.getvalue()
def test_paraphyletic2():
tree_source = "((Ref.byre-2b, Sample.bar-2b), (Ref.baz-2c, (Ref.foo-1a, Sample.floop-1a)));"
report = StringIO()
expected_report = """\
2 paraphyletic Ref.foo-1a, Sample.floop-1a
/-Ref.byre-2b
/-|
| \-Sample.bar-2b
--|
| /-Ref.baz-2c
\-|
| /-Ref.foo-1a
\-|
\-Sample.floop-1a
"""
check_tree(tree_source, report)
assert expected_report == report.getvalue()
def test_polyphyletic():
tree_source = "((Ref.foo-1a, Sample.bar-2b), (Sample.floop-1a, Ref.baz-2c));"
report = StringIO()
expected_report = \
r"""1a polyphyletic Ref.baz-2c, Sample.bar-2b
1 polyphyletic Ref.baz-2c, Sample.bar-2b
2 polyphyletic Ref.foo-1a, Sample.floop-1a
Sample.bar-2b treed with 1a
Sample.floop-1a treed with 2c
/-Ref.foo-1a
/-|
| \-Sample.bar-2b
--|
| /-Sample.floop-1a
\-|
\-Ref.baz-2c
"""
check_tree(tree_source, report)
assert expected_report == report.getvalue()
def test_polyphyletic():
tree_source = "((Ref.foo-1a, Sample.bar-2b), (Sample.floop-1a, Ref.baz-2c));"
report = StringIO()
expected_report = """\
1a polyphyletic Ref.baz-2c, Sample.bar-2b
1 polyphyletic Ref.baz-2c, Sample.bar-2b
2 polyphyletic Ref.foo-1a, Sample.floop-1a
Sample.bar-2b treed with 1a
Sample.floop-1a treed with 2c
/-Ref.foo-1a
/-|
| \-Sample.bar-2b
--|
| /-Sample.floop-1a
\-|
\-Ref.baz-2c
"""
check_tree(tree_source, report)
assert expected_report == report.getvalue()