def test_run_randomise_sample_toobig(self):
# raises ValueError, sample size too big (only 3 trees in this file)
nex = NexusReader(self.filename)
with self.assertRaises(ValueError):
run_random(10, nex)
def test_reader_from_blocks():
n = NexusReader(custom=['begin custom;', '[comment]', 'end;'])
assert hasattr(n, 'custom')
def test_error_on_missing_file(examples):
with pytest.raises(IOError):
NexusReader(examples / 'sausage.nex')
def hash(salt, value):
return hashlib.md5(("%s-%s" % (salt, value)).encode('ascii')).hexdigest()
if __name__ == '__main__': # pragma: no cover
from optparse import OptionParser
parser = OptionParser(usage="usage: %prog fudge.nex output.nex")
options, args = parser.parse_args()
try:
nexusname = args[0]
except IndexError:
print(__doc__)
print("Author: %s\n" % __author__)
parser.print_help()
sys.exit()
try:
newnexus = args[1]
except IndexError:
newnexus = None
nexus = NexusReader(nexusname)
nexus = anonymise(nexus)
if newnexus is not None:
nexus.write_to_file(newnexus)
print("New nexus written to %s" % newnexus)
else:
print(nexus.write_to_file(hash('filename', nexusname)))
def test_error_on_missing_file(self):
with self.assertRaises(IOError):
NexusReader(os.path.join(EXAMPLE_DIR, 'sausage.nex'))
def test_regression(self):
nex = NexusReader(os.path.join(REGRESSION_DIR, 'ape_random.trees'))
assert nex.trees.ntrees == 2
def setUp(self):
self.nex = NexusReader(
os.path.join(REGRESSION_DIR, 'detranslate-with-dash.trees')
)
def glottolog(regression):
"""
Regression: Test that we can read glottolog tree format.
"""
return NexusReader(regression / 'glottolog.trees')
def mesquite_branches(regression):
return NexusReader(regression / 'mesquite_formatted_branches.trees')
def taxlabels(regression):
"""
Regression: Test that we can read taxalabels delimited by spaces not new
lines.
"""
return NexusReader(regression / 'taxlabels.nex')
def mesquite(regression):
return NexusReader(regression / 'mesquite_taxa_block.nex')
def int_length(regression):
return NexusReader(regression / 'branchlengths-in-integers.trees')
def with_dash(regression):
return NexusReader(regression / 'detranslate-with-dash.trees')
def bad_chars(regression):
return NexusReader(regression / 'bad_chars_in_taxaname.trees')
def setUp(self):
self.nex = NexusReader(
os.path.join(REGRESSION_DIR, 'taxlabels.nex')
)
def test_TreeHandler_Regression_RandomAPETrees_regression(regression):
"""Regression: Test that we can parse randomly generated APE/R trees"""
nex = NexusReader(regression / 'ape_random.trees')
assert nex.trees.ntrees == 2
def setUp(self):
self.nex = NexusReader(
os.path.join(REGRESSION_DIR, 'glottolog.trees')
)
def test_detranslate(trees_translated, examples):
assert not trees_translated.trees._been_detranslated
trees_translated.trees.detranslate()
# should NOW be the same as tree 0 in example.trees
other_tree_file = NexusReader(str(examples / 'example.trees'))
assert other_tree_file.trees[0] == trees_translated.trees[0]
def setUp(self):
self.nex = NexusReader(
os.path.join(REGRESSION_DIR, 'bad_chars_in_taxaname.trees')
)
def setUp(self):
self.nex = NexusReader(
os.path.join(EXAMPLE_DIR, 'example-beast.trees')
)
def setUp(self):
self.nex = NexusReader(
os.path.join(REGRESSION_DIR, 'branchlengths-in-integers.trees')
)
def setUp(self):
self.nex = NexusReader(
os.path.join(EXAMPLE_DIR, 'example-translated.trees')
)
def test_read_file(self):
nex = NexusReader(os.path.join(EXAMPLE_DIR, 'example.nex'))
assert 'data' in nex.blocks
assert 'Simon' in nex.blocks['data'].matrix
def setUp(self):
self.nex = NexusReader(os.path.join(EXAMPLE_DIR, 'example2.nex'))
def test_write(self):
nex = NexusReader(os.path.join(EXAMPLE_DIR, 'example.trees'))
with open(os.path.join(EXAMPLE_DIR, 'example.trees')) as handle:
text = handle.read()
assert text == nex.write()
def setUp(self):
self.nex = NexusReader(
os.path.join(REGRESSION_DIR, 'mesquite_taxa_block.nex')
)
def test_roundtrip(examples):
nex = NexusReader(examples.joinpath('example2.nex'))
_ = NexusReader.from_string(nex.write())
def setUp(self):
self.nex = NexusReader(
os.path.join(REGRESSION_DIR, 'mesquite_formatted_branches.trees')
)
def test_write(examples):
nex = NexusReader(examples / 'example.trees')
assert nex.write().startswith('#NEXUS')
assert examples.joinpath('example.trees').read_text(
encoding='utf8') == nex.write()
def test_run_randomise_sample2(self):
nex = NexusReader(self.filename)
new_nex = run_random(2, nex)
assert new_nex.trees.ntrees == len(new_nex.trees.trees) == 2
