def test_multiple(self):
# first test, align string, no output, no input
output = self.run_cli('multiple -s woldemort waldemar walter')
self.assertIn('w\ta\tl\tt\te\t-\t-\tr\t-', output)
# second test, test output as file, no input, vary method as sca
mlt = main('multiple', '-s', 'woldemort', 'waldemar',
'walter', '--method', 'sca', '--output-file',
self.tmp_path('out.msa').as_posix())
assert mlt[0] == list('woldemort')
# third test, test output and input
# second test, test output as file, no input, vary method as sca
mlt = main('multiple', '-i', test_data('harryp.msa'),
'--method', 'sca', '--output-file',
self.tmp_path('out2.msa').as_posix(), '--align-method',
'library')
assert len(mlt[0]) == 7
# fourth test, test output and input with method=basic
mlt = main('multiple', '-i', test_data('harryp.msa'),
'--method', 'basic', '--output-file',
self.tmp_path('out2.msa').as_posix())
assert len(mlt[0]) == 7
assert len([x for x in mlt[1][-1] if x != '-']) == 4
def test_multiple(capsys, test_data, tmppath):
# first test, align string, no output, no input
output = run(capsys, 'multiple -s woldemort waldemar walter')
assert 'w\ta\tl\tt\te\t-\t-\tr\t-' in output
# second test, test output as file, no input, vary method as sca
_ = run(capsys, 'multiple', '-s', 'woldemort', 'waldemar', 'walter',
'--method', 'sca', '--output-file', str(tmppath / 'out.msa'))
# third test, test output and input
# second test, test output as file, no input, vary method as sca
mlt = main('multiple', '-i', str(test_data / 'harryp.msa'), '--method',
'sca', '--output-file', str(tmppath / 'out2.msa'),
'--align-method', 'library')
assert len(mlt[0]) == 7
# fourth test, test output and input with method=basic
mlt = main('multiple', '-i', str(test_data / 'harryp.msa'), '--method',
'basic', '--output-file', str(tmppath / 'out2.msa'))
assert len(mlt[0]) == 7
assert len([x for x in mlt[1][-1] if x != '-']) == 4
def test_multiple(self):
# first test, align string, no output, no input
output = self.run_cli('multiple -s woldemort waldemar walter')
self.assertIn('w\ta\tl\tt\te\t-\t-\tr\t-', output)
# second test, test output as file, no input, vary method as sca
mlt = main('multiple', '-s', 'woldemort', 'waldemar', 'walter',
'--method', 'sca', '--output-file',
self.tmp_path('out.msa').as_posix())
# third test, test output and input
# second test, test output as file, no input, vary method as sca
mlt = main('multiple', '-i', test_data('harryp.msa'), '--method',
'sca', '--output-file',
self.tmp_path('out2.msa').as_posix(), '--align-method',
'library')
assert len(mlt[0]) == 7
# fourth test, test output and input with method=basic
mlt = main('multiple', '-i', test_data('harryp.msa'), '--method',
'basic', '--output-file',
self.tmp_path('out2.msa').as_posix())
assert len(mlt[0]) == 7
assert len([x for x in mlt[1][-1] if x != '-']) == 4
def capture(*args):
out, sys.stdout = sys.stdout, StringIO()
main(*args)
sys.stdout.seek(0)
yield sys.stdout.read()
sys.stdout = out
def test_lexstat(self):
cogs = main('lexstat', '-i',
test_data('KSL.qlc'),
'--output-file', self.tmp_path('lexstat').as_posix())
assert cogs == 1080
from lingpy.cli import main main()
def capture(*args):
out, sys.stdout = sys.stdout, StringIO()
main(*args)
sys.stdout.seek(0)
yield sys.stdout.read()
sys.stdout = out
def test_lexstat(self):
cogs = main('lexstat', '-i', test_data('KSL.qlc'), '--output-file',
self.tmp_path('lexstat').as_posix())
assert cogs == 1080
def test_profile(self):
prf = main('profile', '-i', test_data('KSL.qlc'), '--column', 'ipa')
assert prf == 105
prf = main('profile', '-i', test_data('KSL.qlc'), '--column', 'ipa',
'--language', 'German', '--count')
assert prf == 37
def test_lexstat(self):
# TODO check with other python versions
cogs = main('lexstat', '-i', test_data('KSL.qlc'), '--output-file',
self.tmp_path('lexstat').as_posix())
print(cogs)
assert cogs in [1080, 1081]
def run(capsys, *args):
if len(args) == 1:
args = shlex.split(args[0])
main(*args)
return capsys.readouterr().out
def test_lexstat(test_data, tmppath):
# TODO check with other python versions
cogs = main('lexstat', '-i', str(test_data / 'KSL.qlc'), '--output-file',
str(tmppath / 'lexstat'))
print(cogs)
assert cogs in [1080, 1081]
from lingpy.cli import main main()