def test_tally(capsys, examples):
main(['tally', str(examples / 'example.nex')])
out, _ = capsys.readouterr()
assert '- 0: 0 1' in out
main(['tally', '-t', 'binary', str(examples / 'example.nex')])
out, _ = capsys.readouterr()
assert '2\t2' in out
def test_trees(trees, options, check, capsys, tmpdir):
trees = ['tree {0} = (a[comment]);'.format(t) for t in trees]
x = 'begin trees;\n{0}\nend;\n'.format('\n'.join(trees))
n = _make_nexus(tmpdir,
'begin trees;\n{0}\nend;\n'.format('\n'.join(trees)))
main(['trees', str(n)] + options)
out, _ = capsys.readouterr()
print(out)
assert check(out)
def test_edit(capsys, examples, tmpdir):
with pytest.raises(ValueError):
main(['edit', '-c', str(examples / 'example2.nex')])
main(['edit', '--number', str(examples / 'example.nex')])
out, _ = capsys.readouterr()
assert '0/2' in out
main(['edit', '--stats', str(examples / 'example.nex')])
out, _ = capsys.readouterr()
assert '1x2' in out
nex = _make_nexus(
tmpdir, """Begin data;
Dimensions ntax=4 nchar=5;
Format datatype=standard symbols="01" gap=-;
Matrix
Harry 10-10
Simon 10-01
Betty 10-10
Louise 11-01
;
End;""")
main(['edit', '-c', '-u', '-z', '-x', '4', str(nex)])
out, _ = capsys.readouterr()
assert 'NCHAR=1' in out
def test_multistate2binary(capsys, tmpdir):
M = """
Begin data;
Dimensions ntax=3 nchar=2;
Format datatype=standard symbols="01" gap=-;
Charstatelabels
1 char1, 2 char2;
Matrix
Maori 14
Dutch 25
Latin 36
;"""
in_ = pathlib.Path(str(tmpdir)) / 'in.nex'
in_.write_text(M, encoding='utf8')
main(['multistate2binary', str(in_)])
out, _ = capsys.readouterr()
assert '100100' in out
def test_check(capsys, examples, mocker, tmpdir):
main(['check', '-e', '-a',
str(examples / 'example.nex')],
log=mocker.Mock())
out, _ = capsys.readouterr()
assert '0 errors' in out
n = _make_nexus(
tmpdir, """Begin data;
Dimensions ntax=4 nchar=1;
Format datatype=standard symbols="01" gap=-;
Matrix
Harry 00
Simon 01
Betty 10
Louise 11
;
End;
""")
main(['check', str(n)])
out, _ = capsys.readouterr()
assert 'Warnings encountered' in out
def test_deinterleave(capsys, tmpdir):
M = """
begin data;
dimensions ntax=4 nchar=20;
format datatype=dna gap=- interleave=yes;
matrix
taxon_1 AACGATTCGT
taxon_2 AAGGAT--CA
taxon_3 AACGACTCCT
taxon_4 AAGGATTCCT
taxon_1 TTTTCGAAGC
taxon_2 TTTTCGGAGC
taxon_3 TTTTTGATGC
taxon_4 TTTTCGGAGC
;
end;
"""
in_ = pathlib.Path(str(tmpdir)) / 'in.nex'
in_.write_text(M, encoding='utf8')
main(['deinterleave', str(in_)])
out, _ = capsys.readouterr()
assert 'taxon_1 AACGATTCGTTTTTCGAAGC' in out
def test_describecharacter(capsys, examples):
main(['describecharacter', '0', str(examples / 'example.nex')])
out, _ = capsys.readouterr()
assert 'Harry, Simon' in out
main([
'describecharacter', 'CHAR_A',
str(examples / 'example-characters.nex')
])
out, _ = capsys.readouterr()
assert 'A, B, C' in out
with pytest.raises(IndexError):
main([
'describecharacter', '1',
str(examples / 'example-characters.nex')
])
def test_describetaxa(capsys, examples):
main(['describetaxa', str(examples / 'example.nex')])
out, _ = capsys.readouterr()
assert '0 x 1, 1 x 1' in out
def test_convert(capsys, examples):
main(['convert', str(examples / 'example.nex')])
out, _ = capsys.readouterr()
assert '>Betty' in out
def test_binary2multistate(capsys, examples):
main(['binary2multistate', str(examples / 'example.nex')])
out, _ = capsys.readouterr()
assert 'BEGIN DATA' in out
def test_help(capsys):
main([])
out, _ = capsys.readouterr()
assert 'usage' in out
def test_randomise(capsys, examples):
main(['randomise', '-n', '10', str(examples / 'example.nex')])
out, _ = capsys.readouterr()
assert re.search('[01]{10}', out)
def test_combine(capsys, tmpdir, examples):
o = tmpdir.join('out.nex')
main(['combine', '-o', str(o), str(examples / 'example.nex')])
out, _ = capsys.readouterr()
assert 'out.nex' in out