def test_sequential_phy__with_flag():
expected = \
"""2 15 S
seq1
ACGTTGATAA CCAGG
seq2
TGCAGAGTAC GACGT"""
assert_equal(sequential_phy(_MSA_SHORT_SEQUENCES, add_flag = True), expected)
def test_sequential_phy__short_sequences():
expected = \
"""2 44
seq1
ACGTTGATAA CCAGGAGGGA TTCGCGATTG GTGGTAACGT AGCC
seq2
TGCAGAGTAC GACGTCTCCT AGATCCTGGA CAATTTAAAC CGAA"""
assert_equal(sequential_phy(_MSA_MEDIUM_SEQUENCES), expected)
def test_sequentual_phy__long_names():
expected = \
"""2 15
A_really_long_sequence_name_th
ACGTTGATAA CCAGG
Another_really_long_sequence_n
TGCAGAGTAC GACGT"""
assert_equal(sequential_phy(_MSA_LONG_NAMES), expected)
def test_sequential_phy__short_sequences():
expected = \
"""2 44
seq1
ACGTTGATAA CCAGGAGGGA TTCGCGATTG GTGGTAACGT AGCC
seq2
TGCAGAGTAC GACGTCTCCT AGATCCTGGA CAATTTAAAC CGAA"""
assert_equal(sequential_phy(_MSA_MEDIUM_SEQUENCES), expected)
def test_sequential_phy__with_flag():
expected = \
"""2 15 S
seq1
ACGTTGATAA CCAGG
seq2
TGCAGAGTAC GACGT"""
assert_equal(sequential_phy(_MSA_SHORT_SEQUENCES, add_flag=True), expected)
def test_sequentual_phy__long_names():
expected = \
"""2 15
A_really_long_sequence_name_th
ACGTTGATAA CCAGG
Another_really_long_sequence_n
TGCAGAGTAC GACGT"""
assert_equal(sequential_phy(_MSA_LONG_NAMES), expected)
def _run(self, _config, temp):
# Read and check that MSAs share groups
msas = [MSA.from_file(filename) for filename in sorted(self.input_files)]
MSA.validate(*msas)
blocks = []
for msa in msas:
blocks.append(sequential_phy(msa, add_flag = self._add_flag))
with open(reroot_path(temp, self._out_phy), "w") as output:
output.write("\n\n".join(blocks))
def _run(self, _config, temp):
# Read and check that MSAs share groups
msas = [read_msa(filename) for filename in sorted(self.input_files)]
join_msa(*msas)
blocks = []
for msa in msas:
blocks.append(sequential_phy(msa, add_flag = self._add_flag))
with open(reroot_path(temp, self._out_phy), "w") as output:
output.write("\n\n".join(blocks))
def test_sequential_phy__multi_line_sequences():
expected = \
"""2 140
seq1
CGGATCTGCT CCTCCACTGG CCACGTTTAC TGTCCCCCAA CCGTTCGTCC CGACCTAGTT
ATACTTCTTA GCAAGGTGTA AAACCAGAGA TTGAGGTTAT AACGTTCCTA ATCAGTTATT
AAATTACCGC GCCCCGACAG
seq2
AGTTGAAGAG GCGGAACGTT TGTAAACCGC GCTAACGTAG TTCTACAACC AGCCACCCGG
TTCGAAGGAA CAACTGGTCG CCATAATTAG GCGAAACGAT AGTGCACTAA GGTCAGGTGC
GCCCCTGTAA ATAATTAGAT"""
assert_equal(sequential_phy(_MSA_LONG_SEQUENCES), expected)
def test_sequential_phy__multi_line_sequences():
expected = \
"""2 140
seq1
CGGATCTGCT CCTCCACTGG CCACGTTTAC TGTCCCCCAA CCGTTCGTCC CGACCTAGTT
ATACTTCTTA GCAAGGTGTA AAACCAGAGA TTGAGGTTAT AACGTTCCTA ATCAGTTATT
AAATTACCGC GCCCCGACAG
seq2
AGTTGAAGAG GCGGAACGTT TGTAAACCGC GCTAACGTAG TTCTACAACC AGCCACCCGG
TTCGAAGGAA CAACTGGTCG CCATAATTAG GCGAAACGAT AGTGCACTAA GGTCAGGTGC
GCCCCTGTAA ATAATTAGAT"""
assert_equal(sequential_phy(_MSA_LONG_SEQUENCES), expected)
def test_sequential_phy__different_lengths():
_mock = flexmock(MSA).should_receive('validate').at_least.once
sequential_phy(_MSA_MEDIUM_NAMES)
def test_sequential_phy__different_lengths():
_mock = flexmock(MSA).should_receive('validate').at_least.once
sequential_phy(_MSA_MEDIUM_NAMES)