class PartitonsTest(ExpectingTestCase):
def setUp(self):
if not os.path.exists(temp_dir):
os.makedirs(temp_dir)
self.aln_obj = AlignmentList(dna_data_fas, sql_db=sql_db)
self.aln_obj.partitions.reset(cur=self.aln_obj.cur, )
def tearDown(self):
self.aln_obj.clear_alignments()
self.aln_obj.con.close()
shutil.rmtree(temp_dir)
def test_read_from_nexus(self):
self.aln_obj.partitions.read_from_file(concatenated_small_parNex[0],
no_aln_check=True)
self.assertEqual(len(self.aln_obj.partitions.partitions), 7)
def test_read_from_phylip(self):
self.aln_obj.partitions.read_from_file(concatenated_small_par[0],
no_aln_check=True)
self.assertEqual(len(self.aln_obj.partitions.partitions), 7)
def test_bad_partitions_phy(self):
e = self.aln_obj.partitions.read_from_file(partition_bad_phy[0],
no_aln_check=True)
self.assertTrue(isinstance(e, InvalidPartitionFile))
def test_unsorted_part_phylip(self):
self.aln_obj.partitions.read_from_file(partition_unsorted_phy[0],
no_aln_check=True)
data = [
self.aln_obj.partitions.partitions.keys(),
self.aln_obj.partitions.counter
]
self.assertEqual(data, [[
"BaseConc1.fas", "BaseConc2.fas", "BaseConc3.fas", "BaseConc4.fas",
"BaseConc5.fas", "BaseConc6.fas", "BaseConc7.fas"
], 595])
def test_phylip_dot_notation(self):
self.aln_obj.partitions.read_from_file(partition_dot_not[0],
no_aln_check=True)
data = [
self.aln_obj.partitions.partitions.keys(),
self.aln_obj.partitions.counter
]
self.assertEqual(data, [[
"BaseConc1.fas", "BaseConc2.fas", "BaseConc3.fas", "BaseConc4.fas",
"BaseConc5.fas", "BaseConc6.fas", "BaseConc7.fas"
], 595])
def test_nexus_dot_notation(self):
self.aln_obj.partitions.read_from_file(dot_notation_nex[0],
no_aln_check=True)
data = [
self.aln_obj.partitions.partitions.keys(),
self.aln_obj.partitions.counter
]
self.assertEqual(data, [[
"BaseConc1.fas", "BaseConc2.fas", "BaseConc3.fas", "BaseConc4.fas",
"BaseConc5.fas", "BaseConc6.fas", "BaseConc7.fas"
], 595])
def test_bad_dot_notation(self):
e = self.aln_obj.partitions.read_from_file(bad_dot_notation_nex[0],
no_aln_check=True)
self.assertTrue(isinstance(e, InvalidPartitionFile))
def test_import_new_partscheme(self):
self.aln_obj.clear_alignments()
self.aln_obj.con.close()
self.aln_obj = AlignmentList(concatenated_medium_nexus, sql_db=sql_db)
self.aln_obj.partitions.reset()
self.aln_obj.partitions.read_from_file(concatenated_small_par[0],
no_aln_check=True)
res = self.aln_obj.partitions.get_partition_names()
self.assertEqual(res, [
"BaseConc1.fas", "BaseConc2.fas", "BaseConc3.fas", "BaseConc4.fas",
"BaseConc5.fas", "BaseConc6.fas", "BaseConc7.fas"
])
def test_add_duplicate_name(self):
self.aln_obj.partitions.read_from_file(concatenated_small_par[0],
no_aln_check=True)
self.assertRaises(
PartitionException,
self.aln_obj.partitions.add_partition("BaseCond1.fas", length=100))
def test_get_partition_names(self):
self.aln_obj.partitions.read_from_file(concatenated_small_par[0],
no_aln_check=True)
res = self.aln_obj.partitions.get_partition_names()
self.assertEqual(res, [
"BaseConc1.fas", "BaseConc2.fas", "BaseConc3.fas", "BaseConc4.fas",
"BaseConc5.fas", "BaseConc6.fas", "BaseConc7.fas"
])
def test_get_partition_names_withCodon(self):
self.aln_obj.partitions.read_from_file(
concatenated_smallCodon_parNex[0], no_aln_check=True)
res = self.aln_obj.partitions.get_partition_names()
self.assertEqual(res, [
"BaseConc1.fas_1_1", "BaseConc1.fas_1_2", "BaseConc1.fas_1_3",
"BaseConc2.fas", "BaseConc3.fas", "BaseConc4.fas", "BaseConc5.fas",
"BaseConc6.fas", "BaseConc7.fas"
])
def test_single_partition(self):
self.aln_obj = AlignmentList([dna_data_fas[0]],
db_con=self.aln_obj.con,
db_cur=self.aln_obj.cur,
sql_db=sql_db)
self.assertTrue(self.aln_obj.partitions.is_single())
def test_multiple_partitions(self):
self.assertFalse(self.aln_obj.partitions.is_single())
def test_remove_partition_from_file_original(self):
self.aln_obj.clear_alignments()
self.aln_obj.con.close()
self.aln_obj = AlignmentList(dna_data_fas, sql_db=sql_db)
self.aln_obj.partitions.remove_partition(
file_name="trifusion/tests/data/BaseConc3.fas")
# Check if remaining partition ranges are continuous
cont = True
prev = 0
for r in self.aln_obj.partitions.partitions.values():
if r[0][0][0] == prev:
prev = r[0][0][1] + 1
else:
cont = False
self.expect_equal(cont, True)
def test_remove_partition_from_name(self):
self.aln_obj.partitions.read_from_file(concatenated_small_parNex[0],
no_aln_check=True)
self.aln_obj.partitions.remove_partition("BaseConc3.fas")
# Check keys from _partitions, partitions_alignment and models
key_data = [
list(self.aln_obj.partitions.partitions.keys()),
list(self.aln_obj.partitions.partitions_alignments.keys()),
list(self.aln_obj.partitions.models.keys())
]
self.expect_equal(key_data, [[
"BaseConc1.fas", "BaseConc2.fas", "BaseConc4.fas", "BaseConc5.fas",
"BaseConc6.fas", "BaseConc7.fas"
]] * 3)
# Check if remaining partition ranges are continuous
cont = True
prev = 0
for r in self.aln_obj.partitions.partitions.values():
if r[0][0][0] == prev:
prev = r[0][0][1] + 1
else:
cont = False
self.expect_equal(cont, True)
def test_remove_partition_from_file(self):
self.aln_obj.partitions.read_from_file(concatenated_small_parNex[0],
no_aln_check=True)
self.aln_obj.partitions.remove_partition(file_name="BaseConc3.fas")
# Check keys from _partitions, partitions_alignment and models
key_data = [
list(self.aln_obj.partitions.partitions.keys()),
list(self.aln_obj.partitions.partitions_alignments.keys()),
list(self.aln_obj.partitions.models.keys())
]
self.expect_equal(key_data, [[
"BaseConc1.fas", "BaseConc2.fas", "BaseConc4.fas", "BaseConc5.fas",
"BaseConc6.fas", "BaseConc7.fas"
]] * 3)
# Check if remaining partition ranges are continuous
cont = True
prev = 0
for r in self.aln_obj.partitions.partitions.values():
if r[0][0][0] == prev:
prev = r[0][0][1] + 1
else:
cont = False
self.expect_equal(cont, True)
def test_change_name(self):
self.aln_obj.partitions.read_from_file(concatenated_small_parNex[0],
no_aln_check=True)
self.aln_obj.partitions.change_name("BaseConc1.fas", "OtherName")
key_data = [
list(self.aln_obj.partitions.partitions.keys()),
list(self.aln_obj.partitions.partitions_alignments.keys()),
list(self.aln_obj.partitions.models.keys())
]
self.expect_equal(key_data, [[
"BaseConc2.fas", "BaseConc3.fas", "BaseConc4.fas", "BaseConc5.fas",
"BaseConc6.fas", "BaseConc7.fas", "OtherName"
]] * 3)
# Check if remaining partition ranges are continuous
cont = True
prev = 0
self.aln_obj.partitions.partitions = OrderedDict(
sorted(self.aln_obj.partitions.partitions.iteritems(),
key=lambda x: x[1][0]))
for r in self.aln_obj.partitions.partitions.values():
if r[0][0][0] == prev:
prev = r[0][0][1] + 1
else:
cont = False
self.expect_equal(cont, True)
def test_merge_partitions(self):
self.aln_obj.partitions.read_from_file(concatenated_small_parNex[0],
no_aln_check=True)
self.aln_obj.partitions.merge_partitions([
"BaseConc1.fas", "BaseConc2.fas", "BaseConc3.fas", "BaseConc4.fas",
"BaseConc5.fas", "BaseConc6.fas", "BaseConc7.fas"
], "New_part")
key_data = [
list(self.aln_obj.partitions.partitions.keys()),
list(self.aln_obj.partitions.partitions_alignments.keys()),
list(self.aln_obj.partitions.models.keys())
]
self.assertEqual(key_data, [["New_part"]] * 3)
def test_split_partition(self):
self.aln_obj.partitions.read_from_file(concatenated_small_parNex[0],
no_aln_check=True)
self.aln_obj.partitions.split_partition("BaseConc1.fas",
[[0, 50], [51, 84]],
["part1", "part2"])
key_data = [
list(self.aln_obj.partitions.partitions.keys()),
list(self.aln_obj.partitions.partitions_alignments.keys()),
list(self.aln_obj.partitions.models.keys())
]
self.expect_equal(key_data, [[
"part1", "part2", "BaseConc2.fas", "BaseConc3.fas",
"BaseConc4.fas", "BaseConc5.fas", "BaseConc6.fas", "BaseConc7.fas"
]] * 3)
# Check if remaining partition ranges are continuous
cont = True
prev = 0
self.aln_obj.partitions.partitions = OrderedDict(
sorted(self.aln_obj.partitions.partitions.iteritems(),
key=lambda x: x[1][0]))
for r in self.aln_obj.partitions.partitions.values():
print(r)
if r[0][0][0] == prev:
prev = r[0][0][1] + 1
else:
cont = False
self.expect_equal(cont, True)
def test_merge_and_split(self):
self.aln_obj.partitions.read_from_file(concatenated_small_parNex[0],
no_aln_check=True)
self.aln_obj.partitions.merge_partitions(
["BaseConc1.fas", "BaseConc2.fas", "BaseConc3.fas"], "new_part")
self.aln_obj.partitions.split_partition("new_part")
key_data = [
sorted(self.aln_obj.partitions.partitions.keys()),
sorted(self.aln_obj.partitions.partitions_alignments.keys()),
sorted(self.aln_obj.partitions.models.keys())
]
self.expect_equal(key_data, [[
"BaseConc1.fas", "BaseConc2.fas", "BaseConc3.fas", "BaseConc4.fas",
"BaseConc5.fas", "BaseConc6.fas", "BaseConc7.fas"
]] * 3)
def test_merge_and_custom_split1(self):
self.aln_obj.partitions.read_from_file(concatenated_small_parNex[0],
no_aln_check=True)
self.aln_obj.partitions.merge_partitions(
["BaseConc1.fas", "BaseConc2.fas", "BaseConc3.fas"], "new_part")
self.aln_obj.partitions.split_partition("new_part", [(0, 50),
(51, 254)],
["one", "two"])
key_data = [
self.aln_obj.partitions.partitions_alignments["one"],
self.aln_obj.partitions.partitions_alignments["two"]
]
self.assertEqual(key_data,
[['BaseConc1.fas'],
['BaseConc1.fas', 'BaseConc3.fas', 'BaseConc2.fas']])
def test_merge_and_custom_split2(self):
self.aln_obj.partitions.read_from_file(concatenated_small_parNex[0],
no_aln_check=True)
self.aln_obj.partitions.merge_partitions(
["BaseConc1.fas", "BaseConc2.fas", "BaseConc3.fas"], "new_part")
self.aln_obj.partitions.split_partition("new_part", [(0, 84),
(85, 254)],
["one", "two"])
key_data = [
self.aln_obj.partitions.partitions_alignments["one"],
self.aln_obj.partitions.partitions_alignments["two"]
]
self.assertEqual(
key_data, [['BaseConc1.fas'], ['BaseConc3.fas', 'BaseConc2.fas']])
def test_concat_custom_fileset_from_phy_partfile(self):
self.aln_obj.clear_alignments()
self.aln_obj.con.close()
self.aln_obj = AlignmentList(dna_data_fas, sql_db=sql_db)
self.aln_obj.partitions.read_from_file(concatenated_small_par[0])
self.aln_obj.update_active_alignments([
join(data_path, "BaseConc1.fas"),
join(data_path, "BaseConc2.fas")
])
self.aln_obj.concatenate()
key_data = [
sorted(self.aln_obj.partitions.partitions.keys()),
sorted(self.aln_obj.partitions.partitions_alignments.keys()),
sorted(self.aln_obj.partitions.models.keys())
]
self.expect_equal(key_data, [["BaseConc1.fas", "BaseConc2.fas"]] * 3)
def test_concat_custom_fileset_from_phy_partfile(self):
self.aln_obj.clear_alignments()
self.aln_obj.con.close()
self.aln_obj = AlignmentList(dna_data_fas, sql_db=sql_db)
self.aln_obj.partitions.read_from_file(concatenated_small_parNex[0])
self.aln_obj.update_active_alignments([
join(data_path, "BaseConc1.fas"),
join(data_path, "BaseConc2.fas")
])
self.aln_obj.concatenate()
key_data = [
sorted(self.aln_obj.partitions.partitions.keys()),
sorted(self.aln_obj.partitions.partitions_alignments.keys()),
sorted(self.aln_obj.partitions.models.keys())
]
self.expect_equal(key_data, [["BaseConc1.fas", "BaseConc2.fas"]] * 3)
def test_merge_with_custom_fileset(self):
self.aln_obj.clear_alignments()
self.aln_obj.con.close()
self.aln_obj = AlignmentList(dna_data_fas, sql_db=sql_db)
self.aln_obj.partitions.read_from_file(concatenated_small_parNex[0])
self.aln_obj.partitions.merge_partitions(
["BaseConc1.fas", "BaseConc2.fas", "BaseConc3.fas"], "new_part")
self.aln_obj.update_active_alignments([
join(data_path, "BaseConc1.fas"),
join(data_path, "BaseConc5.fas")
])
self.aln_obj.concatenate()
key_data = [
sorted(self.aln_obj.partitions.partitions.keys()),
sorted(self.aln_obj.partitions.partitions_alignments.keys()),
sorted(self.aln_obj.partitions.models.keys())
]
self.expect_equal(key_data, [["BaseConc1.fas", "BaseConc5.fas"]] * 3)
def test_model_detection(self):
self.aln_obj.clear_alignments()
self.aln_obj = AlignmentList(models_nexus_data,
db_con=self.aln_obj.con,
db_cur=self.aln_obj.cur,
sql_db=sql_db)
self.assertEqual(
self.aln_obj.partitions.models,
OrderedDict([
('Teste1.fas', [[['nst=6', 'statefreqpr=dirichlet(1,1,1,1)']],
[None], []]),
('Teste2.fas', [[['nst=6', 'statefreqpr=dirichlet(1,1,1,1)']],
[None], []]),
('Teste3.fas', [[['nst=6', 'statefreqpr=dirichlet(1,1,1,1)']],
[None], []]),
('Teste4.fas', [[['nst=6', 'statefreqpr=dirichlet(1,1,1,1)']],
[None], []]),
('Teste5.fas', [[['nst=6', 'statefreqpr=dirichlet(1,1,1,1)']],
[None], []]),
('Teste6.fas', [[['nst=6', 'statefreqpr=dirichlet(1,1,1,1)']],
[None], []]),
('Teste7.fas', [[['nst=6', 'statefreqpr=dirichlet(1,1,1,1)']],
[None], []])
]))
def test_model_detection_codons(self):
self.aln_obj.clear_alignments()
self.aln_obj = AlignmentList(models_codon_nexus_data,
db_cur=self.aln_obj.cur,
db_con=self.aln_obj.con,
sql_db=sql_db)
self.assertEqual(
self.aln_obj.partitions.models,
OrderedDict([('Teste1.fas_1',
[[['nst=2', 'statefreqpr=dirichlet(1,1,1,1)'],
['nst=6', 'statefreqpr=fixed(equal)'],
['nst=6', 'statefreqpr=dirichlet(1,1,1,1)']],
[None, None, None], []]),
('Teste2.fas_86',
[[['nst=2', 'statefreqpr=dirichlet(1,1,1,1)'],
['nst=6', 'statefreqpr=fixed(equal)'],
['nst=6', 'statefreqpr=dirichlet(1,1,1,1)']],
[None, None, None], []]),
('Teste3.fas_171',
[[['nst=2', 'statefreqpr=dirichlet(1,1,1,1)'],
['nst=6', 'statefreqpr=fixed(equal)'],
['nst=6', 'statefreqpr=dirichlet(1,1,1,1)']],
[None, None, None], []]),
('Teste4.fas_256',
[[['nst=2', 'statefreqpr=dirichlet(1,1,1,1)'],
['nst=6', 'statefreqpr=fixed(equal)'],
['nst=6', 'statefreqpr=dirichlet(1,1,1,1)']],
[None, None, None], []]),
('Teste5.fas_341',
[[['nst=2', 'statefreqpr=dirichlet(1,1,1,1)'],
['nst=6', 'statefreqpr=fixed(equal)'],
['nst=6', 'statefreqpr=dirichlet(1,1,1,1)']],
[None, None, None], []]),
('Teste6.fas_426',
[[['nst=2', 'statefreqpr=dirichlet(1,1,1,1)'],
['nst=6', 'statefreqpr=fixed(equal)'],
['nst=6', 'statefreqpr=dirichlet(1,1,1,1)']],
[None, None, None], []]),
('Teste7.fas_511',
[[['nst=2', 'statefreqpr=dirichlet(1,1,1,1)'],
['nst=6', 'statefreqpr=fixed(equal)'],
['nst=6', 'statefreqpr=dirichlet(1,1,1,1)']],
[None, None, None], []])]))
def test_set_model(self):
self.aln_obj.partitions.read_from_file(concatenated_small_parNex[0],
no_aln_check=True)
self.aln_obj.partitions.set_model("BaseConc1.fas", ["GTR"])
self.assertEqual(
self.aln_obj.partitions.models,
OrderedDict([('BaseConc1.fas', [[[]], ['GTR'], []]),
('BaseConc2.fas', [[[]], [None], []]),
('BaseConc3.fas', [[[]], [None], []]),
('BaseConc4.fas', [[[]], [None], []]),
('BaseConc5.fas', [[[]], [None], []]),
('BaseConc6.fas', [[[]], [None], []]),
('BaseConc7.fas', [[[]], [None], []])]))
def test_set_model_all(self):
self.aln_obj.partitions.read_from_file(concatenated_small_parNex[0],
no_aln_check=True)
self.aln_obj.partitions.set_model("BaseConc1.fas", ["GTR"],
apply_all=True)
self.assertEqual(
self.aln_obj.partitions.models,
OrderedDict([('BaseConc1.fas', [[[]], ['GTR'], []]),
('BaseConc2.fas', [[[]], ['GTR'], []]),
('BaseConc3.fas', [[[]], ['GTR'], []]),
('BaseConc4.fas', [[[]], ['GTR'], []]),
('BaseConc5.fas', [[[]], ['GTR'], []]),
('BaseConc6.fas', [[[]], ['GTR'], []]),
('BaseConc7.fas', [[[]], ['GTR'], []])]))
def test_set_model_codon(self):
self.aln_obj.partitions.read_from_file(concatenated_small_parNex[0],
no_aln_check=True)
self.aln_obj.partitions.set_model("BaseConc1.fas", ["GTR", "SYM"],
links=["12", "3"],
apply_all=True)
self.assertEqual(
self.aln_obj.partitions.models,
OrderedDict([
('BaseConc1.fas', [[[]], ['GTR', 'SYM'], ['12', '3']]),
('BaseConc2.fas', [[[]], ['GTR', 'SYM'], ['12', '3']]),
('BaseConc3.fas', [[[]], ['GTR', 'SYM'], ['12', '3']]),
('BaseConc4.fas', [[[]], ['GTR', 'SYM'], ['12', '3']]),
('BaseConc5.fas', [[[]], ['GTR', 'SYM'], ['12', '3']]),
('BaseConc6.fas', [[[]], ['GTR', 'SYM'], ['12', '3']]),
('BaseConc7.fas', [[[]], ['GTR', 'SYM'], ['12', '3']])
]))
class SeconaryOpsTest(unittest.TestCase):
def setUp(self):
if not os.path.exists(temp_dir):
os.makedirs(temp_dir)
self.aln_obj = AlignmentList(dna_data_fas, sql_db=sql_db)
def tearDown(self):
self.aln_obj.clear_alignments()
self.aln_obj.con.close()
shutil.rmtree(temp_dir)
def test_summary_stats_all(self):
sum_table, table_data = self.aln_obj.get_summary_stats()
self.assertEqual(
[sum_table, table_data],
[{
'missing': '5 (0.04%)',
'taxa': 24,
'genes': 7,
'informative': '0 (0.0%)',
'gaps': '0 (0.0%)',
'avg_gaps': 0.0,
'avg_missing': 1.0,
'variable': '7 (1.18%)',
'seq_len': 595,
'avg_var': 1.0,
'avg_inf': 0.0
},
[[
'Genes', 'Taxa', 'Alignment length', 'Gaps', 'Gaps per gene',
'Missing data', 'Missing data per gene', 'Variable sites',
'Variable sites per gene', 'Informative sites',
'Informative sites per gene'
],
[
7, 24, 595, '0 (0.0%)', 0.0, '5 (0.04%)', 1.0, '7 (1.18%)',
1.0, '0 (0.0%)', 0.0
]]])
def test_summary_stats_one_active(self):
sum_table, table_data = self.aln_obj.get_summary_stats(
[join(data_path, "BaseConc1.fas")])
self.assertEqual(
[sum_table, table_data],
[{
'missing': '1 (0.05%)',
'taxa': 24,
'genes': 1,
'informative': '0 (0.0%)',
'gaps': '0 (0.0%)',
'avg_gaps': 0.0,
'avg_missing': 1.0,
'variable': '1 (1.18%)',
'seq_len': 85,
'avg_var': 1.0,
'avg_inf': 0.0
},
[[
'Genes', 'Taxa', 'Alignment length', 'Gaps', 'Gaps per gene',
'Missing data', 'Missing data per gene', 'Variable sites',
'Variable sites per gene', 'Informative sites',
'Informative sites per gene'
],
[
1, 24, 85, '0 (0.0%)', 0.0, '1 (0.05%)', 1.0, '1 (1.18%)',
1.0, '0 (0.0%)', 0.0
]]])
def test_single_aln_outlier_mdata(self):
self.aln_obj.update_active_alignments([dna_data_fas[0]])
self.assertEqual(self.aln_obj.outlier_missing_data(),
{"exception": "single_alignment"})
def test_single_aln_outlier_mdata_sp(self):
self.aln_obj.update_active_alignments([dna_data_fas[0]])
print(self.aln_obj.alignments)
self.assertEqual(self.aln_obj.outlier_missing_data_sp(),
{"exception": "single_alignment"})
def test_single_aln_outlier_seg(self):
self.aln_obj.update_active_alignments([dna_data_fas[0]])
self.assertEqual(self.aln_obj.outlier_segregating(),
{"exception": "single_alignment"})
def test_single_aln_outlier_seg_sp(self):
self.aln_obj.update_active_alignments([dna_data_fas[0]])
print(self.aln_obj.alignments)
self.assertEqual(self.aln_obj.outlier_segregating_sp(),
{"exception": "single_alignment"})
def test_single_aln_outlier_seqsize(self):
self.aln_obj.update_active_alignments([dna_data_fas[0]])
self.assertEqual(self.aln_obj.outlier_sequence_size(),
{"exception": "single_alignment"})
def test_single_aln_outlier_seqsize_sp(self):
self.aln_obj.update_active_alignments([dna_data_fas[0]])
self.assertEqual(self.aln_obj.outlier_sequence_size_sp(),
{"exception": "single_alignment"})
def test_single_aln_average_seqsize_per_species(self):
self.aln_obj.update_active_alignments([dna_data_fas[0]])
self.assertEqual(self.aln_obj.average_seqsize_per_species(),
{"exception": "single_alignment"})
def test_single_aln_average_seqsize(self):
self.aln_obj.update_active_alignments([dna_data_fas[0]])
self.assertEqual(self.aln_obj.average_seqsize(),
{"exception": "single_alignment"})
def test_single_aln_sequence_similarity(self):
self.aln_obj.update_active_alignments([dna_data_fas[0]])
self.assertEqual(self.aln_obj.sequence_similarity(),
{"exception": "single_alignment"})
def test_single_aln_sequence_segregation(self):
self.aln_obj.update_active_alignments([dna_data_fas[0]])
self.assertEqual(self.aln_obj.sequence_segregation(),
{"exception": "single_alignment"})
def test_single_aln_length_polymorphism_correlation(self):
self.aln_obj.update_active_alignments([dna_data_fas[0]])
self.assertEqual(self.aln_obj.length_polymorphism_correlation(),
{"exception": "single_alignment"})
def test_single_aln_taxa_distribution(self):
self.aln_obj.update_active_alignments([dna_data_fas[0]])
self.assertEqual(self.aln_obj.taxa_distribution(),
{"exception": "single_alignment"})
def test_single_aln_cumulative_missing_genes(self):
self.aln_obj.update_active_alignments([dna_data_fas[0]])
self.assertEqual(self.aln_obj.cumulative_missing_genes(),
{"exception": "single_alignment"})
def test_single_aln_gene_occupancy(self):
self.aln_obj.update_active_alignments([dna_data_fas[0]])
self.assertEqual(self.aln_obj.gene_occupancy(),
{"exception": "single_alignment"})
def test_single_aln_missing_data_distribution(self):
self.aln_obj.update_active_alignments([dna_data_fas[0]])
self.assertEqual(self.aln_obj.missing_data_distribution(),
{"exception": "single_alignment"})
def test_single_aln_missing_genes_average(self):
self.aln_obj.update_active_alignments([dna_data_fas[0]])
self.assertEqual(self.aln_obj.missing_genes_average(),
{"exception": "single_alignment"})
def test_no_data(self):
self.aln_obj = AlignmentList([], sql_db=sql_db)
self.assertEqual(self.aln_obj.gene_occupancy(),
{'exception': "empty_data"})
def test_gene_occupancy(self):
self.assertTrue(self.aln_obj.gene_occupancy())
def test_missing_data_distribution(self):
self.assertTrue(self.aln_obj.missing_data_distribution())
def test_missing_data_per_species(self):
self.assertTrue(self.aln_obj.missing_data_per_species())
def test_missing_genes_per_species(self):
self.assertTrue(self.aln_obj.missing_genes_per_species())
def test_missing_genes_average(self):
self.assertTrue(self.aln_obj.missing_genes_average())
def test_average_seqsize_per_species(self):
self.assertTrue(self.aln_obj.average_seqsize_per_species())
def test_average_seqsize(self):
self.assertTrue(self.aln_obj.average_seqsize())
def test_characters_proportion(self):
self.assertTrue(self.aln_obj.characters_proportion())
def test_characters_proportion_per_species(self):
self.assertTrue(self.aln_obj.characters_proportion_per_species())
def test_characters_proportion_gene(self):
self.assertTrue(
self.aln_obj.characters_proportion_gene(
join(data_path, "BaseConc1.fas"), 10))
def test_sequence_similarity(self):
self.assertTrue(self.aln_obj.sequence_similarity())
def test_sequence_similarity_per_species(self):
self.assertTrue(self.aln_obj.sequence_similarity_per_species())
def test_sequence_similarity_gene(self):
self.assertTrue(
self.aln_obj.sequence_similarity_gene(
join(data_path, "BaseConc1.fas"), 10))
def test_sequence_conservation(self):
self.assertTrue(
self.aln_obj.sequence_conservation_gnp(
join(data_path, "BaseConc1.fas"), 10))
def test_sequence_segregation(self):
self.assertTrue(self.aln_obj.sequence_segregation())
def test_sequence_segregation_per_species(self):
self.assertTrue(self.aln_obj.sequence_segregation_per_species())
def test_sequence_segregation_gene(self):
self.assertTrue(
self.aln_obj.sequence_segregation_gene(
join(data_path, "BaseConc1.fas"), 10))
def test_length_polymorphism_correlation(self):
self.assertTrue(self.aln_obj.length_polymorphism_correlation())
def test_allele_frequency_spectrum(self):
self.assertTrue(self.aln_obj.allele_frequency_spectrum())
def test_allele_frequency_spectrum_gene(self):
self.assertTrue(
self.aln_obj.allele_frequency_spectrum_gene(
join(data_path, "BaseConc1.fas"), None))
def test_taxa_distribution(self):
self.assertTrue(self.aln_obj.taxa_distribution())
def test_cumulative_missing_genes(self):
self.assertTrue(self.aln_obj.cumulative_missing_genes())
def test_outlier_missing_data(self):
self.assertTrue(self.aln_obj.outlier_missing_data())
def test_outlier_missing_data_sp(self):
self.assertTrue(self.aln_obj.outlier_missing_data_sp())
def test_outlier_segregating(self):
self.assertTrue(self.aln_obj.outlier_segregating())
def test_outlier_segregating_sp(self):
self.assertTrue(self.aln_obj.outlier_segregating_sp())
def test_outlier_sequence_size(self):
self.assertTrue(self.aln_obj.outlier_sequence_size())
def test_outlier_sequence_size_sp(self):
self.assertTrue(self.aln_obj.outlier_sequence_size_sp())
class AlignmentManipulationTest(unittest.TestCase):
def setUp(self):
self.aln_obj = AlignmentList(dna_data_fas, sql_db=sql_db)
def tearDown(self):
try:
self.aln_obj.clear_alignments()
except:
pass
self.aln_obj.con.close()
os.remove(sql_db)
def test_clear_alns(self):
self.aln_obj.clear_alignments()
aln = AlignmentList([], sql_db=sql_db)
self.assertTrue(
compare_inst(self.aln_obj, aln, [
"log_progression", "locus_length", "partitions", "cur", "con"
]))
def test_update_act_anls(self):
self.aln_obj.update_active_alignments([
join(data_path, "BaseConc1.fas"),
join(data_path, "BaseConc2.fas")
])
self.assertEqual(list(self.aln_obj.alignments.keys()), [
join(data_path, "BaseConc1.fas"),
join(data_path, "BaseConc2.fas")
])
def test_update_act_alns_err(self):
self.aln_obj.update_active_alignments([
join(data_path, "BaseConc1.fas"),
join(data_path, "BaseConc2.fas"),
join(data_path, "Wrong_name")
])
self.assertEqual(list(self.aln_obj.alignments.keys()), [
join(data_path, "BaseConc1.fas"),
join(data_path, "BaseConc2.fas")
])
def test_update_aln_shelve(self):
self.aln_obj.update_active_alignment(join(data_path, "BaseConc1.fas"),
"shelve")
self.assertEqual(list(self.aln_obj.alignments.keys()), [
join(data_path, "BaseConc2.fas"),
join(data_path, "BaseConc3.fas"),
join(data_path, "BaseConc4.fas"),
join(data_path, "BaseConc5.fas"),
join(data_path, "BaseConc6.fas"),
join(data_path, "BaseConc7.fas")
])
def test_update_aln_act(self):
self.aln_obj.update_active_alignments([])
self.aln_obj.update_active_alignment(join(data_path, "BaseConc1.fas"),
"active")
self.assertEqual(list(self.aln_obj.alignments.keys()),
[join(data_path, "BaseConc1.fas")])
def test_add_aln_obj(self):
fl = self.aln_obj.alignments.keys()
aln = Alignment(dna_data_loci[0], sql_cursor=self.aln_obj.cur)
self.aln_obj.add_alignments([aln])
self.assertEqual(self.aln_obj.alignments.keys(),
fl + [join(data_path, "c97d5m4p2.loci")])
def test_remove_taxa_from_list(self):
taxa_list = [
"1285_RAD_original", "130a_RAD_original", "137a_RAD_original",
"1427_RAD_original", "167a_RAD_original"
]
expected_taxa = [
tx for tx in self.aln_obj.taxa_names if tx not in taxa_list
]
self.aln_obj.remove_taxa(taxa_list)
self.assertEqual(self.aln_obj.taxa_names, expected_taxa)
def test_remove_taxa_from_file(self):
taxa_list = [
"1285_RAD_original", "130a_RAD_original", "137a_RAD_original",
"1427_RAD_original", "167a_RAD_original"
]
expected_taxa = [
tx for tx in self.aln_obj.taxa_names if tx not in taxa_list
]
self.aln_obj.remove_taxa(taxa_to_remove)
self.assertEqual(self.aln_obj.taxa_names, expected_taxa)
def test_remove_taxa_from_list_inverse(self):
taxa_list = [
"1285_RAD_original", "130a_RAD_original", "137a_RAD_original",
"1427_RAD_original", "167a_RAD_original"
]
expected_taxa = [
tx for tx in self.aln_obj.taxa_names if tx not in taxa_list
]
self.aln_obj.remove_taxa(taxa_list, mode="inverse")
self.assertEqual(self.aln_obj.taxa_names, taxa_list)
#
# def test_retrieve_alignment(self):
#
# aln = self.aln_obj.retrieve_alignment("BaseConc1.fas")
#
# aln2 = Alignment(dna_data_fas[0], dest="new_one")
#
# self.assertTrue(compare_inst(aln, aln2,
# ["log_progression", "locus_length",
# "partitions"]))
def test_concatenation(self):
aln = self.aln_obj.concatenate(alignment_name="test")
aln.write_to_file(["fasta"], "test")
with open("trifusion/tests/data/BaseConcatenation.fas") as fh1, \
open("test.fas") as fh2:
self.assertEqual(fh1.read(), fh2.read())
os.remove("test.fas")
class SeconaryOpsTest(unittest.TestCase):
def setUp(self):
if not os.path.exists(temp_dir):
os.makedirs(temp_dir)
self.aln_obj = AlignmentList(dna_data_fas, sql_db=sql_db)
def tearDown(self):
self.aln_obj.clear_alignments()
self.aln_obj.con.close()
shutil.rmtree(temp_dir)
def test_summary_stats_all(self):
sum_table, table_data = self.aln_obj.get_summary_stats()
self.assertEqual([sum_table, table_data],
[{'missing': '5 (0.04%)', 'taxa': 24, 'genes': 7,
'informative': '0 (0.0%)', 'gaps': '0 (0.0%)',
'avg_gaps': 0.0, 'avg_missing': 1.0, 'variable': '7 (1.18%)',
'seq_len': 595, 'avg_var': 1.0, 'avg_inf': 0.0},
[['Genes', 'Taxa', 'Alignment length', 'Gaps',
'Gaps per gene', 'Missing data',
'Missing data per gene', 'Variable sites',
'Variable sites per gene', 'Informative sites',
'Informative sites per gene'],
[7, 24, 595, '0 (0.0%)', 0.0, '5 (0.04%)', 1.0,
'7 (1.18%)', 1.0, '0 (0.0%)', 0.0]]])
def test_summary_stats_one_active(self):
sum_table, table_data = self.aln_obj.get_summary_stats([
join(data_path, "BaseConc1.fas")])
self.assertEqual([sum_table, table_data],
[{'missing': '1 (0.05%)', 'taxa': 24, 'genes': 1,
'informative': '0 (0.0%)', 'gaps': '0 (0.0%)',
'avg_gaps': 0.0, 'avg_missing': 1.0, 'variable': '1 (1.18%)',
'seq_len': 85, 'avg_var': 1.0, 'avg_inf': 0.0},
[['Genes', 'Taxa', 'Alignment length', 'Gaps',
'Gaps per gene', 'Missing data',
'Missing data per gene', 'Variable sites',
'Variable sites per gene', 'Informative sites',
'Informative sites per gene'],
[1, 24, 85, '0 (0.0%)', 0.0, '1 (0.05%)', 1.0,
'1 (1.18%)', 1.0, '0 (0.0%)', 0.0]]])
def test_single_aln_outlier_mdata(self):
self.aln_obj.update_active_alignments([dna_data_fas[0]])
self.assertEqual(self.aln_obj.outlier_missing_data(),
{"exception": "single_alignment"})
def test_single_aln_outlier_mdata_sp(self):
self.aln_obj.update_active_alignments([dna_data_fas[0]])
print(self.aln_obj.alignments)
self.assertEqual(self.aln_obj.outlier_missing_data_sp(),
{"exception": "single_alignment"})
def test_single_aln_outlier_seg(self):
self.aln_obj.update_active_alignments([dna_data_fas[0]])
self.assertEqual(self.aln_obj.outlier_segregating(),
{"exception": "single_alignment"})
def test_single_aln_outlier_seg_sp(self):
self.aln_obj.update_active_alignments([dna_data_fas[0]])
print(self.aln_obj.alignments)
self.assertEqual(self.aln_obj.outlier_segregating_sp(),
{"exception": "single_alignment"})
def test_single_aln_outlier_seqsize(self):
self.aln_obj.update_active_alignments([dna_data_fas[0]])
self.assertEqual(self.aln_obj.outlier_sequence_size(),
{"exception": "single_alignment"})
def test_single_aln_outlier_seqsize_sp(self):
self.aln_obj.update_active_alignments([dna_data_fas[0]])
self.assertEqual(self.aln_obj.outlier_sequence_size_sp(),
{"exception": "single_alignment"})
def test_single_aln_average_seqsize_per_species(self):
self.aln_obj.update_active_alignments([dna_data_fas[0]])
self.assertEqual(self.aln_obj.average_seqsize_per_species(),
{"exception": "single_alignment"})
def test_single_aln_average_seqsize(self):
self.aln_obj.update_active_alignments([dna_data_fas[0]])
self.assertEqual(self.aln_obj.average_seqsize(),
{"exception": "single_alignment"})
def test_single_aln_sequence_similarity(self):
self.aln_obj.update_active_alignments([dna_data_fas[0]])
self.assertEqual(self.aln_obj.sequence_similarity(),
{"exception": "single_alignment"})
def test_single_aln_sequence_segregation(self):
self.aln_obj.update_active_alignments([dna_data_fas[0]])
self.assertEqual(self.aln_obj.sequence_segregation(),
{"exception": "single_alignment"})
def test_single_aln_length_polymorphism_correlation(self):
self.aln_obj.update_active_alignments([dna_data_fas[0]])
self.assertEqual(self.aln_obj.length_polymorphism_correlation(),
{"exception": "single_alignment"})
def test_single_aln_taxa_distribution(self):
self.aln_obj.update_active_alignments([dna_data_fas[0]])
self.assertEqual(self.aln_obj.taxa_distribution(),
{"exception": "single_alignment"})
def test_single_aln_cumulative_missing_genes(self):
self.aln_obj.update_active_alignments([dna_data_fas[0]])
self.assertEqual(self.aln_obj.cumulative_missing_genes(),
{"exception": "single_alignment"})
def test_single_aln_gene_occupancy(self):
self.aln_obj.update_active_alignments([dna_data_fas[0]])
self.assertEqual(self.aln_obj.gene_occupancy(),
{"exception": "single_alignment"})
def test_single_aln_missing_data_distribution(self):
self.aln_obj.update_active_alignments([dna_data_fas[0]])
self.assertEqual(self.aln_obj.missing_data_distribution(),
{"exception": "single_alignment"})
def test_single_aln_missing_genes_average(self):
self.aln_obj.update_active_alignments([dna_data_fas[0]])
self.assertEqual(self.aln_obj.missing_genes_average(),
{"exception": "single_alignment"})
def test_no_data(self):
self.aln_obj = AlignmentList([], sql_db=sql_db)
self.assertEqual(self.aln_obj.gene_occupancy(),
{'exception': "empty_data"})
def test_gene_occupancy(self):
self.assertTrue(self.aln_obj.gene_occupancy())
def test_missing_data_distribution(self):
self.assertTrue(self.aln_obj.missing_data_distribution())
def test_missing_data_per_species(self):
self.assertTrue(self.aln_obj.missing_data_per_species())
def test_missing_genes_per_species(self):
self.assertTrue(self.aln_obj.missing_genes_per_species())
def test_missing_genes_average(self):
self.assertTrue(self.aln_obj.missing_genes_average())
def test_average_seqsize_per_species(self):
self.assertTrue(self.aln_obj.average_seqsize_per_species())
def test_average_seqsize(self):
self.assertTrue(self.aln_obj.average_seqsize())
def test_characters_proportion(self):
self.assertTrue(self.aln_obj.characters_proportion())
def test_characters_proportion_per_species(self):
self.assertTrue(self.aln_obj.characters_proportion_per_species())
def test_characters_proportion_gene(self):
self.assertTrue(self.aln_obj.characters_proportion_gene(
join(data_path, "BaseConc1.fas"), 10
))
def test_sequence_similarity(self):
self.assertTrue(self.aln_obj.sequence_similarity())
def test_sequence_similarity_per_species(self):
self.assertTrue(self.aln_obj.sequence_similarity_per_species())
def test_sequence_similarity_gene(self):
self.assertTrue(self.aln_obj.sequence_similarity_gene(
join(data_path, "BaseConc1.fas"), 10))
def test_sequence_conservation(self):
self.assertTrue(self.aln_obj.sequence_conservation_gnp(
join(data_path, "BaseConc1.fas"), 10
))
def test_sequence_segregation(self):
self.assertTrue(self.aln_obj.sequence_segregation())
def test_sequence_segregation_per_species(self):
self.assertTrue(self.aln_obj.sequence_segregation_per_species())
def test_sequence_segregation_gene(self):
self.assertTrue(self.aln_obj.sequence_segregation_gene(
join(data_path, "BaseConc1.fas"), 10))
def test_length_polymorphism_correlation(self):
self.assertTrue(self.aln_obj.length_polymorphism_correlation())
def test_allele_frequency_spectrum(self):
self.assertTrue(self.aln_obj.allele_frequency_spectrum())
def test_allele_frequency_spectrum_gene(self):
self.assertTrue(self.aln_obj.allele_frequency_spectrum_gene(
join(data_path, "BaseConc1.fas"), None))
def test_taxa_distribution(self):
self.assertTrue(self.aln_obj.taxa_distribution())
def test_cumulative_missing_genes(self):
self.assertTrue(self.aln_obj.cumulative_missing_genes())
def test_outlier_missing_data(self):
self.assertTrue(self.aln_obj.outlier_missing_data())
def test_outlier_missing_data_sp(self):
self.assertTrue(self.aln_obj.outlier_missing_data_sp())
def test_outlier_segregating(self):
self.assertTrue(self.aln_obj.outlier_segregating())
def test_outlier_segregating_sp(self):
self.assertTrue(self.aln_obj.outlier_segregating_sp())
def test_outlier_sequence_size(self):
self.assertTrue(self.aln_obj.outlier_sequence_size())
def test_outlier_sequence_size_sp(self):
self.assertTrue(self.aln_obj.outlier_sequence_size_sp())
class PartitonsTest(ExpectingTestCase):
def setUp(self):
if not os.path.exists(temp_dir):
os.makedirs(temp_dir)
self.aln_obj = AlignmentList(dna_data_fas, sql_db=sql_db)
self.aln_obj.partitions.reset(cur=self.aln_obj.cur,)
def tearDown(self):
self.aln_obj.clear_alignments()
self.aln_obj.con.close()
shutil.rmtree(temp_dir)
def test_read_from_nexus(self):
self.aln_obj.partitions.read_from_file(concatenated_small_parNex[0],
no_aln_check=True)
self.assertEqual(len(self.aln_obj.partitions.partitions), 7)
def test_read_from_phylip(self):
self.aln_obj.partitions.read_from_file(concatenated_small_par[0],
no_aln_check=True)
self.assertEqual(len(self.aln_obj.partitions.partitions), 7)
def test_bad_partitions_phy(self):
e = self.aln_obj.partitions.read_from_file(partition_bad_phy[0],
no_aln_check=True)
self.assertTrue(isinstance(e, InvalidPartitionFile))
def test_unsorted_part_phylip(self):
self.aln_obj.partitions.read_from_file(partition_unsorted_phy[0],
no_aln_check=True)
data = [self.aln_obj.partitions.partitions.keys(),
self.aln_obj.partitions.counter]
self.assertEqual(data, [["BaseConc1.fas", "BaseConc2.fas",
"BaseConc3.fas", "BaseConc4.fas",
"BaseConc5.fas", "BaseConc6.fas",
"BaseConc7.fas"],
595])
def test_phylip_dot_notation(self):
self.aln_obj.partitions.read_from_file(partition_dot_not[0],
no_aln_check=True)
data = [self.aln_obj.partitions.partitions.keys(),
self.aln_obj.partitions.counter]
self.assertEqual(data, [["BaseConc1.fas", "BaseConc2.fas",
"BaseConc3.fas", "BaseConc4.fas",
"BaseConc5.fas", "BaseConc6.fas",
"BaseConc7.fas"],
595])
def test_nexus_dot_notation(self):
self.aln_obj.partitions.read_from_file(dot_notation_nex[0],
no_aln_check=True)
data = [self.aln_obj.partitions.partitions.keys(),
self.aln_obj.partitions.counter]
self.assertEqual(data, [["BaseConc1.fas", "BaseConc2.fas",
"BaseConc3.fas", "BaseConc4.fas",
"BaseConc5.fas", "BaseConc6.fas",
"BaseConc7.fas"],
595])
def test_import_new_partscheme(self):
self.aln_obj.clear_alignments()
self.aln_obj.con.close()
self.aln_obj = AlignmentList(concatenated_medium_nexus,
sql_db=sql_db)
self.aln_obj.partitions.reset()
self.aln_obj.partitions.read_from_file(concatenated_small_par[0],
no_aln_check=True)
res = self.aln_obj.partitions.get_partition_names()
self.assertEqual(res, ["BaseConc1.fas", "BaseConc2.fas",
"BaseConc3.fas", "BaseConc4.fas",
"BaseConc5.fas", "BaseConc6.fas",
"BaseConc7.fas"])
def test_add_duplicate_name(self):
self.aln_obj.partitions.read_from_file(concatenated_small_par[0],
no_aln_check=True)
self.assertRaises(PartitionException,
self.aln_obj.partitions.add_partition(
"BaseCond1.fas", length=100))
def test_get_partition_names(self):
self.aln_obj.partitions.read_from_file(concatenated_small_par[0],
no_aln_check=True)
res = self.aln_obj.partitions.get_partition_names()
self.assertEqual(res, ["BaseConc1.fas", "BaseConc2.fas",
"BaseConc3.fas", "BaseConc4.fas",
"BaseConc5.fas", "BaseConc6.fas",
"BaseConc7.fas"])
def test_get_partition_names_withCodon(self):
self.aln_obj.partitions.read_from_file(
concatenated_smallCodon_parNex[0], no_aln_check=True)
res = self.aln_obj.partitions.get_partition_names()
self.assertEqual(res, ["BaseConc1.fas_1_1", "BaseConc1.fas_1_2",
"BaseConc1.fas_1_3", "BaseConc2.fas",
"BaseConc3.fas", "BaseConc4.fas",
"BaseConc5.fas", "BaseConc6.fas",
"BaseConc7.fas"])
def test_single_partition(self):
self.aln_obj = AlignmentList([dna_data_fas[0]],
db_con=self.aln_obj.con,
db_cur=self.aln_obj.cur,
sql_db=sql_db)
self.assertTrue(self.aln_obj.partitions.is_single())
def test_multiple_partitions(self):
self.assertFalse(self.aln_obj.partitions.is_single())
def test_remove_partition_from_file_original(self):
self.aln_obj.clear_alignments()
self.aln_obj.con.close()
self.aln_obj = AlignmentList(dna_data_fas, sql_db=sql_db)
self.aln_obj.partitions.remove_partition(
file_name="trifusion/tests/data/BaseConc3.fas")
# Check if remaining partition ranges are continuous
cont = True
prev = 0
for r in self.aln_obj.partitions.partitions.values():
if r[0][0][0] == prev:
prev = r[0][0][1] + 1
else:
cont = False
self.expect_equal(cont, True)
def test_remove_partition_from_name(self):
self.aln_obj.partitions.read_from_file(concatenated_small_parNex[0],
no_aln_check=True)
self.aln_obj.partitions.remove_partition("BaseConc3.fas")
# Check keys from _partitions, partitions_alignment and models
key_data = [list(self.aln_obj.partitions.partitions.keys()),
list(self.aln_obj.partitions.partitions_alignments.keys()),
list(self.aln_obj.partitions.models.keys())]
self.expect_equal(key_data,
[["BaseConc1.fas", "BaseConc2.fas",
"BaseConc4.fas",
"BaseConc5.fas", "BaseConc6.fas",
"BaseConc7.fas"]] * 3)
# Check if remaining partition ranges are continuous
cont = True
prev = 0
for r in self.aln_obj.partitions.partitions.values():
if r[0][0][0] == prev:
prev = r[0][0][1] + 1
else:
cont = False
self.expect_equal(cont, True)
def test_remove_partition_from_file(self):
self.aln_obj.partitions.read_from_file(concatenated_small_parNex[0],
no_aln_check=True)
self.aln_obj.partitions.remove_partition(file_name="BaseConc3.fas")
# Check keys from _partitions, partitions_alignment and models
key_data = [list(self.aln_obj.partitions.partitions.keys()),
list(self.aln_obj.partitions.partitions_alignments.keys()),
list(self.aln_obj.partitions.models.keys())]
self.expect_equal(key_data,
[["BaseConc1.fas", "BaseConc2.fas",
"BaseConc4.fas",
"BaseConc5.fas", "BaseConc6.fas",
"BaseConc7.fas"]] * 3)
# Check if remaining partition ranges are continuous
cont = True
prev = 0
for r in self.aln_obj.partitions.partitions.values():
if r[0][0][0] == prev:
prev = r[0][0][1] + 1
else:
cont = False
self.expect_equal(cont, True)
def test_change_name(self):
self.aln_obj.partitions.read_from_file(concatenated_small_parNex[0],
no_aln_check=True)
self.aln_obj.partitions.change_name("BaseConc1.fas", "OtherName")
key_data = [list(self.aln_obj.partitions.partitions.keys()),
list(self.aln_obj.partitions.partitions_alignments.keys()),
list(self.aln_obj.partitions.models.keys())]
self.expect_equal(key_data,
[["BaseConc2.fas",
"BaseConc3.fas", "BaseConc4.fas",
"BaseConc5.fas", "BaseConc6.fas",
"BaseConc7.fas", "OtherName"]] * 3)
# Check if remaining partition ranges are continuous
cont = True
prev = 0
self.aln_obj.partitions.partitions = OrderedDict(sorted(
self.aln_obj.partitions.partitions.iteritems(),
key=lambda x: x[1][0]
))
for r in self.aln_obj.partitions.partitions.values():
if r[0][0][0] == prev:
prev = r[0][0][1] + 1
else:
cont = False
self.expect_equal(cont, True)
def test_merge_partitions(self):
self.aln_obj.partitions.read_from_file(concatenated_small_parNex[0],
no_aln_check=True)
self.aln_obj.partitions.merge_partitions(
["BaseConc1.fas", "BaseConc2.fas", "BaseConc3.fas", "BaseConc4.fas",
"BaseConc5.fas", "BaseConc6.fas", "BaseConc7.fas"], "New_part")
key_data = [list(self.aln_obj.partitions.partitions.keys()),
list(self.aln_obj.partitions.partitions_alignments.keys()),
list(self.aln_obj.partitions.models.keys())]
self.assertEqual(key_data, [["New_part"]] * 3)
def test_split_partition(self):
self.aln_obj.partitions.read_from_file(concatenated_small_parNex[0],
no_aln_check=True)
self.aln_obj.partitions.split_partition("BaseConc1.fas",
[[0, 50], [51, 84]],
["part1", "part2"])
key_data = [list(self.aln_obj.partitions.partitions.keys()),
list(self.aln_obj.partitions.partitions_alignments.keys()),
list(self.aln_obj.partitions.models.keys())]
self.expect_equal(key_data,
[["part1", "part2", "BaseConc2.fas",
"BaseConc3.fas", "BaseConc4.fas",
"BaseConc5.fas", "BaseConc6.fas",
"BaseConc7.fas"]] * 3)
# Check if remaining partition ranges are continuous
cont = True
prev = 0
self.aln_obj.partitions.partitions = OrderedDict(sorted(
self.aln_obj.partitions.partitions.iteritems(),
key=lambda x: x[1][0]
))
for r in self.aln_obj.partitions.partitions.values():
print(r)
if r[0][0][0] == prev:
prev = r[0][0][1] + 1
else:
cont = False
self.expect_equal(cont, True)
def test_merge_and_split(self):
self.aln_obj.partitions.read_from_file(concatenated_small_parNex[0],
no_aln_check=True)
self.aln_obj.partitions.merge_partitions(
["BaseConc1.fas", "BaseConc2.fas", "BaseConc3.fas"], "new_part")
self.aln_obj.partitions.split_partition("new_part")
key_data = [sorted(self.aln_obj.partitions.partitions.keys()),
sorted(self.aln_obj.partitions.partitions_alignments.keys()),
sorted(self.aln_obj.partitions.models.keys())]
self.expect_equal(key_data, [["BaseConc1.fas", "BaseConc2.fas",
"BaseConc3.fas", "BaseConc4.fas",
"BaseConc5.fas", "BaseConc6.fas",
"BaseConc7.fas"]] * 3)
def test_merge_and_custom_split1(self):
self.aln_obj.partitions.read_from_file(concatenated_small_parNex[0],
no_aln_check=True)
self.aln_obj.partitions.merge_partitions(
["BaseConc1.fas", "BaseConc2.fas", "BaseConc3.fas"], "new_part")
self.aln_obj.partitions.split_partition("new_part",
[(0, 50), (51, 254)],
["one", "two"])
key_data = [self.aln_obj.partitions.partitions_alignments["one"],
self.aln_obj.partitions.partitions_alignments["two"]]
self.assertEqual(key_data,
[['BaseConc1.fas'],
['BaseConc1.fas', 'BaseConc3.fas', 'BaseConc2.fas']])
def test_merge_and_custom_split2(self):
self.aln_obj.partitions.read_from_file(concatenated_small_parNex[0],
no_aln_check=True)
self.aln_obj.partitions.merge_partitions(
["BaseConc1.fas", "BaseConc2.fas", "BaseConc3.fas"], "new_part")
self.aln_obj.partitions.split_partition("new_part",
[(0, 84), (85, 254)],
["one", "two"])
key_data = [self.aln_obj.partitions.partitions_alignments["one"],
self.aln_obj.partitions.partitions_alignments["two"]]
self.assertEqual(key_data,
[['BaseConc1.fas'],
['BaseConc3.fas', 'BaseConc2.fas']])
def test_concat_custom_fileset_from_phy_partfile(self):
self.aln_obj.clear_alignments()
self.aln_obj.con.close()
self.aln_obj = AlignmentList(dna_data_fas, sql_db=sql_db)
self.aln_obj.partitions.read_from_file(concatenated_small_par[0])
self.aln_obj.update_active_alignments(
[join(data_path, "BaseConc1.fas"),
join(data_path, "BaseConc2.fas")])
self.aln_obj.concatenate()
key_data = [
sorted(self.aln_obj.partitions.partitions.keys()),
sorted(self.aln_obj.partitions.partitions_alignments.keys()),
sorted(self.aln_obj.partitions.models.keys())]
self.expect_equal(key_data, [["BaseConc1.fas", "BaseConc2.fas"]] * 3)
def test_concat_custom_fileset_from_phy_partfile(self):
self.aln_obj.clear_alignments()
self.aln_obj.con.close()
self.aln_obj = AlignmentList(dna_data_fas, sql_db=sql_db)
self.aln_obj.partitions.read_from_file(concatenated_small_parNex[0])
self.aln_obj.update_active_alignments(
[join(data_path, "BaseConc1.fas"),
join(data_path, "BaseConc2.fas")])
self.aln_obj.concatenate()
key_data = [
sorted(self.aln_obj.partitions.partitions.keys()),
sorted(self.aln_obj.partitions.partitions_alignments.keys()),
sorted(self.aln_obj.partitions.models.keys())]
self.expect_equal(key_data, [["BaseConc1.fas", "BaseConc2.fas"]] * 3)
def test_merge_with_custom_fileset(self):
self.aln_obj.clear_alignments()
self.aln_obj.con.close()
self.aln_obj = AlignmentList(dna_data_fas, sql_db=sql_db)
self.aln_obj.partitions.read_from_file(concatenated_small_parNex[0])
self.aln_obj.partitions.merge_partitions(
["BaseConc1.fas", "BaseConc2.fas", "BaseConc3.fas"], "new_part")
self.aln_obj.update_active_alignments(
[join(data_path, "BaseConc1.fas"),
join(data_path, "BaseConc5.fas")])
self.aln_obj.concatenate()
key_data = [
sorted(self.aln_obj.partitions.partitions.keys()),
sorted(self.aln_obj.partitions.partitions_alignments.keys()),
sorted(self.aln_obj.partitions.models.keys())]
self.expect_equal(key_data, [["BaseConc1.fas", "BaseConc5.fas"]] * 3)
def test_model_detection(self):
self.aln_obj.clear_alignments()
self.aln_obj = AlignmentList(models_nexus_data,
db_con=self.aln_obj.con,
db_cur=self.aln_obj.cur,
sql_db=sql_db)
self.assertEqual(self.aln_obj.partitions.models,
OrderedDict([('Teste1.fas', [
[['nst=6', 'statefreqpr=dirichlet(1,1,1,1)']],
[None], []]), ('Teste2.fas', [
[['nst=6', 'statefreqpr=dirichlet(1,1,1,1)']],
[None], []]), ('Teste3.fas', [
[['nst=6', 'statefreqpr=dirichlet(1,1,1,1)']],
[None], []]), ('Teste4.fas', [
[['nst=6', 'statefreqpr=dirichlet(1,1,1,1)']],
[None], []]), ('Teste5.fas', [
[['nst=6', 'statefreqpr=dirichlet(1,1,1,1)']],
[None], []]), ('Teste6.fas', [
[['nst=6', 'statefreqpr=dirichlet(1,1,1,1)']],
[None], []]), ('Teste7.fas', [
[['nst=6', 'statefreqpr=dirichlet(1,1,1,1)']],
[None], []])]))
def test_model_detection_codons(self):
self.aln_obj.clear_alignments()
self.aln_obj = AlignmentList(models_codon_nexus_data,
db_cur=self.aln_obj.cur,
db_con=self.aln_obj.con,
sql_db=sql_db)
self.assertEqual(self.aln_obj.partitions.models,
OrderedDict([('Teste1.fas_1', [
[['nst=2', 'statefreqpr=dirichlet(1,1,1,1)'],
['nst=6', 'statefreqpr=fixed(equal)'],
['nst=6', 'statefreqpr=dirichlet(1,1,1,1)']],
[None, None, None], []]), ('Teste2.fas_86', [
[['nst=2', 'statefreqpr=dirichlet(1,1,1,1)'],
['nst=6', 'statefreqpr=fixed(equal)'],
['nst=6', 'statefreqpr=dirichlet(1,1,1,1)']],
[None, None, None], []]), ('Teste3.fas_171', [
[['nst=2', 'statefreqpr=dirichlet(1,1,1,1)'],
['nst=6', 'statefreqpr=fixed(equal)'],
['nst=6', 'statefreqpr=dirichlet(1,1,1,1)']],
[None, None, None], []]), ('Teste4.fas_256', [
[['nst=2', 'statefreqpr=dirichlet(1,1,1,1)'],
['nst=6', 'statefreqpr=fixed(equal)'],
['nst=6', 'statefreqpr=dirichlet(1,1,1,1)']],
[None, None, None], []]), ('Teste5.fas_341', [
[['nst=2', 'statefreqpr=dirichlet(1,1,1,1)'],
['nst=6', 'statefreqpr=fixed(equal)'],
['nst=6', 'statefreqpr=dirichlet(1,1,1,1)']],
[None, None, None], []]), ('Teste6.fas_426', [
[['nst=2', 'statefreqpr=dirichlet(1,1,1,1)'],
['nst=6', 'statefreqpr=fixed(equal)'],
['nst=6', 'statefreqpr=dirichlet(1,1,1,1)']],
[None, None, None], []]), ('Teste7.fas_511', [
[['nst=2', 'statefreqpr=dirichlet(1,1,1,1)'],
['nst=6', 'statefreqpr=fixed(equal)'],
['nst=6', 'statefreqpr=dirichlet(1,1,1,1)']],
[None, None, None], []])]))
def test_set_model(self):
self.aln_obj.partitions.read_from_file(concatenated_small_parNex[0],
no_aln_check=True)
self.aln_obj.partitions.set_model("BaseConc1.fas", ["GTR"])
self.assertEqual(self.aln_obj.partitions.models,
OrderedDict([('BaseConc1.fas', [[[]], ['GTR'], []]),
('BaseConc2.fas', [[[]], [None], []]),
('BaseConc3.fas', [[[]], [None], []]),
('BaseConc4.fas', [[[]], [None], []]),
('BaseConc5.fas', [[[]], [None], []]),
('BaseConc6.fas', [[[]], [None], []]),
('BaseConc7.fas', [[[]], [None], []])])
)
def test_set_model_all(self):
self.aln_obj.partitions.read_from_file(concatenated_small_parNex[0],
no_aln_check=True)
self.aln_obj.partitions.set_model("BaseConc1.fas", ["GTR"],
apply_all=True)
self.assertEqual(self.aln_obj.partitions.models,
OrderedDict([('BaseConc1.fas', [[[]], ['GTR'], []]),
('BaseConc2.fas', [[[]], ['GTR'], []]),
('BaseConc3.fas', [[[]], ['GTR'], []]),
('BaseConc4.fas', [[[]], ['GTR'], []]),
('BaseConc5.fas', [[[]], ['GTR'], []]),
('BaseConc6.fas', [[[]], ['GTR'], []]),
('BaseConc7.fas', [[[]], ['GTR'], []])])
)
def test_set_model_codon(self):
self.aln_obj.partitions.read_from_file(concatenated_small_parNex[0],
no_aln_check=True)
self.aln_obj.partitions.set_model("BaseConc1.fas", ["GTR", "SYM"],
links=["12", "3"],
apply_all=True)
self.assertEqual(self.aln_obj.partitions.models,
OrderedDict([('BaseConc1.fas',
[[[]], ['GTR', 'SYM'], ['12', '3']]), (
'BaseConc2.fas',
[[[]], ['GTR', 'SYM'], ['12', '3']]), (
'BaseConc3.fas',
[[[]], ['GTR', 'SYM'], ['12', '3']]), (
'BaseConc4.fas',
[[[]], ['GTR', 'SYM'], ['12', '3']]), (
'BaseConc5.fas',
[[[]], ['GTR', 'SYM'], ['12', '3']]), (
'BaseConc6.fas',
[[[]], ['GTR', 'SYM'], ['12', '3']]), (
'BaseConc7.fas',
[[[]], ['GTR', 'SYM'], ['12', '3']])]))
class AlignmentManipulationTest(unittest.TestCase):
def setUp(self):
if not os.path.exists(temp_dir):
os.makedirs(temp_dir)
self.aln_obj = AlignmentList(dna_data_fas, sql_db=sql_db)
def tearDown(self):
try:
self.aln_obj.clear_alignments()
except:
pass
self.aln_obj.con.close()
shutil.rmtree(temp_dir)
def test_clear_alns(self):
self.aln_obj.clear_alignments()
aln = AlignmentList([], sql_db=sql_db)
self.assertTrue(compare_inst(self.aln_obj, aln, ["log_progression",
"locus_length",
"partitions",
"cur",
"con"]))
def test_update_act_anls(self):
self.aln_obj.update_active_alignments([join(data_path,
"BaseConc1.fas"),
join(data_path,
"BaseConc2.fas")])
self.assertEqual(list(self.aln_obj.alignments.keys()),
[join(data_path, "BaseConc1.fas"),
join(data_path, "BaseConc2.fas")])
def test_update_act_alns_err(self):
self.aln_obj.update_active_alignments([join(data_path,
"BaseConc1.fas"),
join(data_path,
"BaseConc2.fas"),
join(data_path,
"Wrong_name")])
self.assertEqual(list(self.aln_obj.alignments.keys()),
[join(data_path, "BaseConc1.fas"),
join(data_path, "BaseConc2.fas")])
def test_update_aln_shelve(self):
self.aln_obj.update_active_alignment(join(data_path, "BaseConc1.fas"),
"shelve")
self.assertEqual(list(self.aln_obj.alignments.keys()),
[join(data_path, "BaseConc2.fas"),
join(data_path, "BaseConc3.fas"),
join(data_path, "BaseConc4.fas"),
join(data_path, "BaseConc5.fas"),
join(data_path, "BaseConc6.fas"),
join(data_path, "BaseConc7.fas")])
def test_update_aln_act(self):
self.aln_obj.update_active_alignments([])
self.aln_obj.update_active_alignment(join(data_path, "BaseConc1.fas"),
"active")
self.assertEqual(list(self.aln_obj.alignments.keys()),
[join(data_path, "BaseConc1.fas")])
def test_add_aln_obj(self):
fl = self.aln_obj.alignments.keys()
aln = Alignment(dna_data_loci[0], sql_cursor=self.aln_obj.cur,
sql_con=self.aln_obj.con,
db_idx=self.aln_obj._idx + 1, temp_dir=temp_dir)
self.aln_obj.add_alignments([aln])
self.assertEqual(self.aln_obj.alignments.keys(),
fl + [join(data_path, "c97d5m4p2.loci")])
def test_remove_taxa_from_list(self):
taxa_list = [
"1285_RAD_original",
"130a_RAD_original",
"137a_RAD_original",
"1427_RAD_original",
"167a_RAD_original"
]
expected_taxa = [tx for tx in self.aln_obj.taxa_names if
tx not in taxa_list]
self.aln_obj.remove_taxa(taxa_list)
self.assertEqual(self.aln_obj.taxa_names, expected_taxa)
def test_remove_taxa_from_file(self):
taxa_list = [
"1285_RAD_original",
"130a_RAD_original",
"137a_RAD_original",
"1427_RAD_original",
"167a_RAD_original"
]
expected_taxa = [tx for tx in self.aln_obj.taxa_names if
tx not in taxa_list]
self.aln_obj.remove_taxa(taxa_to_remove)
self.assertEqual(self.aln_obj.taxa_names, expected_taxa)
def test_remove_taxa_from_list_inverse(self):
taxa_list = [
"1285_RAD_original",
"130a_RAD_original",
"137a_RAD_original",
"1427_RAD_original",
"167a_RAD_original"
]
expected_taxa = [tx for tx in self.aln_obj.taxa_names if
tx not in taxa_list]
self.aln_obj.remove_taxa(taxa_list, mode="inverse")
self.assertEqual(self.aln_obj.taxa_names, taxa_list)
#
# def test_retrieve_alignment(self):
#
# aln = self.aln_obj.retrieve_alignment("BaseConc1.fas")
#
# aln2 = Alignment(dna_data_fas[0], dest="new_one")
#
# self.assertTrue(compare_inst(aln, aln2,
# ["log_progression", "locus_length",
# "_partitions"]))
def test_concatenation(self):
self.aln_obj.concatenate()
self.aln_obj.write_to_file(["fasta"], output_file="test")
with open("trifusion/tests/data/BaseConcatenation.fas") as fh1, \
open("test.fas") as fh2:
self.assertEqual(sorted(fh1.readlines()), sorted(fh2.readlines()))
os.remove("test.fas")
def test_concatention_after_removal(self):
fl = [x for x in self.aln_obj.alignments][3:]
self.aln_obj.remove_file(fl)
self.aln_obj.concatenate()
self.assertEqual(len(self.aln_obj.alignments), 1)
