class SeconaryOpsTest(unittest.TestCase):
def setUp(self):
if not os.path.exists(temp_dir):
os.makedirs(temp_dir)
self.aln_obj = AlignmentList([], sql_db=sql_db)
def tearDown(self):
self.aln_obj.clear_alignments()
self.aln_obj.con.close()
shutil.rmtree(temp_dir)
def test_collapse_single(self):
self.aln_obj.add_alignment_files([variable_data[0]])
if not os.path.exists("test_collapse"):
os.makedirs("test_collapse")
self.aln_obj.collapse(haplotype_name="Testing",
haplotypes_file="teste",
dest="test_collapse",
use_main_table=True)
aln = self.aln_obj.alignments.values()[0]
tn = len(list(aln.iter_sequences()))
self.assertEqual(tn, 1)
shutil.rmtree("test_collapse")
def test_collapse_with_variation(self):
self.aln_obj.add_alignment_files([variable_data[1]])
if not os.path.exists("test_collapse"):
os.makedirs("test_collapse")
self.aln_obj.collapse(haplotype_name="Testing",
haplotypes_file="teste",
dest="test_collapse",
use_main_table=True)
aln = self.aln_obj.alignments.values()[0]
tn = len(list(aln.iter_sequences()))
self.assertEqual(tn, 4)
shutil.rmtree("test_collapse")
def test_collapse_after_concatenation(self):
self.aln_obj.add_alignment_files(variable_data)
if not os.path.exists("test_collapse"):
os.makedirs("test_collapse")
self.aln_obj.concatenate()
self.aln_obj.collapse(haplotype_name="Testing",
haplotypes_file="teste",
dest="test_collapse",
table_out="collapse")
tn = len(list(self.aln_obj.iter_alignments("collapse")))
self.assertEqual(tn, 8)
shutil.rmtree("test_collapse")
def test_gcoder(self):
self.aln_obj.add_alignment_files(gcode_data)
self.aln_obj.code_gaps(use_main_table=True)
s = []
for aln in self.aln_obj:
for seq in aln.iter_sequences():
s.append(seq)
res = [
"aaaaaaaa-aaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaa10000",
"aaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaa---aaaaaaaaaaa01000",
"aaaaaaaaaaaa--aaaaaaaaaaaaaaaaaaaaa---aaaaaaaaaaa01100",
"aaaaaaaaaaaa--aaaaaaaaaaaaaaaaaaaaa---aaaaaaaaaaa01100",
"aaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaa---aaaaaaaaaaa01000",
"aaaaaaaaaaaaaaaaaaaaaa----aaaaaaaaa---aaaaaaaaaaa01010",
"aaaaaaaaaaaaaaaaaaaaaaaaaaaaaaa-aaa---aaaaaaaaaaa01001",
"aaaaaaaaaaaaaaaaaaaaaa----aaaaaaaaa---aaaaaaaaaaa01010",
"aaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaa---aaaaaaaaaaa01000",
"aaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaa---aaaaaaaaaaa01000"
]
self.assertEqual(sorted(s), sorted(res))
def test_consensus_multi_file(self):
self.aln_obj.add_alignment_files(dna_data_fas)
self.aln_obj.consensus("IUPAC", use_main_table=True)
s = []
for aln in self.aln_obj:
s.append(len(aln.taxa_idx))
self.assertEqual(s, [1] * 7)
def test_consensus_single_file(self):
self.aln_obj.add_alignment_files(dna_data_fas)
self.aln_obj.consensus("IUPAC", single_file=True)
self.assertEqual(len(self.aln_obj.taxa_names), 7)
def test_consensus_soft_mask(self):
self.aln_obj.add_alignment_files(dna_data_fas)
self.aln_obj.consensus("Soft mask", use_main_table=True)
s = []
for aln in self.aln_obj:
s.append(len(aln.taxa_idx))
self.assertEqual(s, [1] * 7)
def test_consensus_remove(self):
self.aln_obj.add_alignment_files(dna_data_fas)
self.aln_obj.consensus("Remove", use_main_table=True)
s = []
for aln in self.aln_obj:
s.append(len(aln.taxa_idx))
self.assertEqual(s, [1] * 7)
def test_consensus_first_seq(self):
self.aln_obj.add_alignment_files(dna_data_fas)
self.aln_obj.consensus("First sequence", use_main_table=True)
s = []
for aln in self.aln_obj:
s.append(len(aln.taxa_idx))
self.assertEqual(s, [1] * 7)
def test_consensus_first_seq2(self):
self.aln_obj.add_alignment_files(dna_data_fas)
self.aln_obj.consensus("First sequence", use_main_table=True)
s = 0
for _ in self.aln_obj.iter_alignments():
s += 1
self.assertEqual(s, 7)
def test_reverse_concatenate(self):
self.aln_obj.add_alignment_files(concatenated_small_phy)
self.aln_obj.partitions.read_from_file(concatenated_small_par[0])
self.aln_obj.reverse_concatenate()
self.assertEqual(len(self.aln_obj.alignments), 7)
def test_zorro(self):
self.aln_obj.add_alignment_files(zorro_data_fas)
# Generate zorro output
zorro_data = Zorro(self.aln_obj, "_zorro")
zorro_data.write_to_file("test")
# Read zorro and reference files
zorro_content = open("test_zorro.out").read()
reference = open(zorro_out).read()
self.assertEqual(zorro_content, reference)
os.remove("test_zorro.out")
def test_zorro_with_dir(self):
self.aln_obj.add_alignment_files(zorro_data_fas)
# Generate zorro output
zorro_data = Zorro(self.aln_obj, "_zorro", "trifusion/tests/data")
zorro_data.write_to_file("test")
# Read zorro and reference files
zorro_content = open("test_zorro.out").read()
reference = open(zorro_out).read()
self.assertEqual(zorro_content, reference)
os.remove("test_zorro.out")
def test_iter_columns(self):
self.aln_obj = AlignmentList([variable_data[1]])
s = 0
for col, aln_idx in self.aln_obj.iter_columns():
if len(set(col)) > 1:
s += 1
self.assertEqual(s, 3)
def test_iter_columns_with_active_tx(self):
self.aln_obj = AlignmentList([variable_data[1]])
self.aln_obj.update_taxa_names(self.aln_obj.taxa_names[1:])
s = 0
for col, aln_idx in self.aln_obj.iter_columns():
if len(set(col)) > 1:
s += 1
self.assertEqual(s, 2)
class SeconaryOpsTest(unittest.TestCase):
def setUp(self):
self.aln_obj = AlignmentList([], sql_db=sql_db)
def tearDown(self):
self.aln_obj.clear_alignments()
self.aln_obj.con.close()
os.remove(sql_db)
def test_collapse_single(self):
self.aln_obj.add_alignment_files([variable_data[0]])
if not os.path.exists("test_collapse"):
os.makedirs("test_collapse")
self.aln_obj.collapse(haplotype_name="Testing",
haplotypes_file="teste",
dest="test_collapse",
use_main_table=True)
aln = self.aln_obj.alignments.values()[0]
tn = len(list(aln.iter_sequences(table_suffix="_collapse")))
self.assertEqual(tn, 1)
shutil.rmtree("test_collapse")
def test_collapse_with_variation(self):
self.aln_obj.add_alignment_files([variable_data[1]])
if not os.path.exists("test_collapse"):
os.makedirs("test_collapse")
self.aln_obj.collapse(haplotype_name="Testing",
haplotypes_file="teste",
dest="test_collapse",
use_main_table=True)
aln = self.aln_obj.alignments.values()[0]
tn = len(list(aln.iter_sequences(table_suffix="_collapse")))
self.assertEqual(tn, 4)
shutil.rmtree("test_collapse")
def test_collapse_after_concatenation(self):
self.aln_obj.add_alignment_files(variable_data)
if not os.path.exists("test_collapse"):
os.makedirs("test_collapse")
aln = self.aln_obj.concatenate(alignment_name="test")
aln.collapse(haplotype_name="Testing",
haplotypes_file="teste",
dest="test_collapse",
table_out="_collapse")
tn = len(list(aln.iter_sequences(table_suffix="_collapse")))
self.assertEqual(tn, 7)
shutil.rmtree("test_collapse")
def test_gcoder(self):
self.aln_obj.add_alignment_files(gcode_data)
self.aln_obj.code_gaps(use_main_table=True)
s = []
for aln in self.aln_obj:
for seq in aln.iter_sequences():
s.append(seq)
res = [
"aaaaaaaa-aaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaa10000",
"aaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaa---aaaaaaaaaaa01000",
"aaaaaaaaaaaa--aaaaaaaaaaaaaaaaaaaaa---aaaaaaaaaaa01100",
"aaaaaaaaaaaa--aaaaaaaaaaaaaaaaaaaaa---aaaaaaaaaaa01100",
"aaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaa---aaaaaaaaaaa01000",
"aaaaaaaaaaaaaaaaaaaaaa----aaaaaaaaa---aaaaaaaaaaa01010",
"aaaaaaaaaaaaaaaaaaaaaaaaaaaaaaa-aaa---aaaaaaaaaaa01001",
"aaaaaaaaaaaaaaaaaaaaaa----aaaaaaaaa---aaaaaaaaaaa01010",
"aaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaa---aaaaaaaaaaa01000",
"aaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaa---aaaaaaaaaaa01000"
]
self.assertEqual(sorted(s), sorted(res))
def test_consensus_multi_file(self):
self.aln_obj.add_alignment_files(dna_data_fas)
self.aln_obj.consensus("IUPAC", use_main_table=True)
s = []
for aln in self.aln_obj:
s.append(len(aln.taxa_list))
self.assertEqual(s, [1] * 7)
def test_consensus_single_file(self):
self.aln_obj.add_alignment_files(dna_data_fas)
aln = self.aln_obj.consensus("IUPAC", single_file=True)
self.assertEqual(len(aln.taxa_list), 7)
def test_consensus_soft_mask(self):
self.aln_obj.add_alignment_files(dna_data_fas)
self.aln_obj.consensus("Soft mask", use_main_table=True)
s = []
for aln in self.aln_obj:
s.append(len(aln.taxa_list))
self.assertEqual(s, [1] * 7)
def test_consensus_remove(self):
self.aln_obj.add_alignment_files(dna_data_fas)
self.aln_obj.consensus("Remove", use_main_table=True)
s = []
for aln in self.aln_obj:
s.append(len(aln.taxa_list))
self.assertEqual(s, [1] * 7)
def test_consensus_first_seq(self):
self.aln_obj.add_alignment_files(dna_data_fas)
self.aln_obj.consensus("First sequence", use_main_table=True)
s = []
for aln in self.aln_obj:
s.append(len(aln.taxa_list))
self.assertEqual(s, [1] * 7)
def test_reverse_concatenate(self):
self.aln_obj.add_alignment_files(concatenated_small_phy)
partition_obj = Partitions()
# In case the partitions file is badly formatted or invalid, the
# exception will be returned by the read_from_file method.
partition_obj.read_from_file(concatenated_small_par[0])
aln = self.aln_obj.concatenate(alignment_name="test")
aln.set_partitions(partition_obj)
alns = aln.reverse_concatenate(table_in="concatenation",
db_con=self.aln_obj.con)
self.assertEqual(len(alns.alignments), 7)
def test_zorro(self):
self.aln_obj.add_alignment_files(zorro_data_fas)
# Generate zorro output
zorro_data = Zorro(self.aln_obj, "_zorro")
zorro_data.write_to_file("test")
# Read zorro and reference files
zorro_content = open("test_zorro.out").read()
reference = open(zorro_out).read()
self.assertEqual(zorro_content, reference)
os.remove("test_zorro.out")
def test_zorro_with_dir(self):
self.aln_obj.add_alignment_files(zorro_data_fas)
# Generate zorro output
zorro_data = Zorro(self.aln_obj, "_zorro", "trifusion/tests/data")
zorro_data.write_to_file("test")
# Read zorro and reference files
zorro_content = open("test_zorro.out").read()
reference = open(zorro_out).read()
self.assertEqual(zorro_content, reference)
os.remove("test_zorro.out")
class SeconaryOpsTest(unittest.TestCase):
def setUp(self):
if not os.path.exists(temp_dir):
os.makedirs(temp_dir)
self.aln_obj = AlignmentList([], sql_db=sql_db)
def tearDown(self):
self.aln_obj.clear_alignments()
self.aln_obj.con.close()
shutil.rmtree(temp_dir)
def test_collapse_single(self):
self.aln_obj.add_alignment_files([variable_data[0]])
if not os.path.exists("test_collapse"):
os.makedirs("test_collapse")
self.aln_obj.collapse(haplotype_name="Testing",
haplotypes_file="teste",
dest="test_collapse",
use_main_table=True)
aln = self.aln_obj.alignments.values()[0]
tn = len(list(aln.iter_sequences()))
self.assertEqual(tn, 1)
shutil.rmtree("test_collapse")
def test_collapse_with_variation(self):
self.aln_obj.add_alignment_files([variable_data[1]])
if not os.path.exists("test_collapse"):
os.makedirs("test_collapse")
self.aln_obj.collapse(haplotype_name="Testing",
haplotypes_file="teste",
dest="test_collapse",
use_main_table=True)
aln = self.aln_obj.alignments.values()[0]
tn = len(list(aln.iter_sequences()))
self.assertEqual(tn, 4)
shutil.rmtree("test_collapse")
def test_collapse_after_concatenation(self):
self.aln_obj.add_alignment_files(variable_data)
if not os.path.exists("test_collapse"):
os.makedirs("test_collapse")
self.aln_obj.concatenate()
self.aln_obj.collapse(haplotype_name="Testing",
haplotypes_file="teste",
dest="test_collapse",
table_out="collapse")
tn = len(list(self.aln_obj.iter_alignments("collapse")))
self.assertEqual(tn, 8)
shutil.rmtree("test_collapse")
def test_gcoder(self):
self.aln_obj.add_alignment_files(gcode_data)
self.aln_obj.code_gaps(use_main_table=True)
s = []
for aln in self.aln_obj:
for seq in aln.iter_sequences():
s.append(seq)
res = [
"aaaaaaaa-aaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaa10000",
"aaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaa---aaaaaaaaaaa01000",
"aaaaaaaaaaaa--aaaaaaaaaaaaaaaaaaaaa---aaaaaaaaaaa01100",
"aaaaaaaaaaaa--aaaaaaaaaaaaaaaaaaaaa---aaaaaaaaaaa01100",
"aaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaa---aaaaaaaaaaa01000",
"aaaaaaaaaaaaaaaaaaaaaa----aaaaaaaaa---aaaaaaaaaaa01010",
"aaaaaaaaaaaaaaaaaaaaaaaaaaaaaaa-aaa---aaaaaaaaaaa01001",
"aaaaaaaaaaaaaaaaaaaaaa----aaaaaaaaa---aaaaaaaaaaa01010",
"aaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaa---aaaaaaaaaaa01000",
"aaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaa---aaaaaaaaaaa01000"
]
self.assertEqual(sorted(s), sorted(res))
def test_consensus_multi_file(self):
self.aln_obj.add_alignment_files(dna_data_fas)
self.aln_obj.consensus("IUPAC", use_main_table=True)
s = []
for aln in self.aln_obj:
s.append(len(aln.taxa_idx))
self.assertEqual(s, [1] * 7)
def test_consensus_single_file(self):
self.aln_obj.add_alignment_files(dna_data_fas)
self.aln_obj.consensus("IUPAC", single_file=True)
self.assertEqual(len(self.aln_obj.taxa_names), 7)
def test_consensus_soft_mask(self):
self.aln_obj.add_alignment_files(dna_data_fas)
self.aln_obj.consensus("Soft mask", use_main_table=True)
s = []
for aln in self.aln_obj:
s.append(len(aln.taxa_idx))
self.assertEqual(s, [1] * 7)
def test_consensus_remove(self):
self.aln_obj.add_alignment_files(dna_data_fas)
self.aln_obj.consensus("Remove", use_main_table=True)
s = []
for aln in self.aln_obj:
s.append(len(aln.taxa_idx))
self.assertEqual(s, [1] * 7)
def test_consensus_first_seq(self):
self.aln_obj.add_alignment_files(dna_data_fas)
self.aln_obj.consensus("First sequence", use_main_table=True)
s = []
for aln in self.aln_obj:
s.append(len(aln.taxa_idx))
self.assertEqual(s, [1] * 7)
def test_consensus_first_seq2(self):
self.aln_obj.add_alignment_files(dna_data_fas)
self.aln_obj.consensus("First sequence", use_main_table=True)
s = 0
for _ in self.aln_obj.iter_alignments():
s += 1
self.assertEqual(s, 7)
def test_reverse_concatenate(self):
self.aln_obj.add_alignment_files(concatenated_small_phy)
self.aln_obj.partitions.read_from_file(concatenated_small_par[0])
self.aln_obj.reverse_concatenate()
self.assertEqual(len(self.aln_obj.alignments), 7)
def test_zorro(self):
self.aln_obj.add_alignment_files(zorro_data_fas)
# Generate zorro output
zorro_data = Zorro(self.aln_obj, "_zorro")
zorro_data.write_to_file("test")
# Read zorro and reference files
zorro_content = open("test_zorro.out").read()
reference = open(zorro_out).read()
self.assertEqual(zorro_content, reference)
os.remove("test_zorro.out")
def test_zorro_with_dir(self):
self.aln_obj.add_alignment_files(zorro_data_fas)
# Generate zorro output
zorro_data = Zorro(self.aln_obj, "_zorro", "trifusion/tests/data")
zorro_data.write_to_file("test")
# Read zorro and reference files
zorro_content = open("test_zorro.out").read()
reference = open(zorro_out).read()
self.assertEqual(zorro_content, reference)
os.remove("test_zorro.out")
def test_iter_columns(self):
self.aln_obj = AlignmentList([variable_data[1]])
s = 0
for col, aln_idx in self.aln_obj.iter_columns():
if len(set(col)) > 1:
s += 1
self.assertEqual(s, 3)
def test_iter_columns_with_active_tx(self):
self.aln_obj = AlignmentList([variable_data[1]])
self.aln_obj.update_taxa_names(
self.aln_obj.taxa_names[1:])
s = 0
for col, aln_idx in self.aln_obj.iter_columns():
if len(set(col)) > 1:
s += 1
self.assertEqual(s, 2)