def test_treefile_source(self):
"""
Test PhyTrees.from_treefile() and PhyTrees.write() methods.
"""
infile = 'Newick/f002.trees.newick'
self.assertTrue(os.path.isfile(infile))
tree_db = PhyTrees.from_treefile(infile, 'newick')
outfile = 'tmp_test.newick'
outrepfile = 'tmp_test.rep'
self.files_to_clean.add(outfile)
self.files_to_clean.add(outrepfile)
tree_db.write(outfile)
self.assertTrue(os.path.isfile(outfile))
# Check the content of both sequence files
self.assertEqual(len(list(Phylo.parse(infile, 'newick'))),
len(list(Phylo.parse(outfile, 'newick'))))
# Check the content of the report file
with open(outrepfile, 'r') as repfile:
for line in repfile.readlines():
self.assertTrue(
('Num. trees: 9' in line) or ('History:' in line) or (bool(
re.match(
r"""\d\d\d\d/\d\d/\d\d\ \d\d:\d\d:\d\d[ ]+
[ ]+.*Tests/Newick/f002\.trees\.newick
\ +newick""", line, re.VERBOSE))))
def test_join ( self ) :
"""
Test PhyTrees.join() method.
"""
infile1 = 'Newick/f002.trees.newick'
infile2 = 'Nexus/f005.trees.nexus'
self.assertTrue(os.path.isfile(infile1))
self.assertTrue(os.path.isfile(infile2))
tree_db = PhyTrees.from_treefile(infile1, 'newick')
extra_db = PhyTrees.from_treefile(infile2, 'nexus')
tree_db.join(extra_db)
# Check the sequence data
inlist1 = [tree for tree in Phylo.parse(infile1, 'newick')]
inlist2 = [tree for tree in Phylo.parse(infile2, 'nexus')]
self.assertEqual(len(inlist1) + len(inlist2), len(tree_db))
# Check the report information
self.assertIn('Tests/Newick/f002.trees.newick', tree_db._report[0][1])
self.assertIn('newick', tree_db._report[0][2])
self.assertIn('Tests/Nexus/f005.trees.nexus', tree_db._report[1][1])
self.assertIn('nexus', tree_db._report[1][2])
def test_join(self):
"""
Test PhyTrees.join() method.
"""
infile1 = 'Newick/f002.trees.newick'
infile2 = 'Nexus/f005.trees.nexus'
self.assertTrue(os.path.isfile(infile1))
self.assertTrue(os.path.isfile(infile2))
tree_db = PhyTrees.from_treefile(infile1, 'newick')
extra_db = PhyTrees.from_treefile(infile2, 'nexus')
tree_db.join(extra_db)
# Check the sequence data
inlist1 = [tree for tree in Phylo.parse(infile1, 'newick')]
inlist2 = [tree for tree in Phylo.parse(infile2, 'nexus')]
self.assertEqual(len(inlist1) + len(inlist2), len(tree_db))
# Check the report information
self.assertIn('Tests/Newick/f002.trees.newick', tree_db._report[0][1])
self.assertIn('newick', tree_db._report[0][2])
self.assertIn('Tests/Nexus/f005.trees.nexus', tree_db._report[1][1])
self.assertIn('nexus', tree_db._report[1][2])
def test_statistics ( self ) :
"""
Test PhyTrees.statistics() method.
"""
infile = 'Newick/f002.trees.newick'
self.assertTrue(os.path.isfile(infile))
tree_db = PhyTrees.from_treefile(infile, 'newick')
nseqs, mean, minimum, maximum = tree_db.statistics()
# Check the resultant values
self.assertEqual(nseqs, len(tree_db))
self.assertEqual(mean, 10.0)
self.assertEqual(minimum, 10)
self.assertEqual(maximum, 10)
def test_statistics(self):
"""
Test PhyTrees.statistics() method.
"""
infile = 'Newick/f002.trees.newick'
self.assertTrue(os.path.isfile(infile))
tree_db = PhyTrees.from_treefile(infile, 'newick')
nseqs, mean, minimum, maximum = tree_db.statistics()
# Check the resultant values
self.assertEqual(nseqs, len(tree_db))
self.assertEqual(mean, 10.0)
self.assertEqual(minimum, 10)
self.assertEqual(maximum, 10)
def test_str ( self ) :
"""
Test str() property.
"""
infile = 'Newick/f002.trees.newick'
self.assertTrue(os.path.isfile(infile))
tree_db = PhyTrees.from_treefile(infile, 'newick')
outstr = str(tree_db)
# Check the output string
lines = outstr.split('\n')
self.assertEqual(lines[0], 'Num. trees: 9')
self.assertEqual(lines[1], 'History:')
self.assertTrue(bool(re.match(r"""\d\d\d\d/\d\d/\d\d\ \d\d:\d\d:\d\d[ ]+
[ ]+.*Tests/Newick/f002\.trees\.newick[ ]+newick""", lines[2],
re.VERBOSE)))
def test_str(self):
"""
Test str() property.
"""
infile = 'Newick/f002.trees.newick'
self.assertTrue(os.path.isfile(infile))
tree_db = PhyTrees.from_treefile(infile, 'newick')
outstr = str(tree_db)
# Check the output string
lines = outstr.split('\n')
self.assertEqual(lines[0], 'Num. trees: 9')
self.assertEqual(lines[1], 'History:')
self.assertTrue(
bool(
re.match(
r"""\d\d\d\d/\d\d/\d\d\ \d\d:\d\d:\d\d[ ]+
[ ]+.*Tests/Newick/f002\.trees\.newick[ ]+newick""", lines[2],
re.VERBOSE)))
def test_bioseqs_source ( self ) :
"""
Test PhyTrees.from_bioseqs() method and len() property.
"""
infile = 'PhyTrees/f002.trees.newick'
inrepfile = 'PhyTrees/f002.trees.rep'
self.assertTrue(os.path.isfile(infile))
self.assertTrue(os.path.isfile(inrepfile))
tree_db = PhyTrees.from_phytrees(infile)
# Check the content of the PhyTrees' object
self.assertEqual(len(tree_db), len(list(Phylo.parse(infile, 'newick'))))
# Check the content of the PhyTrees' report
with open(inrepfile, 'r') as repfile :
line = repfile.readline().strip() # Num. trees: 9
self.assertEqual(len(tree_db), int(line[-2:]))
line = repfile.readline() # History:
line = repfile.readline().strip() # [First source information]
source_info = line.split(' ')
self.assertEqual(tree_db._report[0], tuple(source_info))
def test_bioseqs_source(self):
"""
Test PhyTrees.from_bioseqs() method and len() property.
"""
infile = 'PhyTrees/f002.trees.newick'
inrepfile = 'PhyTrees/f002.trees.rep'
self.assertTrue(os.path.isfile(infile))
self.assertTrue(os.path.isfile(inrepfile))
tree_db = PhyTrees.from_phytrees(infile)
# Check the content of the PhyTrees' object
self.assertEqual(len(tree_db), len(list(Phylo.parse(infile,
'newick'))))
# Check the content of the PhyTrees' report
with open(inrepfile, 'r') as repfile:
line = repfile.readline().strip() # Num. trees: 9
self.assertEqual(len(tree_db), int(line[-2:]))
line = repfile.readline() # History:
line = repfile.readline().strip() # [First source information]
source_info = line.split(' ')
self.assertEqual(tree_db._report[0], tuple(source_info))
def test_treefile_source ( self ) :
"""
Test PhyTrees.from_treefile() and PhyTrees.write() methods.
"""
infile = 'Newick/f002.trees.newick'
self.assertTrue(os.path.isfile(infile))
tree_db = PhyTrees.from_treefile(infile, 'newick')
outfile = 'tmp_test.newick'
outrepfile = 'tmp_test.rep'
self.files_to_clean.add(outfile)
self.files_to_clean.add(outrepfile)
tree_db.write(outfile)
self.assertTrue(os.path.isfile(outfile))
# Check the content of both sequence files
self.assertEqual(len(list(Phylo.parse(infile, 'newick'))),
len(list(Phylo.parse(outfile, 'newick'))))
# Check the content of the report file
with open(outrepfile, 'r') as repfile :
for line in repfile.readlines() :
self.assertTrue(('Num. trees: 9' in line) or
('History:' in line) or
(bool(re.match(r"""\d\d\d\d/\d\d/\d\d\ \d\d:\d\d:\d\d[ ]+
[ ]+.*Tests/Newick/f002\.trees\.newick
\ +newick""", line, re.VERBOSE))))