def test_speed(self):
_LINE_LENGTH = 100
sym_count = 1
while sym_count < 100000:
sym_count *= 10
with TempDirectory() as tmp:
t1 = time.clock()
for p in ('a.fa', 'b.fa'):
with open(os.path.join(tmp.path, p), 'w', sym_count) as f:
f.write('> seq\n')
for j in xrange(sym_count):
f.write(random.choice(['a', 'c', 't', 'g', '-']))
if (j + 1) % _LINE_LENGTH == 0:
f.write('\n')
f.write('\n')
t2 = time.clock()
ZipDirectory.create_original_sequences(
tmp.path, os.path.join(tmp.path, 'a.fa'),
os.path.join(tmp.path, 'b.fa'))
t3 = time.clock()
self.assertTrue(t1 < t2 < t3)
def test_create_cache(self):
with TempDirectory() as temp:
directory = create_ziphmm_directory(temp.path)
xdir = ZipDirectory(directory)
self.assertFalse(xdir.is_cached(3))
xdir.create_cache(3)
self.assertTrue(xdir.is_cached(3))
def test_speed(self):
_LINE_LENGTH = 100
sym_count = 1
while sym_count < 100000:
sym_count *= 10
with TempDirectory() as tmp:
t1 = time.clock()
for p in ('a.fa', 'b.fa'):
with open(os.path.join(tmp.path, p), 'w', sym_count) as f:
f.write('> seq\n')
for j in xrange(sym_count):
f.write(random.choice(['a', 'c', 't', 'g', '-']))
if (j + 1) % _LINE_LENGTH == 0:
f.write('\n')
f.write('\n')
t2 = time.clock()
ZipDirectory.create_original_sequences(
tmp.path,
os.path.join(tmp.path, 'a.fa'),
os.path.join(tmp.path, 'b.fa'))
t3 = time.clock()
self.assertTrue(t1 < t2 < t3)
def _init_alignments(options, fasta_index1, fasta_index2, group_dir):
assert os.path.isdir(options.exp_folder), \
'Directory not found: {0}'.format(options.exp_folder)
assert len(options.fasta) > fasta_index1, \
'Not enough FASTA files specified'
assert len(options.fasta) > fasta_index2, \
'Not enough FASTA files specified'
root_dir = _get_ziphmm_root_dir(options, group_dir)
if not os.path.isdir(root_dir):
print '# Creating directory: {0}'.format(root_dir)
os.mkdir(root_dir)
ZipDirectory.create_original_sequences(
root_dir,
options.fasta[fasta_index1],
options.fasta[fasta_index2],
options.chunk_size,
sys.stdout)
ziphmm_dirs = map(ZipDirectory, glob.glob(os.path.join(root_dir, '*')))
for ziphmm_dir in ziphmm_dirs:
if not ziphmm_dir.is_cached(NUM_STATES):
print '# Creating {0}-state alignment in directory: {1}'.format(
NUM_STATES, ziphmm_dir.path)
ziphmm_dir.create_cache(NUM_STATES)
def _init_alignments(options, fasta_index1, fasta_index2, group_dir):
assert os.path.isdir(options.exp_folder), \
'Directory not found: {0}'.format(options.exp_folder)
assert len(options.fasta) > fasta_index1, \
'Not enough FASTA files specified'
assert len(options.fasta) > fasta_index2, \
'Not enough FASTA files specified'
root_dir = _get_ziphmm_root_dir(options, group_dir)
if not os.path.isdir(root_dir):
print '# Creating directory: {0}'.format(root_dir)
os.mkdir(root_dir)
ZipDirectory.create_original_sequences(root_dir,
options.fasta[fasta_index1],
options.fasta[fasta_index2],
options.chunk_size, sys.stdout)
ziphmm_dirs = map(ZipDirectory, glob.glob(os.path.join(root_dir, '*')))
for ziphmm_dir in ziphmm_dirs:
if not ziphmm_dir.is_cached(NUM_STATES):
print '# Creating {0}-state alignment in directory: {1}'.format(
NUM_STATES, ziphmm_dir.path)
ziphmm_dir.create_cache(NUM_STATES)
def test_clear_cache(self):
with TempDirectory() as temp:
directory = create_ziphmm_directory(temp.path)
xdir = ZipDirectory(directory)
self.assertTrue(os.path.isfile(
os.path.join(directory, 'data_structure')))
xdir.clear_cache()
self.assertFalse(os.path.isfile(
os.path.join(directory, 'data_structure')))
def test_clear_cache(self):
with TempDirectory() as temp:
directory = create_ziphmm_directory(temp.path)
xdir = ZipDirectory(directory)
self.assertTrue(
os.path.isfile(os.path.join(directory, 'data_structure')))
xdir.clear_cache()
self.assertFalse(
os.path.isfile(os.path.join(directory, 'data_structure')))
def test_is_cached(self):
with TempDirectory() as temp:
directory = create_ziphmm_directory(temp.path)
xdir = ZipDirectory(directory)
self.assertTrue(xdir.is_cached(2))
self.assertFalse(xdir.is_cached(3))
xdir.create_cache(3)
self.assertTrue(xdir.is_cached(2))
self.assertTrue(xdir.is_cached(3))
xdir.clear_cache()
self.assertFalse(xdir.is_cached(2))
self.assertFalse(xdir.is_cached(3))
def test_init_without_data(self):
with TempDirectory() as temp:
directory = create_ziphmm_directory(temp.path)
data_structure_path = os.path.join(directory, 'data_structure')
os.remove(data_structure_path)
xdir = ZipDirectory(directory)
self.assertEqual(directory, xdir.path)
def test_create_original_sequences(self):
with TempDirectory() as temp:
ZipDirectory.create_original_sequences(temp.path,
locate("inputs/a.fa"),
locate("inputs/b.fa"),
chunk_size=10)
def test(name, expected):
path = os.path.join(temp.path, name, 'original_sequence')
self.assertTrue(os.path.isfile(path))
actual = open(path, 'r').read()
self.assertEqual(expected, actual)
test('s1.ziphmm0', '0 0 0 0 1 1 1 1 0 0 ')
test('s1.ziphmm1', '0 0 1 1 1 1 0 0 0 0 ')
test('s1.ziphmm2', '1 1 2 1 ')
test('s2.ziphmm0', '0 0 0 0 1 1 0 0 0 0 ')
test('s2.ziphmm1', '1 1 0 0 0 0 1 1 ')
def test_load(self):
with TempDirectory() as temp:
directory = create_ziphmm_directory(temp.path)
xdir = ZipDirectory(directory)
self.assertTrue(xdir.is_cached(2))
xseq2 = xdir.load(2)
self.assertEqual(2, xseq2.state_count)
self.assertTrue(xdir.is_cached(2))
self.assertFalse(xdir.is_cached(3))
xseq3 = xdir.load(3)
self.assertEqual(3, xseq3.state_count)
self.assertTrue(xdir.is_cached(3))
self.assertFalse(xdir.is_cached(4))
xseq4 = xdir.load(4)
self.assertEqual(4, xseq4.state_count)
self.assertTrue(xdir.is_cached(4))
def test_create_original_sequences(self):
with TempDirectory() as temp:
ZipDirectory.create_original_sequences(
temp.path,
locate("inputs/a.fa"),
locate("inputs/b.fa"),
chunk_size=10)
def test(name, expected):
path = os.path.join(temp.path, name, 'original_sequence')
self.assertTrue(os.path.isfile(path))
actual = open(path, 'r').read()
self.assertEqual(expected, actual)
test('s1.ziphmm0', '0 0 0 0 1 1 1 1 0 0 ')
test('s1.ziphmm1', '0 0 1 1 1 1 0 0 0 0 ')
test('s1.ziphmm2', '1 1 2 1 ')
test('s2.ziphmm0', '0 0 0 0 1 1 0 0 0 0 ')
test('s2.ziphmm1', '1 1 0 0 0 0 1 1 ')
def test_has_original_sequence(self):
with TempDirectory() as temp:
self.assertFalse(ZipDirectory.has_original_sequence(temp.path))
directory = create_ziphmm_directory(temp.path)
self.assertTrue(ZipDirectory.has_original_sequence(directory))
def test_load(self):
with TempDirectory() as temp:
directory = create_ziphmm_directory(temp.path)
xdir = ZipDirectory(directory)
self.assertTrue(xdir.is_cached(2))
xseq2 = xdir.load(2)
self.assertEqual(2, xseq2.state_count)
self.assertTrue(xdir.is_cached(2))
self.assertFalse(xdir.is_cached(3))
xseq3 = xdir.load(3)
self.assertEqual(3, xseq3.state_count)
self.assertTrue(xdir.is_cached(3))
self.assertFalse(xdir.is_cached(4))
xseq4 = xdir.load(4)
self.assertEqual(4, xseq4.state_count)
self.assertTrue(xdir.is_cached(4))
def test_init_with_data(self):
with TempDirectory() as temp:
directory = create_ziphmm_directory(temp.path)
xdir = ZipDirectory(directory)
self.assertEqual(directory, xdir.path)
def test_has_original_sequence(self):
with TempDirectory() as temp:
self.assertFalse(ZipDirectory.has_original_sequence(temp.path))
directory = create_ziphmm_directory(temp.path)
self.assertTrue(ZipDirectory.has_original_sequence(directory))