class Test_seq_align(TestCase):
"""Unit tests for the data.seq_align relax module."""
def setUp(self):
"""Set 'self.seq_align' to an empty instance of the Sequence_alignments class."""
self.seq_align = Sequence_alignments()
def generate_ids(self, object_ids, models, molecules):
"""Generate the expected IDs."""
# Generate the IDs.
ids = []
for i in range(len(object_ids)):
ids.append("Object '%s'" % object_ids[i])
if models[i] != None:
ids[-1] += "; Model %i" % models[i]
ids[-1] += "; Molecule '%s'" % molecules[i]
# Return the IDs.
return ids
def return_align_data(self):
"""Return a data set for alignment testing."""
# The data.
object_ids = ['frame_order', 'ensemble', 'ensemble', 'ensemble', 'ensemble', 'ensemble', 'ensemble', 'ensemble']
models = [None, 1, 1, 1, 1, 1, 1, 1]
molecules = [
'N-dom',
'ensemble 4M A',
'ensemble 4M B',
'ensemble 4M C',
'ensemble 4M D',
'CaM-IQ A',
'CaM-IQ B',
'CaM-IQ C'
]
sequences = [
'LTEEQIAEFKEAFSLFDKDGDGTITTKELGTVMRSLGQNPTEAELQDMINEVDADGNGTIDFPEFLTMMARK*****',
'*DQLTEEQIAEFKEAFSLFDKDGDGTITTKELGTVMRSLGQNPTEAELQDMINEVDADGNGTIDFPEFLTMMARKMKDTDSEEEIREAFRVFDKDGNGYISAAELRHVMTNLGEKLTDEEVDEMIREADIDGDGQVNYEEFVQMMTA*****',
'*DQLTEEQIAEFKEAFSLFDKDGDGTITTKELGTVMRSLGQNPTEAELQDMINEVDADGNGTIDFPEFLTMMARKMKDTDSEEEIREAFRVFDKDGNGYISAAELRHVMTNLGEKLTDEEVDEMIREADIDGDGQVNYEEFVQMMTA*****',
'*DQLTEEQIAEFKEAFSLFDKDGDGTITTKELGTVMRSLGQNPTEAELQDMINEVDADGNGTIDFPEFLTMMARKMKDTDSEEEIREAFRVFDKDGNGYISAAELRHVMTNLGEKLTDEEVDEMIREADIDGDGQVNYEEFVQMMTA*****',
'*DQLTEEQIAEFKEAFSLFDKDGDGTITTKELGTVMRSLGQNPTEAELQDMINEVDADGNGTIDFPEFLTMMARKMKDTDSEEEIREAFRVFDKDGNGYISAAELRHVMTNLGEKLTDEEVDEMIREADIDGDGQVNYEEFVQMMTA*****',
' QLTEEQIAEFKEAFSLFDKDGDGTITTKELGTVMRSLGQNPTEAELQDMINEVDADGNGTIDFPEFLTMMARKMKSEEEIREAFRVFDKDGNGYISAAELRHVMTNLGEKLTDEEVDEMIREADIDGDGQVNYEEFVQMMT*****',
' LTEEQIAEFKEAFSLFDKDGDGTITTKELGTVMRSLGQNPTEAELQDMINEVDADGNGTIDFPEFLTMMARKMKDEEEIREAFRVFDKDGNGYISAAELRHVMTNLGEKLTDEEVDEMIREADIDGDGQVNYEEFVQMMT*****',
' LTEEQIAEFKEAFSLFDKDGDGTITTKELGTVMRSLGQNPTEAELQDMINEVDADGNGTIDFPEFLTMMARKEEEIREAFRVFDKDGNGYISAAELRHVMTNLGEKLTDEEVDEMIREADIDGDGQVNYEEFVQMMT*****',
'TEEQIAEFKEAFSLFDKDGDGTITTKELGTVMRSLGQNPTEAELQDMINEVDADG',
'ADQLTEEQIAEFKEAFSLFDKDGDGTITTKELGTVMRSLGQNPTEAELQDMINEVDADGNGTIDFPEFLTMMARKM',
'LTEEQIAEFKEAFSLFDKDGDGTITTKELGTVMRSLGQNPTEAELQDMINEVDADGNGTIDFPEFLTMMAR'
]
strings = [
'---LTEEQIAEFKEAFSLFDKDGDGTITTKELGTVMRSLGQNPTEAELQDMINEVDADGNGTIDFPEFLTMMARK------------------------------------------------------------------------*****----------------------------------------------------------------------------',
'*DQLTEEQIAEFKEAFSLFDKDGDGTITTKELGTVMRSLGQNPTEAELQDMINEVDADGNGTIDFPEFLTMMARK----------------------------------------------------------------------------MKDTDSEEEIREAFRVFDKDGNGYISAAELRHVMTNLGEKLTDEEVDEMIREADIDGDGQVNYEEFVQMMTA*****',
'*DQLTEEQIAEFKEAFSLFDKDGDGTITTKELGTVMRSLGQNPTEAELQDMINEVDADGNGTIDFPEFLTMMARKMKDTDSEEEIREAFRVFDKDGNGYISAAELRHVMTNLGEKLTDEEVDEMIREADIDGDGQVNYEEFVQMMTA*****----------------------------------------------------------------------------',
'*DQLTEEQIAEFKEAFSLFDKDGDGTITTKELGTVMRSLGQNPTEAELQDMINEVDADGNGTIDFPEFLTMMARKMKDTDSEEEIREAFRVFDKDGNGYISAAELRHVMTNLGEKLTDEEVDEMIREADIDGDGQVNYEEFVQMMTA*****----------------------------------------------------------------------------',
'*DQLTEEQIAEFKEAFSLFDKDGDGTITTKELGTVMRSLGQNPTEAELQDMINEVDADGNGTIDFPEFLTMMARKMKDTDSEEEIREAFRVFDKDGNGYISAAELRHVMTNLGEKLTDEEVDEMIREADIDGDGQVNYEEFVQMMTA*****----------------------------------------------------------------------------',
'--QLTEEQIAEFKEAFSLFDKDGDGTITTKELGTVMRSLGQNPTEAELQDMINEVDADGNGTIDFPEFLTMMARK----MKSEEEIREAFRVFDKDGNGYISAAELRHVMTNLGEKLTDEEVDEMIREADIDGDGQVNYEEFVQMMT*****----------------------------------------------------------------------------',
'---LTEEQIAEFKEAFSLFDKDGDGTITTKELGTVMRSLGQNPTEAELQDMINEVDADGNGTIDFPEFLTMMARK----MKDEEEIREAFRVFDKDGNGYISAAELRHVMTNLGEKLTDEEVDEMIREADIDGDGQVNYEEFVQMMT*****----------------------------------------------------------------------------',
'---LTEEQIAEFKEAFSLFDKDGDGTITTKELGTVMRSLGQNPTEAELQDMINEVDADGNGTIDFPEFLTMMARK-------EEEIREAFRVFDKDGNGYISAAELRHVMTNLGEKLTDEEVDEMIREADIDGDGQVNYEEFVQMMT*****----------------------------------------------------------------------------',
]
gaps = []
for i in range(len(strings)):
gaps.append([])
for j in range(len(strings[0])):
if strings[i][j] == '-':
gaps[i].append(1)
else:
gaps[i].append(0)
msa_algorithm = 'Central Star'
pairwise_algorithm = 'NW70'
matrix = 'BLOSUM62'
gap_open_penalty = 10.0
gap_extend_penalty = 1.0
end_gap_open_penalty = 0.0
end_gap_extend_penalty = 0.0
# Return the data.
return object_ids, models, molecules, sequences, strings, gaps, msa_algorithm, pairwise_algorithm, matrix, gap_open_penalty, gap_extend_penalty, end_gap_open_penalty, end_gap_extend_penalty
def test_alignment_addition(self):
"""Test the creation of a new sequence alignment object."""
# The data.
object_ids, models, molecules, sequences, strings, gaps, msa_algorithm, pairwise_algorithm, matrix, gap_open_penalty, gap_extend_penalty, end_gap_open_penalty, end_gap_extend_penalty = self.return_align_data()
# Add the alignment.
self.seq_align.add(object_ids=object_ids, models=models, molecules=molecules, sequences=sequences, strings=strings, gaps=gaps, msa_algorithm=msa_algorithm, pairwise_algorithm=pairwise_algorithm, matrix=matrix, gap_open_penalty=gap_open_penalty, gap_extend_penalty=gap_extend_penalty, end_gap_open_penalty=end_gap_open_penalty, end_gap_extend_penalty=end_gap_extend_penalty)
# Generate the expected IDs.
ids = self.generate_ids(object_ids, models, molecules)
# Check the data.
for i in range(8):
print("Checking \"%s\"" % ids[i])
self.assertEqual(self.seq_align[0].ids[i], ids[i])
self.assertEqual(self.seq_align[0].object_ids[i], object_ids[i])
self.assertEqual(self.seq_align[0].models[i], models[i])
self.assertEqual(self.seq_align[0].molecules[i], molecules[i])
self.assertEqual(self.seq_align[0].sequences[i], sequences[i])
self.assertEqual(self.seq_align[0].strings[i], strings[i])
self.assertEqual(self.seq_align[0].gaps[i], gaps[i])
self.assertEqual(self.seq_align[0].msa_algorithm, msa_algorithm)
self.assertEqual(self.seq_align[0].pairwise_algorithm, pairwise_algorithm)
self.assertEqual(self.seq_align[0].matrix, matrix)
self.assertEqual(self.seq_align[0].gap_open_penalty, gap_open_penalty)
self.assertEqual(self.seq_align[0].gap_extend_penalty, gap_extend_penalty)
self.assertEqual(self.seq_align[0].end_gap_open_penalty, end_gap_open_penalty)
self.assertEqual(self.seq_align[0].end_gap_extend_penalty, end_gap_extend_penalty)
def test_find_alignment(self):
"""Test the retrieval of pre-existing alignment."""
# Execute the body of the test_alignment_addition() unit test to set up the object.
self.test_alignment_addition()
# The identifying data.
object_ids, models, molecules, sequences, strings, gaps, msa_algorithm, pairwise_algorithm, matrix, gap_open_penalty, gap_extend_penalty, end_gap_open_penalty, end_gap_extend_penalty = self.return_align_data()
# Retrieve the alignment.
align = self.seq_align.find_alignment(object_ids=object_ids, models=models, molecules=molecules, sequences=sequences, msa_algorithm=msa_algorithm, pairwise_algorithm=pairwise_algorithm, matrix=matrix, gap_open_penalty=gap_open_penalty, gap_extend_penalty=gap_extend_penalty, end_gap_open_penalty=end_gap_open_penalty, end_gap_extend_penalty=end_gap_extend_penalty)
# Check that something was returned.
self.assertNotEqual(align, None)
# Generate the expected IDs.
ids = self.generate_ids(object_ids, models, molecules)
# Check some of the data.
for i in range(8):
print("Checking \"%s\"" % ids[i])
self.assertEqual(self.seq_align[0].object_ids[i], object_ids[i])
self.assertEqual(self.seq_align[0].models[i], models[i])
self.assertEqual(self.seq_align[0].molecules[i], molecules[i])
def test_find_missing_alignment(self):
"""Test the retrieval of non-existent alignment."""
# Execute the body of the test_alignment_addition() unit test to set up the object.
self.test_alignment_addition()
# The identifying data.
object_ids, models, molecules, sequences, strings, gaps, msa_algorithm, pairwise_algorithm, matrix, gap_open_penalty, gap_extend_penalty, end_gap_open_penalty, end_gap_extend_penalty = self.return_align_data()
# Change a gap penalty.
gap_open_penalty = 0.5
# Retrieve the alignment.
align = self.seq_align.find_alignment(object_ids=object_ids, models=models, molecules=molecules, sequences=sequences, msa_algorithm=msa_algorithm, pairwise_algorithm=pairwise_algorithm, matrix=matrix, gap_open_penalty=gap_open_penalty, gap_extend_penalty=gap_extend_penalty, end_gap_open_penalty=end_gap_open_penalty, end_gap_extend_penalty=end_gap_extend_penalty)
# Check that nothing was returned.
self.assertEqual(align, None)
