def setup(self):
self.seqs = ['waldemar','woldemort','vladimir']
self.msa = Multiple(self.seqs)
def msa(seqs):
return Multiple(seqs)
class TestMultiple(object):
def setup(self):
self.seqs = ['waldemar','woldemort','vladimir']
self.msa = Multiple(self.seqs)
def test_prog_align(self):
self.msa.prog_align()
assert self.msa.alm_matrix[0] == list('wal-demar-')
def test_lib_align(self):
self.msa.lib_align()
assert self.msa.alm_matrix[0] == list('w-aldemar-')
def test_get_pid(self):
self.msa.prog_align()
pid = int(self.msa.get_pid() * 100)
assert pid == 63
def test_swap_check(self):
self.msa.prog_align()
assert self.msa.swap_check()
def test_iterate_all_sequences(self):
self.msa.prog_align()
first = ''.join(self.msa.alm_matrix[0])
self.msa.iterate_all_sequences()
secnd = ''.join(self.msa.alm_matrix[0])
assert first == secnd
def test_iterate_orphans(self):
self.msa.prog_align()
first = ''.join(self.msa.alm_matrix[0])
self.msa.iterate_orphans(0.5)
secnd = ''.join(self.msa.alm_matrix[0])
assert first == secnd
def test_iterate_similar_gap_sites(self):
self.msa.prog_align()
first = ''.join(self.msa.alm_matrix[0])
self.msa.iterate_similar_gap_sites()
secnd = ''.join(self.msa.alm_matrix[0])
assert first == secnd
def test_iterate_clusters(self):
self.msa.prog_align()
first = ''.join(self.msa.alm_matrix[0])
self.msa.iterate_clusters(0.5)
secnd = ''.join(self.msa.alm_matrix[0])
assert first == secnd
def test_sum_of_pairs(self):
self.msa.prog_align()
assert 8 > self.msa.sum_of_pairs() > 7
def test_get_pairwise_alignments(self):
self.msa.prog_align()
self.msa.get_pairwise_alignments()
assert hasattr(self.msa,'alignments')
def test_get_peaks(self):
self.msa.prog_align()
assert self.msa.get_peaks()[2] == 10
def test_get_local_peaks(self):
self.msa.prog_align()
self.msa.get_local_peaks()
assert self.msa.local[0] == 0
def setUp(self):
self.seqs = ['waldemar', 'woldemort', 'vladimir']
self.msa = Multiple(self.seqs)
class Tests(TestCase):
def setUp(self):
self.seqs = ['waldemar', 'woldemort', 'vladimir']
self.msa = Multiple(self.seqs)
def test_mult_align(self):
self.assertEqual(
''.join(mult_align(['waldemar', 'woldemort', 'vladimir'])[0]),
'wal-demar-')
def test___get__(self):
self.msa.lib_align()
assert self.msa[0]
assert self.msa[0, 0]
def test_prog_align(self):
self.msa.prog_align()
assert self.msa.alm_matrix[0] == list('wal-demar-')
self.msa.prog_align(
sonars=[[1, 2, 3, 4, 1, 2, 3, 4], [1, 2, 3, 4, 5, 1, 2, 3, 4],
[1, 1, 1, 1, 1, 1, 1, 1]])
assert self.msa.alm_matrix[0] == list('wal-demar-')
def test_lib_align(self):
self.msa.lib_align()
assert self.msa.alm_matrix[0] == list('w-aldemar-')
def test_get_pid(self):
self.msa.prog_align()
pid = int(self.msa.get_pid() * 100)
assert pid == 63
def test_swap_check(self):
self.msa.prog_align()
assert self.msa.swap_check()
def test_iterate_all_sequences(self):
self.msa.prog_align()
first = ''.join(self.msa.alm_matrix[0])
self.msa.iterate_all_sequences()
secnd = ''.join(self.msa.alm_matrix[0])
assert first == secnd
def test_iterate_orphans(self):
self.msa.prog_align()
first = ''.join(self.msa.alm_matrix[0])
self.msa.iterate_orphans(0.5)
secnd = ''.join(self.msa.alm_matrix[0])
assert first == secnd
def test_iterate_similar_gap_sites(self):
self.msa.prog_align()
first = ''.join(self.msa.alm_matrix[0])
self.msa.iterate_similar_gap_sites()
secnd = ''.join(self.msa.alm_matrix[0])
assert first == secnd
def test_iterate_clusters(self):
self.msa.prog_align()
first = ''.join(self.msa.alm_matrix[0])
self.msa.iterate_clusters(0.5)
secnd = ''.join(self.msa.alm_matrix[0])
assert first == secnd
def test_sum_of_pairs(self):
self.msa.prog_align()
assert 8 > self.msa.sum_of_pairs() > 7
def test_get_pairwise_alignments(self):
self.msa.prog_align()
self.msa.get_pairwise_alignments()
assert hasattr(self.msa, 'alignments')
def test_get_peaks(self):
self.msa.prog_align()
assert self.msa.get_peaks()[2] == 10
def test_get_local_peaks(self):
self.msa.prog_align()
self.msa.get_local_peaks()
assert self.msa.local[0] == 0
class TestMultiple(object):
def setup(self):
self.seqs = ['waldemar', 'woldemort', 'vladimir']
self.msa = Multiple(self.seqs)
def test_prog_align(self):
self.msa.prog_align()
assert self.msa.alm_matrix[0] == list('wal-demar-')
def test_lib_align(self):
self.msa.lib_align()
assert self.msa.alm_matrix[0] == list('w-aldemar-')
def test_get_pid(self):
self.msa.prog_align()
pid = int(self.msa.get_pid() * 100)
assert pid == 63
def test_swap_check(self):
self.msa.prog_align()
assert self.msa.swap_check()
def test_iterate_all_sequences(self):
self.msa.prog_align()
first = ''.join(self.msa.alm_matrix[0])
self.msa.iterate_all_sequences()
secnd = ''.join(self.msa.alm_matrix[0])
assert first == secnd
def test_iterate_orphans(self):
self.msa.prog_align()
first = ''.join(self.msa.alm_matrix[0])
self.msa.iterate_orphans(0.5)
secnd = ''.join(self.msa.alm_matrix[0])
assert first == secnd
def test_iterate_similar_gap_sites(self):
self.msa.prog_align()
first = ''.join(self.msa.alm_matrix[0])
self.msa.iterate_similar_gap_sites()
secnd = ''.join(self.msa.alm_matrix[0])
assert first == secnd
def test_iterate_clusters(self):
self.msa.prog_align()
first = ''.join(self.msa.alm_matrix[0])
self.msa.iterate_clusters(0.5)
secnd = ''.join(self.msa.alm_matrix[0])
assert first == secnd
def test_sum_of_pairs(self):
self.msa.prog_align()
assert 8 > self.msa.sum_of_pairs() > 7
def test_get_pairwise_alignments(self):
self.msa.prog_align()
self.msa.get_pairwise_alignments()
assert hasattr(self.msa, 'alignments')
def test_get_peaks(self):
self.msa.prog_align()
assert self.msa.get_peaks()[2] == 10
def test_get_local_peaks(self):
self.msa.prog_align()
self.msa.get_local_peaks()
assert self.msa.local[0] == 0
class Tests(TestCase):
def setUp(self):
self.seqs = ['waldemar', 'woldemort', 'vladimir']
self.msa = Multiple(self.seqs)
def test_mult_align(self):
self.assertEqual(
''.join(mult_align(['waldemar', 'woldemort', 'vladimir'])[0]),
'wal-demar-')
def test___get__(self):
self.msa.lib_align()
assert self.msa[0]
assert self.msa[0, 0]
def test_prog_align(self):
self.msa.prog_align()
assert self.msa.alm_matrix[0] == list('wal-demar-')
self.msa.prog_align(sonars=[
[1, 2, 3, 4, 1, 2, 3, 4],
[1, 2, 3, 4, 5, 1, 2, 3, 4],
[1, 1, 1, 1, 1, 1, 1, 1]])
assert self.msa.alm_matrix[0] == list('wal-demar-')
def test_lib_align(self):
self.msa.lib_align()
assert self.msa.alm_matrix[0] == list('w-aldemar-')
def test_get_pid(self):
self.msa.prog_align()
pid = int(self.msa.get_pid() * 100)
assert pid == 63
def test_swap_check(self):
self.msa.prog_align()
assert self.msa.swap_check()
def test_iterate_all_sequences(self):
self.msa.prog_align()
first = ''.join(self.msa.alm_matrix[0])
self.msa.iterate_all_sequences()
secnd = ''.join(self.msa.alm_matrix[0])
assert first == secnd
def test_iterate_orphans(self):
self.msa.prog_align()
first = ''.join(self.msa.alm_matrix[0])
self.msa.iterate_orphans(0.5)
secnd = ''.join(self.msa.alm_matrix[0])
assert first == secnd
def test_iterate_similar_gap_sites(self):
self.msa.prog_align()
first = ''.join(self.msa.alm_matrix[0])
self.msa.iterate_similar_gap_sites()
secnd = ''.join(self.msa.alm_matrix[0])
assert first == secnd
def test_iterate_clusters(self):
self.msa.prog_align()
first = ''.join(self.msa.alm_matrix[0])
self.msa.iterate_clusters(0.5)
secnd = ''.join(self.msa.alm_matrix[0])
assert first == secnd
def test_sum_of_pairs(self):
self.msa.prog_align()
assert 8 > self.msa.sum_of_pairs() > 7
def test_get_pairwise_alignments(self):
self.msa.prog_align()
self.msa.get_pairwise_alignments()
assert hasattr(self.msa, 'alignments')
def test_get_peaks(self):
self.msa.prog_align()
assert self.msa.get_peaks()[2] == 10
def test_get_local_peaks(self):
self.msa.prog_align()
self.msa.get_local_peaks()
assert self.msa.local[0] == 0