def test_remove_gaps(self):
s1 = ''.join(stats.sample_wr(translate.AAs(), 100))
others = [''.join([mut(x, 0.2,0.1) for x in s1]) for i in range(9)]
seqs = [s1]+others
als = muscle.alignSequences(seqs)
res = len(als) == len(seqs)
for i in range(len(als)):
self.assertTrue(als[i].replace("-",'') == seqs[i].replace("-",''))
def test002():
s1 = ''.join(stats.sample_wr(translate.AAs(), 100))
others = [''.join([mut(x, 0.2,0.1) for x in s1]) for i in range(9)]
seqs = [s1]+others
res = False
try:
als = muscle.alignSequences(seqs, exepath=os.path.expanduser("~/develop/muscle3.8.13/muscle"))
except muscle.MuscleError, me:
res = True
def test001():
s1 = ''.join(stats.sample_wr(translate.AAs(), 100))
others = [''.join([mut(x, 0.2,0.1) for x in s1]) for i in range(9)]
seqs = [s1]+others
als = muscle.alignSequences(seqs)
res = len(als) == len(seqs)
for i in range(len(als)):
res = res and (als[i].replace("-",'') == seqs[i].replace("-",''))
return True
def test001():
s1 = ''.join(stats.sample_wr(translate.AAs(), 100))
others = [''.join([mut(x, 0.2, 0.1) for x in s1]) for i in range(9)]
seqs = [s1] + others
als = muscle.alignSequences(seqs)
res = len(als) == len(seqs)
for i in range(len(als)):
res = res and (als[i].replace("-", '') == seqs[i].replace("-", ''))
return True
def test_remove_gaps(self):
s1 = ''.join(stats.sample_wr(translate.AAs(), 100))
others = [''.join([mut(x, 0.2, 0.1) for x in s1]) for i in range(9)]
seqs = [s1] + others
als = muscle.alignSequences(seqs)
res = len(als) == len(seqs)
for i in range(len(als)):
self.assertTrue(
als[i].replace("-", '') == seqs[i].replace("-", ''))
def test002():
s1 = ''.join(stats.sample_wr(translate.AAs(), 100))
others = [''.join([mut(x, 0.2, 0.1) for x in s1]) for i in range(9)]
seqs = [s1] + others
res = False
try:
als = muscle.alignSequences(
seqs, exepath=os.path.expanduser("~/develop/muscle3.8.13/muscle"))
except muscle.MuscleError, me:
res = True
def test_gapped_index(self):
s1 = ''.join(stats.sample_wr(translate.AAs(), 50))
# No gaps: pgap = 0.0
others = [''.join([mut(x, 0.2,0.0) for x in s1]) for i in range(9)]
seqs = [s1]+others
res = False
try:
als = muscle.alignSequences(seqs)
#print als
self.assertTrue(len(als) == len(seqs))
for (i, s) in enumerate(seqs):
self.assertTrue(s == als[i].replace("-",''))
except muscle.MuscleError as me:
self.assertTrue(False)
def test_gapped_index(self):
s1 = ''.join(stats.sample_wr(translate.AAs(), 50))
# No gaps: pgap = 0.0
others = [''.join([mut(x, 0.2, 0.0) for x in s1]) for i in range(9)]
seqs = [s1] + others
res = False
try:
als = muscle.alignSequences(seqs)
#print als
self.assertTrue(len(als) == len(seqs))
for (i, s) in enumerate(seqs):
self.assertTrue(s == als[i].replace("-", ''))
except muscle.MuscleError as me:
self.assertTrue(False)
def genMotif(aas_list, num_samples_list): """Generate a motif that has""" res = '' for (i,n) in num_samples_list: res += ''.join(stats.sample_wr(aas_list[i],n)) return res
def randomSequence(n, alphabet): return ''.join(stats.sample_wr(alphabet, n))
def randomProtein(L): aas = translate.AAs() return ''.join(stats.sample_wr(aas, L))
def randomSequence(n, alphabet): return ''.join(stats.sample_wr(alphabet, n))
def randomProtein(L):
aas = translate.AAs()
return ''.join(stats.sample_wr(aas, L))
