def test_getIntMap(self):
"""Alignment.getIntMap should return correct mapping."""
aln = Alignment({'seq1':'ACGU','seq2':'CGUA','seq3':'CCGU'})
int_keys = {'seq_0':'seq1','seq_1':'seq2','seq_2':'seq3'}
int_map = {'seq_0':'ACGU','seq_1':'CGUA','seq_2':'CCGU'}
im,ik = aln.getIntMap()
self.assertEqual(ik,int_keys)
self.assertEqual(im,int_map)
def test_distance_matrix(self):
"""distance_matrix should obey RowOrder of alignment"""
#RowOrder=None
aln1_exp = array([[0,2,2],[2,0,1],[2,1,0]])
self.assertEqual(distance_matrix(self.aln1),aln1_exp)
a = Alignment(self.aln1.copy())
a.RowOrder=[1,2,0]
a_exp = array([[0,1,2],[1,0,2],[2,2,0]])
self.assertEqual(distance_matrix(a),a_exp)
def test_columnProbs(self):
"""Alignment.columnProbs should find Pr(symbol) in each column"""
#make an alignment with 4 rows (easy to calculate probabilities)
align = Alignment(["AAA", "ACA", "GGG", "GUC"])
cp = align.columnProbs()
#check that the column probs match the counts we expect
self.assertEqual(cp, map(Freqs, [
{'A':0.5, 'G':0.5},
{'A':0.25, 'C':0.25, 'G':0.25, 'U':0.25},
{'A':0.5, 'G':0.25, 'C':0.25},
]))
def ClustalParser(record, seq_constructor=Sequence, strict=True):
"""Returns contents of record as Alignment object."""
seqs, label_order = MinimalClustalParser(record, strict)
result = Alignment()
for label, seq in seqs.items():
new_seq = seq_constructor(''.join(map(strip, seq)))
try:
new_seq.Label = label
except AttributeError:
pass
result[label] = new_seq
result.RowOrder = label_order
return result
def test_toPhylip(self):
"""Alignment should return PHYLIP string format correctly"""
align_norm = Alignment( ['ACDEFGHIKLMNPQRSTUVWY-',
'ACDEFGHIKLMNPQRSUUVWF-',
'ACDEFGHIKLMNPERSKUVWC-',
'ACNEFGHIKLMNPQRS-UVWP-',
])
phylip_str, id_map = align_norm.toPhylip()
self.assertEqual(phylip_str, """4 22\nseq0000001 ACDEFGHIKLMNPQRSTUVWY-\nseq0000002 ACDEFGHIKLMNPQRSUUVWF-\nseq0000003 ACDEFGHIKLMNPERSKUVWC-\nseq0000004 ACNEFGHIKLMNPQRS-UVWP-""")
self.assertEqual(id_map, {'seq0000004': 3, 'seq0000001': 0, 'seq0000003': 2, 'seq0000002': 1})
align_rag = Alignment( ['ACDEFGHIKLMNPQRSTUVWY-',
'ACDEFGHIKLMNPQRSUUVWF-',
'ACDEFGHIKLMNPERSKUVWC-',
'ACNEFGHIKLMNUVWP-',
])
self.assertRaises(ValueError, align_rag.toPhylip)
def setUp(self):
"""Set up for Voronoi tests"""
self.aln1 = Alignment(['ABC','BCC','BAC'])
self.aln2 = Alignment({'seq1':'GYVGS','seq2':'GFDGF','seq3':'GYDGF',\
'seq4':'GYQGG'},RowOrder=['seq1','seq2','seq3','seq4'])
self.aln3 = Alignment({'seq1':'AA', 'seq2':'AA', 'seq3':'BB'},\
RowOrder=['seq1','seq2','seq3'])
self.aln4 = Alignment({'seq1':'AA', 'seq2':'AA', 'seq3':'BB',\
'seq4':'BB','seq5':'CC'},RowOrder=['seq1','seq2','seq3','seq4','seq5'])
self.aln5 = Alignment(['ABBA','ABCA','CBCB'])
def test_uncertainties(self):
"""Alignment.uncertainties should match hand-calculated values"""
aln = Alignment(['abc', 'axc'])
obs = aln.uncertainties()
self.assertFloatEqual(obs, [0, 1, 0])
#check what happens with only one input sequence
aln = Alignment(['abc'])
obs = aln.uncertainties()
self.assertFloatEqual(obs, [0, 0, 0])
#check that we can screen out bad items OK
aln = Alignment(['abc', 'def', 'ghi', 'jkl', 'GHI'])
obs = aln.uncertainties('abcdefghijklmnop')
self.assertFloatEqual(obs, [2.0] * 3)
class UtilTests(TestCase):
def setUp(self):
"""Set up for Voronoi tests"""
self.aln1 = Alignment(['ABC','BCC','BAC'])
self.aln2 = Alignment({'seq1':'GYVGS','seq2':'GFDGF','seq3':'GYDGF',\
'seq4':'GYQGG'},RowOrder=['seq1','seq2','seq3','seq4'])
self.aln3 = Alignment({'seq1':'AA', 'seq2':'AA', 'seq3':'BB'},\
RowOrder=['seq1','seq2','seq3'])
self.aln4 = Alignment({'seq1':'AA', 'seq2':'AA', 'seq3':'BB',\
'seq4':'BB','seq5':'CC'},RowOrder=['seq1','seq2','seq3','seq4','seq5'])
self.aln5 = Alignment(['ABBA','ABCA','CBCB'])
def test_number_of_pseudo_seqs(self):
"""number_of_pseudo_seqs: should return # of pseudo seqs"""
self.assertEqual(number_of_pseudo_seqs(self.aln1),6)
self.assertEqual(number_of_pseudo_seqs(self.aln2),18)
self.assertEqual(number_of_pseudo_seqs(self.aln3),4)
self.assertEqual(number_of_pseudo_seqs(self.aln4),9)
def test_pseudo_seqs_exact(self):
"""pseudo_seqs_exact: should generate expected pseudo sequences"""
self.assertEqualItems(pseudo_seqs_exact(self.aln1),\
['AAC','ABC','ACC','BAC','BBC','BCC'])
self.assertEqualItems(pseudo_seqs_exact(self.aln3),\
['AA','AB','BA','BB'])
self.assertEqual(len(pseudo_seqs_exact(self.aln2)), 18)
def test_pseudo_seqs_monte_carlo(self):
"""pseudo_seqs_monte_carlo: random sample from all possible pseudo seqs
"""
self.assertEqual(len(list(pseudo_seqs_monte_carlo(self.aln1,n=100))),\
100)
for i in pseudo_seqs_monte_carlo(self.aln3,n=100):
assert i in ['AA','AB','BA','BB']
def test_row_to_vote(self):
"""row_to_vote: should return correct votes for int and float distances
"""
self.assertEqual(row_to_vote(array([2,3,4,5])),array([1,0,0,0]))
self.assertEqual(row_to_vote(array([2,3,2,5])),array([.5,0,0.5,0]))
self.assertEqual(row_to_vote(array([2.3,3.5,2.1,5.8]))\
,array([0,0,1,0]))
def test_distance_matrix(self):
"""distance_matrix should obey RowOrder of alignment"""
#RowOrder=None
aln1_exp = array([[0,2,2],[2,0,1],[2,1,0]])
self.assertEqual(distance_matrix(self.aln1),aln1_exp)
a = Alignment(self.aln1.copy())
a.RowOrder=[1,2,0]
a_exp = array([[0,1,2],[1,0,2],[2,2,0]])
self.assertEqual(distance_matrix(a),a_exp)
def test_eigenvector_for_largest_eigenvalue(self):
"""eigenvector_for_largest_eigenvalue: No idea how to test this"""
pass
def test_distance_to_closest(self):
"""distance_to_closest: should return closest distances"""
self.assertEqual(distance_to_closest(self.aln1),[2,1,1])
self.assertEqual(distance_to_closest(self.aln2),[2,1,1,2])
def test_SeqToProfile(self):
"""SequenceToProfile: should work with different parameter settings
"""
seq = DnaSequence("ATCGRYN-")
#Only non-degenerate bases in the char order, all other
#characters are ignored. In a sequence this means that
#several positions will contain only zeros in the profile.
exp = zeros([len(seq),4],Float64)
for x,y in zip(range(len(seq)),[2,0,1,3]):
exp[x,y] = 1
self.assertEqual(SeqToProfile(seq,char_order="TCAG",\
split_degenerates=False).Data.tolist(),exp.tolist())
#Same thing should work as well when the char order is not passed in
exp = zeros([len(seq),4],Float64)
for x,y in zip(range(len(seq)),[2,0,1,3]):
exp[x,y] = 1
self.assertEqual(SeqToProfile(seq, split_degenerates=False)\
.Data.tolist(),exp.tolist())
#All symbols in the sequence are in the char order, no row
#should contain only zeros. Degenerate symbols are not split.
exp = zeros([len(seq),8],Float64)
for x,y in zip(range(len(seq)),[2,0,1,3,4,5,6,7]):
exp[x,y] = 1
self.assertEqual(SeqToProfile(seq,char_order="TCAGRYN-",\
split_degenerates=False).Data.tolist(), exp.tolist())
#splitting all degenerate symbols, having only non-degenerate symbols
#in the character order (and -)
exp = array([[0,0,1,0,0],[1,0,0,0,0],[0,1,0,0,0],[0,0,0,1,0],
[0,0,.5,.5,0],[.5,.5,0,0,0],[.25,.25,.25,.25,0],[0,0,0,0,1]])
self.assertEqual(SeqToProfile(seq,char_order="TCAG-",\
split_degenerates=True).Data.tolist(),exp.tolist())
#splitting degenerates, but having one of the degenerate
#symbols in the character order. In that case the degenerate symbol
#is not split.
exp = array([[0,0,1,0,0,0],[1,0,0,0,0,0],[0,1,0,0,0,0],[0,0,0,1,0,0],
[0,0,.5,.5,0,0],[.5,.5,0,0,0,0],[0,0,0,0,1,0],[0,0,0,0,0,1]])
self.assertEqual(SeqToProfile(seq,char_order="TCAGN-",\
split_degenerates=True).Data.tolist(),exp.tolist())
def test_AlignmentToProfile_basic(self):
"""AlignmentToProfile: should work under basic conditions
"""
#sequences in the alignment are unweighted
#Alphabet is the alphabet of the sequences (RnaAlphabet)
#CharOrder is set explicitly
#Degenerate bases are split up
#Gaps are ignored
#In all of the columns at least one character is in the CharOrder
a = Alignment({'a':RnaSequence('UCAGRYN-'),'b':RnaSequence('ACUGAAAA')})
exp =\
array([[.5,0,.5,0],
[0,1,0,0],
[.5,0,.5,0],
[0,0,0,1],
[0,0,.75,.25],
[.25,.25,.5,0],
[.125,.125,.625,.125],
[0,0,1,0]])
self.assertEqual(AlnToProfile(a,alphabet=RnaAlphabet,\
split_degenerates=True).Data.tolist(),exp.tolist())
def test_AlignmentToProfile_ignore(self):
"""AlignmentToProfile: should raise an error if too many chars ignored
"""
#Same conditions as previous function, but in the last column
#there are only gaps, so normalization will fail at that position
a = Alignment({'a':RnaSequence('UCAGRYN-'),'b':RnaSequence('ACUGAAA-')})
exp =\
array([[.5,0,.5,0],
[0,1,0,0],
[.5,0,.5,0],
[0,0,0,1],
[0,0,.75,.25],
[.25,.25,.5,0],
[.125,.125,.625,.125],
[0,0,1,0]])
self.assertRaises(ValueError,AlnToProfile,a,alphabet=RnaAlphabet,\
split_degenerates=True)
def test_AlignmentToProfile_weighted(self):
"""AlignmentToProfile: should work when sequences are weighted
"""
#Alignment: sequences are just strings and don't have an alphabet
#Weights: a normal dictionary (could be a real Weights object as well)
a = Alignment({'seq1':'TCAG','seq2':'TAR-','seq3':'YAG-'},\
RowOrder=['seq1','seq2','seq3'])
w = {'seq1':0.5,'seq2':.25,'seq3':.25}
#Error will be raised when no Alphabet is given, since the seqs
#in the alignment are just strings
self.assertRaises(AttributeError,AlnToProfile,a)
#Basic situation in which all letters in the sequences occur in the
#CharOrder, None have to be ignored. In that case it doesn't matter
#whether we set split_degenerates to True or False, because if it's
#True it's overwritten by the fact that the char is in the CharOrder.
exp = array([[0.75,0,0,0,0,.25,0],
[0,0.5,0.5,0,0,0,0],
[0,0.5,0,0.25,0.25,0,0],
[0,0,0,0.5,0,0,0.5]])
#split_degenerates = False
self.assertEqual(AlnToProfile(a,DnaAlphabet, char_order="TACGRY-",\
weights=w, split_degenerates=False).Data.tolist(),exp.tolist())
#split_degenerates = True
self.assertEqual(AlnToProfile(a,DnaAlphabet, char_order="TACGRY-",\
weights=w, split_degenerates=True).Data.tolist(),exp.tolist())
#Only non-degenerate symbols in the CharOrder. Degenerates are split.
#Gaps are ignored
exp = array([[0.875,0,0.125,0],
[0,0.5,0.5,0],
[0,0.625,0,0.375],
[0,0,0,1]])
self.assertEqual(AlnToProfile(a,DnaAlphabet, char_order="TACG",\
weights=w, split_degenerates=True).Data.tolist(),exp.tolist())
#An Error is raised if all chars in an alignment column are ignored
#CharOrder=AT, degenerates are not split.
self.assertRaises(ValueError,AlnToProfile,a,DnaAlphabet,\
char_order="AT",weights=w, split_degenerates=True)
def test_init_dict(self):
"""Alignment init from dict should work as expected"""
d = {'a':'aaaaa', 'b':'bbbbb'}
a = Alignment(d)
self.assertEqual(a, d)
self.assertEqual(a.items(), d.items())
def test_getSimilar(self):
"""Alignment getSimilar should get all sequences close to target seq"""
aln = self.many
x = Rna('gggggggggg')
y = Rna('----------')
#test min and max similarity ranges
result = aln.getSimilar(aln['a'],min_similarity=0.4,max_similarity=0.7)
for seq in 'cefg':
assert seq in result
assert result[seq] == aln[seq]
self.assertEqual(len(result), 4)
result = aln.getSimilar(aln['a'],min_similarity=0.95,max_similarity=1)
for seq in 'a':
assert seq in result
assert result[seq] == aln[seq]
self.assertEqual(len(result), 1)
result = aln.getSimilar(aln['a'], min_similarity=0.75, \
max_similarity=0.85)
for seq in 'bd':
assert seq in result
assert result[seq] == aln[seq]
self.assertEqual(len(result), 2)
result = aln.getSimilar(aln['a'],min_similarity=0,max_similarity=0.2)
self.assertEqual(len(result), 0)
#test some sequence transformations
transform = lambda s: s[1:4]
result = aln.getSimilar(aln['a'], min_similarity=0.5, \
transform=transform)
for seq in 'abdfg':
assert seq in result
assert result[seq] == aln[seq]
self.assertEqual(len(result), 5)
transform = lambda s: s[-3:]
result = aln.getSimilar(aln['a'], min_similarity=0.5, \
transform=transform)
for seq in 'abcde':
assert seq in result
assert result[seq] == aln[seq]
self.assertEqual(len(result), 5)
#test a different distance metric
metric = lambda x, y: x.count('g') + y.count('g')
result = aln.getSimilar(aln['a'], min_similarity=5, max_similarity=10, \
metric=metric)
for seq in 'ef':
assert seq in result
assert result[seq] == aln[seq]
self.assertEqual(len(result), 2)
#test the combination of a transform and a distance metric
aln = Alignment(dict(enumerate(map(Rna, ['aA-ac','A-aAC','aa-aa']))))
transform = lambda s: Rna(s.upper())
metric = RnaSequence.fracSameNonGaps
#first, do it without the transformation
result = aln.getSimilar(aln[0], min_similarity=0.5, metric=metric)
for seq in [0,2]:
assert seq in result
assert result[seq] == aln[seq]
self.assertEqual(len(result), 2)
result = aln.getSimilar(aln[0], min_similarity=0.8, metric=metric)
for seq in [0]:
assert seq in result
assert result[seq] == aln[seq]
self.assertEqual(len(result), 1)
#then, verify that the transform changes the results
result = aln.getSimilar(aln[0], min_similarity=0.5, metric=metric, \
transform=transform)
for seq in [0,1,2]:
assert seq in result
assert result[seq] == aln[seq]
self.assertEqual(len(result), 3)
result = aln.getSimilar(aln[0], min_similarity=0.8, metric=metric, \
transform=transform)
for seq in [0,1]:
assert seq in result
assert result[seq] == aln[seq]
self.assertEqual(len(result), 2)
def setUp(self):
"""Define some standard Alignment objects."""
self.empty = Alignment({})
self.one_seq = Alignment({'a':'aaaaa'})
self.ragged = Alignment({'a':'aaaaaa', 'b':'aaa', 'c':'aaaa'})
self.identical = Alignment({'a':'aaaa','b':'aaaa'})
self.gaps = Alignment({'a':'aaaaaaa','b':'a--a-aa', 'c':'aa-----'})
self.gaps_rna = Alignment({'a':Rna('aaaaaaa'), 'b':Rna('a--a-aa'), \
'c':Rna('aa-----')})
self.unordered = Alignment({'a':'aaaaa','b':'bbbbb'})
self.ordered1 = Alignment({'a':'aaaaa','b':'bbbbb'}, RowOrder=['a','b'])
self.ordered2 = Alignment({'a':'aaaaa','b':'bbbbb'}, RowOrder=['b','a'])
self.mixed = Alignment({'a':'abcde', 'b':'lmnop'})
self.end_gaps = Alignment({'a':'--a-bc-', 'b':'-cb-a--', 'c':'--d-ef-'})
self.many = Alignment({
'a': Rna('ucagucaguu'),
'b': Rna('uccgucaauu'),
'c': Rna('accaucaguc'),
'd': Rna('ucaaucgguu'),
'e': Rna('uugguugggu'),
'f': Rna('ccgggcggcc'),
'g': Rna('ucaaccggaa'),
})
#Additional Alignments for tests added 6/4/04 by Jeremy Widmann
self.integers = Alignment([[1,2,3,4,5],[1,1,1,1,1],[5,4,3,2,1]])
self.sequences = Alignment(map(RnaSequence, ['UCAG', 'UCAG', 'UCAG']))
self.structures = Alignment(map(ViennaStructure,
['(())..', '......', '(....)']), None, str)
self.labeled = Alignment(['abc', 'def'], ['1st', '2nd'])
#Additional Alignment for tests added 1/30/06 by Cathy Lozupone
self.omitRowsTemplate_aln = Alignment({
's1':Rna('UC-----CU---C'),
's2':Rna('UC------U---C'),
's3':Rna('UUCCUUCUU-UUC'),
's4':Rna('UU-UUUU-UUUUC'),
's5':Rna('-------------')
})
class AlignmentTests(TestCase):
"""Tests of the Alignment object."""
def setUp(self):
"""Define some standard Alignment objects."""
self.empty = Alignment({})
self.one_seq = Alignment({'a':'aaaaa'})
self.ragged = Alignment({'a':'aaaaaa', 'b':'aaa', 'c':'aaaa'})
self.identical = Alignment({'a':'aaaa','b':'aaaa'})
self.gaps = Alignment({'a':'aaaaaaa','b':'a--a-aa', 'c':'aa-----'})
self.gaps_rna = Alignment({'a':Rna('aaaaaaa'), 'b':Rna('a--a-aa'), \
'c':Rna('aa-----')})
self.unordered = Alignment({'a':'aaaaa','b':'bbbbb'})
self.ordered1 = Alignment({'a':'aaaaa','b':'bbbbb'}, RowOrder=['a','b'])
self.ordered2 = Alignment({'a':'aaaaa','b':'bbbbb'}, RowOrder=['b','a'])
self.mixed = Alignment({'a':'abcde', 'b':'lmnop'})
self.end_gaps = Alignment({'a':'--a-bc-', 'b':'-cb-a--', 'c':'--d-ef-'})
self.many = Alignment({
'a': Rna('ucagucaguu'),
'b': Rna('uccgucaauu'),
'c': Rna('accaucaguc'),
'd': Rna('ucaaucgguu'),
'e': Rna('uugguugggu'),
'f': Rna('ccgggcggcc'),
'g': Rna('ucaaccggaa'),
})
#Additional Alignments for tests added 6/4/04 by Jeremy Widmann
self.integers = Alignment([[1,2,3,4,5],[1,1,1,1,1],[5,4,3,2,1]])
self.sequences = Alignment(map(RnaSequence, ['UCAG', 'UCAG', 'UCAG']))
self.structures = Alignment(map(ViennaStructure,
['(())..', '......', '(....)']), None, str)
self.labeled = Alignment(['abc', 'def'], ['1st', '2nd'])
#Additional Alignment for tests added 1/30/06 by Cathy Lozupone
self.omitRowsTemplate_aln = Alignment({
's1':Rna('UC-----CU---C'),
's2':Rna('UC------U---C'),
's3':Rna('UUCCUUCUU-UUC'),
's4':Rna('UU-UUUU-UUUUC'),
's5':Rna('-------------')
})
def test_init_dict(self):
"""Alignment init from dict should work as expected"""
d = {'a':'aaaaa', 'b':'bbbbb'}
a = Alignment(d)
self.assertEqual(a, d)
self.assertEqual(a.items(), d.items())
def test_init_seq(self):
"""Alignment init from list of sequences should use indices as keys"""
seqs = ['aaaaa', 'bbbbb', 'ccccc']
a = Alignment(seqs)
self.assertEqual(len(a), 3)
self.assertEqual(a[0], 'aaaaa')
self.assertEqual(a[1], 'bbbbb')
self.assertEqual(a[2], 'ccccc')
self.assertEqual(a.RowOrder, [0,1,2])
self.assertEqual(list(a.Rows), ['aaaaa','bbbbb','ccccc'])
def test_init_pairs(self):
"""Alignment init from list of (key,val) pairs should work correctly"""
seqs = [['x', 'xxx'], ['b','bbb'], ['c','ccc']]
a = Alignment(seqs)
self.assertEqual(len(a), 3)
self.assertEqual(a['x'], 'xxx')
self.assertEqual(a['b'], 'bbb')
self.assertEqual(a['c'], 'ccc')
self.assertEqual(a.RowOrder, ['x','b','c'])
self.assertEqual(list(a.Rows), ['xxx','bbb','ccc'])
def test_init_ordered(self):
"""Alignment should iterate over rows correctly even if ordered"""
first = self.ordered1
sec = self.ordered2
un = self.unordered
self.assertEqual(first.RowOrder, ['a','b'])
self.assertEqual(sec.RowOrder, ['b', 'a'])
self.assertEqual(un.RowOrder, un.keys())
first_list = list(first.Rows)
sec_list = list(sec.Rows)
un_list = list(un.Rows)
self.assertEqual(first_list, ['aaaaa','bbbbb'])
self.assertEqual(sec_list, ['bbbbb','aaaaa'])
#check that the unordered seq matches one of the lists
assert (un_list == first_list) or (un_list == sec_list)
self.assertNotEqual(first_list, sec_list)
def test_SeqLen_get(self):
"""Alignment SeqLen should return length of longest seq"""
self.assertEqual(self.empty.SeqLen, 0)
self.assertEqual(self.one_seq.SeqLen, 5)
self.assertEqual(self.ragged.SeqLen, 6)
self.assertEqual(self.identical.SeqLen, 4)
self.assertEqual(self.gaps.SeqLen, 7)
def test_SeqLen_set(self):
"""Alignment SeqLen assignment should pad or truncate sequences"""
#if there are no sequences, SeqLen will always be 0
a = self.empty
a.SeqLen = 5
self.assertEqual(a.SeqLen, 0)
a = self.one_seq
a.SeqLen = 10
self.assertEqual(a['a'], 'aaaaa-----')
a.SeqLen = 2
self.assertEqual(a['a'], 'aa')
a = self.ragged
a.SeqLen = None
self.assertEqual(a, {'a':'aaaaaa', 'b':'aaa---', 'c':'aaaa--'})
a.SeqLen = 8
self.assertEqual(a, {'a':'aaaaaa--','b':'aaa-----','c':'aaaa----'})
a.SeqLen = 2
self.assertEqual(a, {'a':'aa','b':'aa','c':'aa'})
a.DefaultGap = '~'
a.SeqLen = 4
self.assertEqual(a, {'a':'aa~~','b':'aa~~','c':'aa~~'})
def test_Rows(self):
"""Alignment Rows property should return rows in correct order."""
first = self.ordered1
sec = self.ordered2
un = self.unordered
first_list = list(first.Rows)
sec_list = list(sec.Rows)
un_list = list(un.Rows)
self.assertEqual(first_list, ['aaaaa','bbbbb'])
self.assertEqual(sec_list, ['bbbbb','aaaaa'])
#check that the unordered seq matches one of the lists
assert (un_list == first_list) or (un_list == sec_list)
self.assertNotEqual(first_list, sec_list)
#should work on empty alignment
self.assertEqual(list(self.empty.Rows), [])
#should work on ragged alignment
self.ragged.RowOrder = 'bac'
self.assertEqual(list(self.ragged.Rows), ['aaa', 'aaaaaa', 'aaaa'])
def test_iterRows(self):
"""Alignment iterRows() method should support reordering of rows"""
self.assertEqual(list(self.empty.iterRows()), [])
self.ragged.RowOrder = ['a','b','c']
rows = list(self.ragged.iterRows())
self.assertEqual(rows, ['aaaaaa', 'aaa', 'aaaa'])
rows = list(self.ragged.iterRows(row_order=['b','a','a']))
self.assertEqual(rows, ['aaa', 'aaaaaa', 'aaaaaa'])
assert rows[1] is rows[2]
assert rows[0] is self.ragged['b']
def test_Cols(self):
"""Alignment Cols property should iterate over columns, using self.RowOrder"""
r = self.ragged
self.assertRaises(IndexError, list, r.Cols)
r.SeqLen = None
r.RowOrder = ['a','b','c']
self.assertEqual(list(r.Cols), map(list, \
['aaa','aaa','aaa', 'a-a', 'a--', 'a--']))
#should work on empty alignment
self.assertEqual(list(self.empty.Cols), [])
def test_iterCols(self):
"""Alignment iterCols() method should support reordering of cols"""
r = self.ragged
self.assertRaises(IndexError, list, r.iterCols(col_order=[5,1,3]))
r.RowOrder = 'cb'
r.SeqLen = None
self.assertEqual(list(r.iterCols(col_order=[5,1,3])),\
map(list,['--','aa','a-']))
r.RowOrder = ['a','b','c']
cols = list(self.ragged.iterCols())
self.assertEqual(cols, map(list, ['aaa','aaa','aaa','a-a','a--','a--']))
def test_Items(self):
"""Alignment Items should iterate over items in specified order."""
#should work on empty alignment
self.assertEqual(list(self.empty.Items), [])
#should work if one row
self.assertEqual(list(self.one_seq.Items), ['a']*5)
#should work on ragged alignment
self.assertEqual(list(self.ragged.Items), ['a']*13)
#should take order into account
self.assertEqual(list(self.ordered1.Items), ['a']*5 + ['b']*5)
self.assertEqual(list(self.ordered2.Items), ['b']*5 + ['a']*5)
def test_iterItems(self):
"""Alignment iterItems() should iterate over items in correct order"""
#should work on empty alignment
self.assertEqual(list(self.empty.iterItems()), [])
#should work if one row
self.assertEqual(list(self.one_seq.iterItems()), ['a']*5)
#should work on ragged alignment
self.assertEqual(list(self.ragged.iterItems()), ['a']*13)
#should take order into account
self.assertEqual(list(self.ordered1.iterItems()), ['a']*5 + ['b']*5)
self.assertEqual(list(self.ordered2.iterItems()), ['b']*5 + ['a']*5)
#should allow row and/or col specification
self.assertRaises(IndexError, list, self.ragged.iterItems(\
row_order=['c','b'], col_order=[5,1,3]))
self.ragged.SeqLen = None
self.assertEqual(list(self.ragged.iterItems(row_order=['c','b'], \
col_order=[5,1,3])), list('-aa-a-'))
#should not interfere with superclass iteritems()
i = list(self.ragged.iteritems()) #remember, we padded self.ragged above
i.sort()
self.assertEqual(i, [('a','aaaaaa'),('b','aaa---'),('c','aaaa--')])
def test_getRows(self):
"""Alignment getRows should return new Alignment with selected rows."""
self.assertRaises(KeyError, self.empty.getRows, ['a'])
a = self.ragged.getRows('bc')
assert isinstance(a, Alignment)
self.assertEqual(a, {'b':'aaa','c':'aaaa'})
#should be able to negate
a = self.ragged.getRows('bc', negate=True)
self.assertEqual(a, {'a':'aaaaaa'})
def test_getRowIndices(self):
"""Alignment getRowIndices should return names of rows where f(row) is True"""
is_long = lambda x: len(x) > 10
is_med = lambda x: len(x) > 3
is_any = lambda x: len(x) > 0
self.assertEqual(self.ragged.getRowIndices(is_long), [])
self.ragged.RowOrder = 'cba'
self.assertEqual(self.ragged.getRowIndices(is_med), ['c','a'])
self.ragged.RowOrder = 'abc'
self.assertEqual(self.ragged.getRowIndices(is_med), ['a','c'])
self.assertEqual(self.ragged.getRowIndices(is_any), ['a','b','c'])
#should be able to negate
self.assertEqual(self.ragged.getRowIndices(is_med, negate=True), ['b'])
self.assertEqual(self.ragged.getRowIndices(is_any, negate=True), [])
def test_getRowsIf(self):
"""Alignment getRowsIf should return rows where f(row) is True"""
is_long = lambda x: len(x) > 10
is_med = lambda x: len(x) > 3
is_any = lambda x: len(x) > 0
self.assertEqual(self.ragged.getRowsIf(is_long), {})
self.ragged.RowOrder = 'cba'
self.assertEqual(self.ragged.getRowsIf(is_med), \
{'c':'aaaa','a':'aaaaaa'})
self.ragged.RowOrder = None
self.assertEqual(self.ragged.getRowsIf(is_med), \
{'c':'aaaa','a':'aaaaaa'})
self.assertEqual(self.ragged.getRowsIf(is_any), self.ragged)
assert isinstance(self.ragged.getRowsIf(is_med), Alignment)
#should be able to negate
self.assertEqual(self.ragged.getRowsIf(is_med, negate=True), \
{'b':'aaa'})
def test_getCols(self):
"""Alignment getCols should return new alignment w/ specified columns"""
self.assertEqual(self.empty.getCols([0]), {})
self.assertEqual(self.gaps.getCols([5,4,0], row_constructor=''.join), \
{'a':'aaa','b':'a-a','c':'--a'})
assert isinstance(self.gaps.getCols([0]), Alignment)
#should be able to negate
self.assertEqual(self.gaps.getCols([5,4,0], negate=True, \
row_constructor=''.join),
{'a':'aaaa','b':'--aa','c':'a---'})
def test_getColIndices(self):
"""Alignment getColIndices should return names of cols where f(col) is True"""
gap_1st = lambda x: x[0] == '-'
gap_2nd = lambda x: x[1] == '-'
gap_3rd = lambda x: x[2] == '-'
is_list = lambda x: isinstance(x, list)
self.gaps.RowOrder = 'abc'
self.assertEqual(self.gaps.getColIndices(gap_1st), [])
self.assertEqual(self.gaps.getColIndices(gap_2nd), [1,2,4])
self.assertEqual(self.gaps.getColIndices(gap_3rd), [2,3,4,5,6])
self.assertEqual(self.gaps.getColIndices(is_list), [0,1,2,3,4,5,6])
#should be able to negate
self.assertEqual(self.gaps.getColIndices(gap_2nd, negate=True), \
[0,3,5,6])
self.assertEqual(self.gaps.getColIndices(gap_1st, negate=True), \
[0,1,2,3,4,5,6])
self.assertEqual(self.gaps.getColIndices(is_list, negate=True), [])
def test_getColsIf(self):
"""Alignment getColsIf should return cols where f(col) is True"""
gap_1st = lambda x: x[0] == '-'
gap_2nd = lambda x: x[1] == '-'
gap_3rd = lambda x: x[2] == '-'
is_list = lambda x: isinstance(x, list)
self.gaps.RowOrder = 'abc'
self.assertEqual(self.gaps.getColsIf(gap_1st,row_constructor=''.join),\
{'a':'', 'b':'', 'c':''})
self.assertEqual(self.gaps.getColsIf(gap_2nd,row_constructor=''.join),\
{'a':'aaa', 'b':'---', 'c':'a--'})
self.assertEqual(self.gaps.getColsIf(gap_3rd,row_constructor=''.join),\
{'a':'aaaaa', 'b':'-a-aa', 'c':'-----'})
self.assertEqual(self.gaps.getColsIf(is_list,row_constructor=''.join),\
self.gaps)
assert isinstance(self.gaps.getColsIf(gap_1st), Alignment)
#should be able to negate
self.assertEqual(self.gaps.getColsIf(gap_1st, row_constructor=''.join,\
negate=True), self.gaps)
self.assertEqual(self.gaps.getColsIf(gap_2nd, row_constructor=''.join,\
negate=True), {'a':'aaaa','b':'aaaa','c':'a---'})
self.assertEqual(self.gaps.getColsIf(gap_3rd, row_constructor=''.join,\
negate=True), {'a':'aa','b':'a-','c':'aa'})
def test_getItems(self):
"""Alignment getItems should return list of items from k,v pairs"""
self.assertEqual(self.mixed.getItems([('a',3),('b',4),('a',0)]), \
['d','p','a'])
self.assertRaises(KeyError, self.mixed.getItems, [('x','y')])
self.assertRaises(IndexError, self.mixed.getItems, [('a',1000)])
#should be able to negate -- note that results will have rows in
#arbitrary order
self.assertEqualItems(self.mixed.getItems([('a',3),('b',4),('a',0)], \
negate=True), ['b','c','e','l','m','n','o'])
def test_getItemIndices(self):
"""Alignment getItemIndices should return coordinates of matching items"""
is_vowel = lambda x: x in 'aeiou'
self.mixed.RowOrder = 'ba' #specify reverse order
self.assertEqual(self.mixed.getItemIndices(is_vowel), \
[('b',3),('a',0),('a',4)])
not_vowel = lambda x: not is_vowel(x)
self.assertEqual(self.ragged.getItemIndices(not_vowel), [])
#should be able to negate
self.assertEqualItems(self.mixed.getItemIndices(is_vowel, negate=True),\
[('a',1),('a',2),('a',3),('b',0),('b',1),('b',2),('b',4)])
def test_getItemsIf(self):
"""Alignment getItemsIf should return matching items"""
is_vowel = lambda x: x in 'aeiou'
self.mixed.RowOrder = 'ba'
self.assertEqual(self.mixed.getItemsIf(is_vowel), ['o','a','e'])
self.assertEqual(self.empty.getItemsIf(is_vowel), [])
self.assertEqual(self.one_seq.getItemsIf(is_vowel), list('aaaaa'))
#should be able to negate
self.assertEqualItems(self.mixed.getItemsIf(is_vowel, negate=True), \
list('bcdlmnp'))
def test_getSimilar(self):
"""Alignment getSimilar should get all sequences close to target seq"""
aln = self.many
x = Rna('gggggggggg')
y = Rna('----------')
#test min and max similarity ranges
result = aln.getSimilar(aln['a'],min_similarity=0.4,max_similarity=0.7)
for seq in 'cefg':
assert seq in result
assert result[seq] == aln[seq]
self.assertEqual(len(result), 4)
result = aln.getSimilar(aln['a'],min_similarity=0.95,max_similarity=1)
for seq in 'a':
assert seq in result
assert result[seq] == aln[seq]
self.assertEqual(len(result), 1)
result = aln.getSimilar(aln['a'], min_similarity=0.75, \
max_similarity=0.85)
for seq in 'bd':
assert seq in result
assert result[seq] == aln[seq]
self.assertEqual(len(result), 2)
result = aln.getSimilar(aln['a'],min_similarity=0,max_similarity=0.2)
self.assertEqual(len(result), 0)
#test some sequence transformations
transform = lambda s: s[1:4]
result = aln.getSimilar(aln['a'], min_similarity=0.5, \
transform=transform)
for seq in 'abdfg':
assert seq in result
assert result[seq] == aln[seq]
self.assertEqual(len(result), 5)
transform = lambda s: s[-3:]
result = aln.getSimilar(aln['a'], min_similarity=0.5, \
transform=transform)
for seq in 'abcde':
assert seq in result
assert result[seq] == aln[seq]
self.assertEqual(len(result), 5)
#test a different distance metric
metric = lambda x, y: x.count('g') + y.count('g')
result = aln.getSimilar(aln['a'], min_similarity=5, max_similarity=10, \
metric=metric)
for seq in 'ef':
assert seq in result
assert result[seq] == aln[seq]
self.assertEqual(len(result), 2)
#test the combination of a transform and a distance metric
aln = Alignment(dict(enumerate(map(Rna, ['aA-ac','A-aAC','aa-aa']))))
transform = lambda s: Rna(s.upper())
metric = RnaSequence.fracSameNonGaps
#first, do it without the transformation
result = aln.getSimilar(aln[0], min_similarity=0.5, metric=metric)
for seq in [0,2]:
assert seq in result
assert result[seq] == aln[seq]
self.assertEqual(len(result), 2)
result = aln.getSimilar(aln[0], min_similarity=0.8, metric=metric)
for seq in [0]:
assert seq in result
assert result[seq] == aln[seq]
self.assertEqual(len(result), 1)
#then, verify that the transform changes the results
result = aln.getSimilar(aln[0], min_similarity=0.5, metric=metric, \
transform=transform)
for seq in [0,1,2]:
assert seq in result
assert result[seq] == aln[seq]
self.assertEqual(len(result), 3)
result = aln.getSimilar(aln[0], min_similarity=0.8, metric=metric, \
transform=transform)
for seq in [0,1]:
assert seq in result
assert result[seq] == aln[seq]
self.assertEqual(len(result), 2)
def test_omitGapCols(self):
"""Alignment omitGapCols should return alignment w/o columns of gaps"""
aln = self.end_gaps
#first, check behavior when we're just acting on the cols (and not
#trying to delete the naughty rows).
#default should strip out cols that are 100% gaps
self.assertEqual(aln.omitGapCols(row_constructor=''.join), \
{'a':'-abc', 'b':'cba-', 'c':'-def'})
#if allowed_gap_frac is 1, shouldn't delete anything
self.assertEqual(aln.omitGapCols(1, row_constructor=''.join), \
{'a':'--a-bc-', 'b':'-cb-a--', 'c':'--d-ef-'})
#if allowed_gap_frac is 0, should strip out any cols containing gaps
self.assertEqual(aln.omitGapCols(0, row_constructor=''.join), \
{'a':'ab', 'b':'ba', 'c':'de'})
#intermediate numbers should work as expected
self.assertEqual(aln.omitGapCols(0.4, row_constructor=''.join), \
{'a':'abc', 'b':'ba-', 'c':'def'})
self.assertEqual(aln.omitGapCols(0.7, row_constructor=''.join), \
{'a':'-abc', 'b':'cba-', 'c':'-def'})
#check that it doesn't fail on an empty alignment
self.assertEqual(self.empty.omitGapCols(), {})
#second, need to check behavior when the naughty rows should be
#deleted as well.
#default should strip out cols that are 100% gaps
self.assertEqual(aln.omitGapCols(row_constructor=''.join, \
del_rows=True), {'a':'-abc', 'b':'cba-', 'c':'-def'})
#if allowed_gap_frac is 1, shouldn't delete anything
self.assertEqual(aln.omitGapCols(1, row_constructor=''.join, \
del_rows=True), {'a':'--a-bc-', 'b':'-cb-a--', 'c':'--d-ef-'})
#if allowed_gap_frac is 0, should strip out any cols containing gaps
self.assertEqual(aln.omitGapCols(0, row_constructor=''.join, \
del_rows=True), {}) #everything has at least one naughty non-gap
#intermediate numbers should work as expected
self.assertEqual(aln.omitGapCols(0.4, row_constructor=''.join,
del_rows=True), {'a':'abc', 'c':'def'}) #b has a naughty non-gap
#check that does not delete b if allowed_frac_bad_calls higher than 0.14
self.assertEqual(aln.omitGapCols(0.4, row_constructor=''.join,
del_rows=True, allowed_frac_bad_cols=0.2), \
{'a':'abc', 'b':'ba-','c':'def'})
self.assertEqual(aln.omitGapCols(0.4, row_constructor=''.join,
del_rows=True), {'a':'abc', 'c':'def'}) #b has a naughty non-gap
self.assertEqual(aln.omitGapCols(0.7, row_constructor=''.join,
del_rows=True), {'a':'-abc', 'b':'cba-', 'c':'-def'}) #all ok
#check that it doesn't fail on an empty alignment
self.assertEqual(self.empty.omitGapCols(del_rows=True), {})
#when we increase the number of sequences to 6, more differences
#start to appear.
aln['d'] = '-------'
aln['e'] = 'xyzxyzx'
aln['f'] = 'ab-cdef'
#if no gaps are allowed, everything is deleted...
self.assertEqual(aln.omitGapCols(0, del_rows=False), \
{'a':[], 'b':[], 'c':[], 'd':[], 'e':[], 'f':[]})
#...though not a sequence that's all gaps, since it has no positions
#that are not gaps. This 'feature' should possibly be considered a bug.
self.assertEqual(aln.omitGapCols(0, del_rows=True), {'d':[]})
#if we're deleting only full columns of gaps, del_rows does nothing.
self.assertEqual(aln.omitGapCols(del_rows=True, \
row_constructor=''.join), aln)
#at 50%, should delete a bunch of minority sequences
self.assertEqual(aln.omitGapCols(0.5, del_rows=True, \
row_constructor=''.join), \
{'a':'-abc','b':'cba-','c':'-def','d':'----'})
#shouldn't depend on order of rows
aln.RowOrder = 'fadbec'
self.assertEqual(aln.omitGapCols(0.5, del_rows=True, \
row_constructor=''.join), \
{'a':'-abc','b':'cba-','c':'-def','d':'----'})
def test_omitGapRows(self):
"""Alignment omitGapRows should return alignment w/o rows with gaps"""
#check default params
self.assertEqual(self.gaps.omitGapRows(), self.gaps.omitGapRows(0))
#check for boundary effects
self.assertEqual(self.gaps.omitGapRows(-1), {})
self.assertEqual(self.gaps.omitGapRows(0), {'a':'aaaaaaa'})
self.assertEqual(self.gaps.omitGapRows(0.1), {'a':'aaaaaaa'})
self.assertEqual(self.gaps.omitGapRows(3.0/7 - 0.01), {'a':'aaaaaaa'})
self.assertEqual(self.gaps.omitGapRows(3.0/7), \
{'a':'aaaaaaa','b':'a--a-aa'})
self.assertEqual(self.gaps.omitGapRows(3.0/7 + 0.01), \
{'a':'aaaaaaa','b':'a--a-aa'})
self.assertEqual(self.gaps.omitGapRows(5.0/7 - 0.01), \
{'a':'aaaaaaa','b':'a--a-aa'})
self.assertEqual(self.gaps.omitGapRows(5.0/7 + 0.01), self.gaps)
self.assertEqual(self.gaps.omitGapRows(0.99), self.gaps)
#check new object creation
assert self.gaps.omitGapRows(0.99) is not self.gaps
assert isinstance(self.gaps.omitGapRows(3.0/7), Alignment)
#repeat tests for object that supplies its own gaps
self.assertEqual(self.gaps_rna.omitGapRows(-1), {})
self.assertEqual(self.gaps_rna.omitGapRows(0), {'a':'aaaaaaa'})
self.assertEqual(self.gaps_rna.omitGapRows(0.1), {'a':'aaaaaaa'})
self.assertEqual(self.gaps_rna.omitGapRows(3.0/7 - 0.01), \
{'a':'aaaaaaa'})
self.assertEqual(self.gaps_rna.omitGapRows(3.0/7), \
{'a':'aaaaaaa','b':'a--a-aa'})
self.assertEqual(self.gaps_rna.omitGapRows(3.0/7 + 0.01), \
{'a':'aaaaaaa','b':'a--a-aa'})
self.assertEqual(self.gaps_rna.omitGapRows(5.0/7 - 0.01), \
{'a':'aaaaaaa','b':'a--a-aa'})
self.assertEqual(self.gaps_rna.omitGapRows(5.0/7 + 0.01), self.gaps_rna)
self.assertEqual(self.gaps_rna.omitGapRows(0.99), self.gaps_rna)
assert self.gaps_rna.omitGapRows(0.99) is not self.gaps_rna
assert isinstance(self.gaps_rna.omitGapRows(3.0/7), Alignment)
def test_omitGapRuns(self):
"""Alignment omitGapRuns should return alignment w/o runs of gaps"""
#negative value will still let through ungapped sequences
self.assertEqual(self.gaps.omitGapRuns(-5), {'a':'aaaaaaa'})
#test edge effects
self.assertEqual(self.gaps.omitGapRuns(0), {'a':'aaaaaaa'})
self.assertEqual(self.gaps.omitGapRuns(1), {'a':'aaaaaaa'})
self.assertEqual(self.gaps.omitGapRuns(2),{'a':'aaaaaaa','b':'a--a-aa'})
self.assertEqual(self.gaps.omitGapRuns(3),{'a':'aaaaaaa','b':'a--a-aa'})
self.assertEqual(self.gaps.omitGapRuns(4),{'a':'aaaaaaa','b':'a--a-aa'})
self.assertEqual(self.gaps.omitGapRuns(5), self.gaps)
self.assertEqual(self.gaps.omitGapRuns(6), self.gaps)
self.assertEqual(self.gaps.omitGapRuns(1000), self.gaps)
#test new object creation
assert self.gaps.omitGapRuns(6) is not self.gaps
assert isinstance(self.gaps.omitGapRuns(6), Alignment)
def test_distanceMatrix(self):
"""Alignment distanceMatrix should produce correct scores"""
self.assertEqual(self.empty.distanceMatrix(frac_same), {})
self.assertEqual(self.one_seq.distanceMatrix(frac_same), {'a':{'a':1}})
self.assertEqual(self.gaps.distanceMatrix(frac_same),
{ 'a':{'a':7/7.0,'b':4/7.0,'c':2/7.0},
'b':{'a':4/7.0,'b':7/7.0,'c':3/7.0},
'c':{'a':2/7.0,'b':3/7.0,'c':7/7.0},
})
def test_IUPACConsensus_RNA(self):
"""Alignment IUPACConsensus should use RNA IUPAC symbols correctly"""
alignmentUpper = Alignment( ['UCAGN-UCAGN-UCAGN-UCAGAGCAUN-',
'UUCCAAGGNN--UUCCAAGGNNAGCAG--',
'UUCCAAGGNN--UUCCAAGGNNAGCUA--',
'UUUUCCCCAAAAGGGGNNNN--AGCUA--',
'UUUUCCCCAAAAGGGGNNNN--AGCUA--',
])
alignmentLower = Alignment( ['ucagn-ucagn-ucagn-ucagagcaun-',
'uuccaaggnn--uuccaaggnnagcag--',
'uuccaaggnn--uuccaaggnnagcua--',
'uuuuccccaaaaggggnnnn--agcua--',
'uuuuccccaaaaggggnnnn--agcua--',
])
alignmentMixed = Alignment( ['ucagn-ucagn-ucagn-ucagagcaun-',
'UUCCAAGGNN--UUCCAAGGNNAGCAG--',
'uuccaaggnn--uuccaaggnnagcua--',
'UUUUCCCCAAAAGGGGNNNN--AGCUA--',
'uuuuccccaaaaggggnnnn--agcua--',
])
#following IUPAC consensus calculated by hand
#Test all uppper
self.assertEqual(alignmentUpper.IUPACConsensus(),
'UYHBN?BSNN??KBVSN?NN??AGCWD?-')
#Test all lower
self.assertEqual(alignmentLower.IUPACConsensus(),
'uyhbn?bsnn??kbvsn?nn??agcwd?-')
#Test mixed case
self.assertEqual(alignmentMixed.IUPACConsensus(),
'UYHBN?BSNN??KBVSN?NN??AGCWD?-')
def test_IUPACConsensus_DNA(self):
"""Alignment IUPACConsensus should use DNA IUPAC symbols correctly"""
alignmentUpper = Alignment( ['TCAGN-TCAGN-TCAGN-TCAGAGCATN-',
'TTCCAAGGNN--TTCCAAGGNNAGCAG--',
'TTCCAAGGNN--TTCCAAGGNNAGCTA--',
'TTTTCCCCAAAAGGGGNNNN--AGCTA--',
'TTTTCCCCAAAAGGGGNNNN--AGCTA--',
])
alignmentLower = Alignment( ['tcagn-tcagn-tcagn-tcagagcatn-',
'ttccaaggnn--ttccaaggnnagcag--',
'ttccaaggnn--ttccaaggnnagcta--',
'ttttccccaaaaggggnnnn--agcta--',
'ttttccccaaaaggggnnnn--agcta--',
])
alignmentMixed = Alignment( ['tcagn-tcagn-tcagn-tcagagcatn-',
'TTCCAAGGNN--TTCCAAGGNNAGCAG--',
'ttccaaggnn--ttccaaggnnagcta--',
'TTTTCCCCAAAAGGGGNNNN--AGCTA--',
'ttttccccaaaaggggnnnn--agcta--',
])
#following IUPAC consensus calculated by hand
#Test all uppper
self.assertEqual(alignmentUpper.IUPACConsensus(DnaAlphabet),
'TYHBN?BSNN??KBVSN?NN??AGCWD?-')
#Test all lower
self.assertEqual(alignmentLower.IUPACConsensus(DnaAlphabet),
'tyhbn?bsnn??kbvsn?nn??agcwd?-')
#Test mixed case
self.assertEqual(alignmentMixed.IUPACConsensus(DnaAlphabet),
'TYHBN?BSNN??KBVSN?NN??AGCWD?-')
def test_IUPACConsensus_Protein(self):
"""Alignment IUPACConsensus should use protein IUPAC symbols correctly"""
alignmentUpper = Alignment( ['ACDEFGHIKLMNPQRSTUVWY-',
'ACDEFGHIKLMNPQRSUUVWF-',
'ACDEFGHIKLMNPERSKUVWC-',
'ACNEFGHIKLMNPQRS-UVWP-',
])
alignmentLower = Alignment( ['acdefghiklmnpqrstuvwy-',
'acdefghiklmnpqrsuuvwf-',
'acdefghiklmnperskuvwc-',
'acnefghiklmnpqrs-uvwp-',
])
alignmentMixed = Alignment( ['acdefghiklmnpqrstuvwy-',
'ACDEFGHIKLMNPQRSUUVWF-',
'acdefghiklmnperskuvwc-',
'ACNEFGHIKLMNPQRS-UVWP-',
])
#following IUPAC consensus calculated by hand
#Test all uppper
self.assertEqual(alignmentUpper.IUPACConsensus(ProteinAlphabet),
'ACBEFGHIKLMNPZRS?UVWx-')
#Test all lower
self.assertEqual(alignmentLower.IUPACConsensus(ProteinAlphabet),
'acbefghiklmnpzrs?uvwx-')
#Test mixed case
self.assertEqual(alignmentMixed.IUPACConsensus(ProteinAlphabet),
'ACBEFGHIKLMNPZRS?UVWx-')
def test_toPhylip(self):
"""Alignment should return PHYLIP string format correctly"""
align_norm = Alignment( ['ACDEFGHIKLMNPQRSTUVWY-',
'ACDEFGHIKLMNPQRSUUVWF-',
'ACDEFGHIKLMNPERSKUVWC-',
'ACNEFGHIKLMNPQRS-UVWP-',
])
phylip_str, id_map = align_norm.toPhylip()
self.assertEqual(phylip_str, """4 22\nseq0000001 ACDEFGHIKLMNPQRSTUVWY-\nseq0000002 ACDEFGHIKLMNPQRSUUVWF-\nseq0000003 ACDEFGHIKLMNPERSKUVWC-\nseq0000004 ACNEFGHIKLMNPQRS-UVWP-""")
self.assertEqual(id_map, {'seq0000004': 3, 'seq0000001': 0, 'seq0000003': 2, 'seq0000002': 1})
align_rag = Alignment( ['ACDEFGHIKLMNPQRSTUVWY-',
'ACDEFGHIKLMNPQRSUUVWF-',
'ACDEFGHIKLMNPERSKUVWC-',
'ACNEFGHIKLMNUVWP-',
])
self.assertRaises(ValueError, align_rag.toPhylip)
def test_isRagged(self):
"""Alignment isRagged should return true if ragged alignment"""
assert(self.ragged.isRagged())
assert(not self.identical.isRagged())
assert(not self.gaps.isRagged())
def test_scoreMatrix(self):
"""Alignment scoreMatrix should produce position specific score matrix."""
scoreMatrix = {
0:{'a':1.0,'c':1.0,'u':5.0},
1:{'c':6.0,'u':1.0},
2:{'a':3.0,'c':2.0,'g':2.0},
3:{'a':3.0,'g':4.0},
4:{'c':1.0,'g':1.0,'u':5.0},
5:{'c':6.0,'u':1.0},
6:{'a':3.0,'g':4.0},
7:{'a':1.0,'g':6.0},
8:{'a':1.0,'c':1.0,'g':1.0,'u':4.0},
9:{'a':1.0,'c':2.0,'u':4.0},
}
self.assertEqual(self.many.scoreMatrix(), scoreMatrix)
def test_columnFrequencies(self):
"""Alignment.columnFrequencies should count symbols in each column"""
#calculate by hand what the first and last columns should look like in
#each case
firstvalues = [ [self.integers, Freqs([1,1,5])],
[self.sequences, Freqs('UUU')],
[self.structures, Freqs('(.(')],
]
lastvalues = [ [self.integers, Freqs([5,1,1])],
[self.sequences, Freqs('GGG')],
[self.structures, Freqs('..)')],
]
#check that the first columns are what we expected
for obj, result in firstvalues:
freqs = obj.columnFrequencies()
self.assertEqual(str(freqs[0]), str(result))
#check that the last columns are what we expected
for obj, result in lastvalues:
freqs = obj.columnFrequencies()
self.assertEqual(str(freqs[-1]), str(result))
#check that it works for the empty alignment
freqs = self.empty.columnFrequencies()
self.assertEqual(str(freqs), str([]))
def test_columnProbs(self):
"""Alignment.columnProbs should find Pr(symbol) in each column"""
#make an alignment with 4 rows (easy to calculate probabilities)
align = Alignment(["AAA", "ACA", "GGG", "GUC"])
cp = align.columnProbs()
#check that the column probs match the counts we expect
self.assertEqual(cp, map(Freqs, [
{'A':0.5, 'G':0.5},
{'A':0.25, 'C':0.25, 'G':0.25, 'U':0.25},
{'A':0.5, 'G':0.25, 'C':0.25},
]))
def test_majorityConsensus(self):
"""Alignment.majorityConsensus should return commonest symbol per column"""
#Check the majority consensus in detail for the integer alignment
obs = self.integers.majorityConsensus()
self.assertEqual(obs[0], 1)
assert(obs[1] in [2, 1, 4])
self.assertEqual(obs[2], 3)
assert(obs[3] in [2, 1, 4])
self.assertEqual(obs[4], 1)
#Check the exact strings expected from string transform
self.assertEqual(self.sequences.majorityConsensus(str), 'UCAG')
self.assertEqual(self.structures.majorityConsensus(str), '(.....')
self.assertEqual(str(self.empty.majorityConsensus()), str([]))
def test_uncertainties(self):
"""Alignment.uncertainties should match hand-calculated values"""
aln = Alignment(['abc', 'axc'])
obs = aln.uncertainties()
self.assertFloatEqual(obs, [0, 1, 0])
#check what happens with only one input sequence
aln = Alignment(['abc'])
obs = aln.uncertainties()
self.assertFloatEqual(obs, [0, 0, 0])
#check that we can screen out bad items OK
aln = Alignment(['abc', 'def', 'ghi', 'jkl', 'GHI'])
obs = aln.uncertainties('abcdefghijklmnop')
self.assertFloatEqual(obs, [2.0] * 3)
def test_omitRowsTemplate(self):
"""Alignment.omitRowsTemplate returns new aln with well-aln to temp"""
aln = self.omitRowsTemplate_aln
result = aln.omitRowsTemplate('s3', 0.9, 5)
self.assertEqual(result, {'s3': 'UUCCUUCUU-UUC', \
's4': 'UU-UUUU-UUUUC'})
result2 = aln.omitRowsTemplate('s4', 0.9, 4)
self.assertEqual(result2, {'s3': 'UUCCUUCUU-UUC', \
's4': 'UU-UUUU-UUUUC'})
result3 = aln.omitRowsTemplate('s1', 0.9, 4)
self.assertEqual(result3, {'s2': 'UC------U---C', \
's1': 'UC-----CU---C', 's5': '-------------'})
result4 = aln.omitRowsTemplate('s3', 0.5, 13)
self.assertEqual(result4, {'s3': 'UUCCUUCUU-UUC', \
's4': 'UU-UUUU-UUUUC'})
def test_toFasta(self):
"""toFasta returns a fasta string"""
aln = self.end_gaps
result = aln.toFasta()
self.assertEqual(result, """>a
--a-bc-
>c
--d-ef-
>b
-cb-a--""")
def test_make_gap_filter(self):
"""make_gap_filter returns f(seq) -> True if aligned ok w/ query"""
s1 = Rna('UC-----CU---C')
s3 = Rna('UUCCUUCUU-UUC')
s4 = Rna('UU-UUUU-UUUUC')
#check that the behavior is ok for gap runs
f1 = make_gap_filter(s1, 0.9, 5)
f3 = make_gap_filter(s3, 0.9, 5)
#Should return False since s1 has gap run >= 5 with respect to s3
self.assertEqual(f3(s1), False)
#Should return False since s3 has an insertion run >= 5 to s1
self.assertEqual(f1(s3), False)
#Should retun True since s4 does not have a long enough gap or ins run
self.assertEqual(f3(s4), True)
f3 = make_gap_filter(s3, 0.9, 6)
self.assertEqual(f3(s1), True)
#Check that behavior is ok for gap_fractions
f1 = make_gap_filter(s1, 0.5, 6)
f3 = make_gap_filter(s3, 0.5, 6)
#Should return False since 0.53% of positions are diff for gaps
self.assertEqual(f3(s1), False)
self.assertEqual(f1(s3), False)
self.assertEqual(f3(s4), True)
def test_getIntMap(self):
"""Alignment.getIntMap should return correct mapping."""
aln = Alignment({'seq1':'ACGU','seq2':'CGUA','seq3':'CCGU'})
int_keys = {'seq_0':'seq1','seq_1':'seq2','seq_2':'seq3'}
int_map = {'seq_0':'ACGU','seq_1':'CGUA','seq_2':'CCGU'}
im,ik = aln.getIntMap()
self.assertEqual(ik,int_keys)
self.assertEqual(im,int_map)