def test_pairwise_returns_score(self):
"""exercise pairwise local/global returns alignment score"""
S = make_dna_scoring_dict(10, -1, -8)
aln, score = local_pairwise(seq1, seq2, S, 10, 2, return_score=True)
self.assertTrue(score > 100)
aln, score = global_pairwise(seq1, seq2, S, 10, 2, return_score=True)
self.assertTrue(score > 100)
def pair_hmm_align_unaligned_seqs(seqs, moltype=DNA, params={}):
"""
Checks parameters for pairwise alignment, returns alignment.
Code from Greg Caporaso.
"""
seqs = LoadSeqs(data=seqs, moltype=moltype, aligned=False)
try:
s1, s2 = seqs.values()
except ValueError:
raise ValueError(
"Pairwise aligning of seqs requires exactly two seqs.")
try:
gap_open = params['gap_open']
except KeyError:
gap_open = 5
try:
gap_extend = params['gap_extend']
except KeyError:
gap_extend = 2
try:
score_matrix = params['score_matrix']
except KeyError:
score_matrix = make_dna_scoring_dict(
match=1, transition=-1, transversion=-1)
return local_pairwise(s1, s2, score_matrix, gap_open, gap_extend)
def test_pairwise_returns_score(self):
"""exercise pairwise local/global returns alignment score"""
S = make_dna_scoring_dict(10, -1, -8)
aln, score = local_pairwise(seq1, seq2, S, 10, 2, return_score=True)
self.assertTrue(score > 100)
aln, score = global_pairwise(seq1, seq2, S, 10, 2, return_score=True)
self.assertTrue(score > 100)
def pair_hmm_align_unaligned_seqs(seqs, moltype=DNA, params={}):
"""
Checks parameters for pairwise alignment, returns alignment.
Code from Greg Caporaso.
"""
seqs = LoadSeqs(data=seqs, moltype=moltype, aligned=False)
try:
s1, s2 = seqs.values()
except ValueError:
raise ValueError(
"Pairwise aligning of seqs requires exactly two seqs.")
try:
gap_open = params['gap_open']
except KeyError:
gap_open = 5
try:
gap_extend = params['gap_extend']
except KeyError:
gap_extend = 2
try:
score_matrix = params['score_matrix']
except KeyError:
score_matrix = make_dna_scoring_dict(match=1,
transition=-1,
transversion=-1)
return local_pairwise(s1, s2, score_matrix, gap_open, gap_extend)
def test_local_tiebreak(self):
"""Should pick the first best-equal hit rather than the last one"""
# so that the Pyrex and Python versions give the same result.
score_matrix = make_dna_scoring_dict(match=1, transition=-1,
transversion=-1)
pattern = DNA.makeSequence('cwc', Name='pattern')
two_hit = DNA.makeSequence( 'cactc', Name= 'target')
aln = local_pairwise(pattern, two_hit, score_matrix, 5, 2)
hit = aln.NamedSeqs['target']
self.assertEqual(str(hit).lower(), 'cac')
def test_local_tiebreak(self):
"""Should pick the first best-equal hit rather than the last one"""
# so that the Pyrex and Python versions give the same result.
score_matrix = make_dna_scoring_dict(match=1,
transition=-1,
transversion=-1)
pattern = DNA.makeSequence('cwc', Name='pattern')
two_hit = DNA.makeSequence('cactc', Name='target')
aln = local_pairwise(pattern, two_hit, score_matrix, 5, 2)
hit = aln.NamedSeqs['target']
self.assertEqual(str(hit).lower(), 'cac')
def pair_hmm_align_unaligned_seqs(seqs,
moltype=DNA,
params={}):
"""
Handles pairwise alignment of given sequence pair
seqs: list of [primer, target sequence] in string format
moltype: molecule type tested. Only DNA supported.
params: Used to set parameters for opening, extending gaps and score
matrix if something other than the default given in this function
is desired.
"""
try:
seqs = LoadSeqs(data=seqs,moltype=moltype,aligned=False)
except AlphabetError:
raise AlphabetError,("Error in characters present in primer "+\
"%s and/or sequence %s." % (seqs[0], seqs[1]))
try:
s1, s2 = seqs.values()
except ValueError:
raise ValueError,\
"Pairwise aligning of seqs requires exactly two seqs."
try:
gap_open = params['gap_open']
except KeyError:
gap_open = 5
try:
gap_extend = params['gap_extend']
except KeyError:
gap_extend = 2
try:
score_matrix = params['score_matrix']
except KeyError:
score_matrix = make_dna_scoring_dict(\
match=1, transition=-1, transversion=-1)
return local_pairwise(s1, s2, score_matrix, gap_open, gap_extend)
