def test_needleman_wunsch_align_DNA(self):
"""Test the Needleman-Wunsch sequence alignment for two DNA sequences."""
# The sequences.
seq1 = 'GCATTACT'
seq2 = 'GATTACT'
print("\nIn:")
print(seq1)
print(seq2)
# Perform the alignment.
score, align1, align2, gaps = needleman_wunsch_align(seq1, seq2, sub_matrix=SIMILARITY_DNA, sub_seq=SIMILARITY_DNA_SEQ, gap_open_penalty=1, gap_extend_penalty=1)
print("\nOut:")
print(score)
print(align1)
print(align2)
print(gaps)
print("\n")
# Check the alignment.
self.assertEqual(align1, 'GCATTACT')
self.assertEqual(align2, 'G-ATTACT')
# The gap matrix.
real_gaps = [
[0, 0, 0, 0, 0, 0, 0, 0],
[0, 1, 0, 0, 0, 0, 0, 0]
]
for i in range(2):
for j in range(8):
self.assertEqual(gaps[i, j], real_gaps[i][j])
def test_needleman_wunsch_align_DNA(self):
"""Test the Needleman-Wunsch sequence alignment for two DNA sequences."""
# The sequences.
seq1 = 'GCATTACT'
seq2 = 'GATTACT'
print("\nIn:")
print(seq1)
print(seq2)
# Perform the alignment.
score, align1, align2, gaps = needleman_wunsch_align(
seq1,
seq2,
sub_matrix=SIMILARITY_DNA,
sub_seq=SIMILARITY_DNA_SEQ,
gap_open_penalty=1,
gap_extend_penalty=1)
print("\nOut:")
print(score)
print(align1)
print(align2)
print(gaps)
print("\n")
# Check the alignment.
self.assertEqual(align1, 'GCATTACT')
self.assertEqual(align2, 'G-ATTACT')
# The gap matrix.
real_gaps = [[0, 0, 0, 0, 0, 0, 0, 0], [0, 1, 0, 0, 0, 0, 0, 0]]
for i in range(2):
for j in range(8):
self.assertEqual(gaps[i, j], real_gaps[i][j])
def test_needleman_wunsch_align_NUC_4_4(self):
"""Test the Needleman-Wunsch sequence alignment for two DNA sequences using the NUC 4.4 matrix.
From online servers, the results with a gap open penalty of 5 and gap extend of 1 should be::
https://www.ebi.ac.uk/Tools/psa/emboss_needle/
EMBOSS_001 1 GAAAAAAT 8
| |||
EMBOSS_001 1 G----AAT 4
"""
# The sequences.
seq1 = 'GAAAAAAT'
seq2 = 'GAAT'
print("\nIn:")
print(seq1)
print(seq2)
# Perform the alignment.
score, align1, align2, gaps = needleman_wunsch_align(
seq1,
seq2,
sub_matrix=NUC_4_4,
sub_seq=NUC_4_4_SEQ,
gap_open_penalty=5,
gap_extend_penalty=1)
print("\nOut:")
print(score)
print(align1)
print(align2)
print(gaps)
print("\n")
# Check the alignment.
self.assertEqual(align1, 'GAAAAAAT')
self.assertEqual(align2, 'G----AAT')
# The gap matrix.
real_gaps = [[0, 0, 0, 0, 0, 0, 0, 0], [0, 1, 1, 1, 1, 0, 0, 0]]
for i in range(2):
for j in range(8):
self.assertEqual(gaps[i, j], real_gaps[i][j])
def test_needleman_wunsch_align_NUC_4_4(self):
"""Test the Needleman-Wunsch sequence alignment for two DNA sequences using the NUC 4.4 matrix.
From online servers, the results with a gap open penalty of 5 and gap extend of 1 should be::
https://www.ebi.ac.uk/Tools/psa/emboss_needle/
EMBOSS_001 1 GAAAAAAT 8
| |||
EMBOSS_001 1 G----AAT 4
"""
# The sequences.
seq1 = 'GAAAAAAT'
seq2 = 'GAAT'
print("\nIn:")
print(seq1)
print(seq2)
# Perform the alignment.
score, align1, align2, gaps = needleman_wunsch_align(seq1, seq2, sub_matrix=NUC_4_4, sub_seq=NUC_4_4_SEQ, gap_open_penalty=5, gap_extend_penalty=1)
print("\nOut:")
print(score)
print(align1)
print(align2)
print(gaps)
print("\n")
# Check the alignment.
self.assertEqual(align1, 'GAAAAAAT')
self.assertEqual(align2, 'G----AAT')
# The gap matrix.
real_gaps = [
[0, 0, 0, 0, 0, 0, 0, 0],
[0, 1, 1, 1, 1, 0, 0, 0]
]
for i in range(2):
for j in range(8):
self.assertEqual(gaps[i, j], real_gaps[i][j])
def align_pairwise(sequence1, sequence2, algorithm='NW70', matrix='BLOSUM62', gap_open_penalty=1.0, gap_extend_penalty=1.0, end_gap_open_penalty=0.0, end_gap_extend_penalty=0.0, verbosity=1):
"""Align two protein sequences.
@param sequence1: The first protein sequence as one letter codes.
@type sequence1: str
@param sequence2: The second protein sequence as one letter codes.
@type sequence2: str
@keyword algorithm: The pairwise sequence alignment algorithm to use.
@type algorithm: str
@keyword matrix: The substitution matrix to use.
@type matrix: str
@keyword gap_open_penalty: The penalty for introducing gaps, as a positive number.
@type gap_open_penalty: float
@keyword gap_extend_penalty: The penalty for extending a gap, as a positive number.
@type gap_extend_penalty: float
@keyword end_gap_open_penalty: The optional penalty for opening a gap at the end of a sequence.
@type end_gap_open_penalty: float
@keyword end_gap_extend_penalty: The optional penalty for extending a gap at the end of a sequence.
@type end_gap_extend_penalty: float
@keyword verbosity: The level of verbosity. Setting this to zero silences all printouts.
@type verbosity: int
@return: The alignment score, two alignment strings and the gap matrix.
@rtype: float, str, str, numpy rank-2 int array
"""
# Checks.
allowed_algor = ['NW70']
if algorithm not in allowed_algor:
raise RelaxError("The sequence alignment algorithm '%s' is unknown, it must be one of %s." % (algorithm, allowed_algor))
allowed_matrices = ['BLOSUM62', 'PAM250']
if matrix not in allowed_matrices:
raise RelaxError("The substitution matrix '%s' is unknown, it must be one of %s." % (matrix, allowed_matrices))
# Capitalise the sequences.
sequence1 = sequence1.upper()
sequence2 = sequence2.upper()
# Initial printout.
if verbosity:
sys.stdout.write("\nPairwise protein alignment.\n")
sys.stdout.write("%-30s %s\n" % ("Substitution matrix:", matrix))
sys.stdout.write("%-30s %s\n" % ("Gap opening penalty:", gap_open_penalty))
sys.stdout.write("%-30s %s\n" % ("Gap extend penalty:", gap_extend_penalty))
sys.stdout.write("\n%-30s %s\n" % ("Input sequence 1:", sequence1))
sys.stdout.write("%-30s %s\n" % ("Input sequence 2:", sequence2))
# Select the substitution matrix.
if matrix == 'BLOSUM62':
sub_matrix = BLOSUM62
sub_seq = BLOSUM62_SEQ
elif matrix == 'PAM250':
sub_matrix = PAM250
sub_seq = PAM250_SEQ
# The alignment.
if algorithm == 'NW70':
score, align1, align2, gaps = needleman_wunsch_align(sequence1, sequence2, sub_matrix=sub_matrix, sub_seq=sub_seq, 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)
# Final printout.
if verbosity:
sys.stdout.write("\n%-30s %s\n" % ("Aligned sequence 1:", align1))
sys.stdout.write("%-30s %s\n" % ("Aligned sequence 2:", align2))
sys.stdout.write("%-30s " % "")
for i in range(len(align1)):
if align1[i] == align2[i]:
sys.stdout.write("*")
else:
sys.stdout.write(" ")
sys.stdout.write("\n\n")
# Return the results.
return score, align1, align2, gaps
