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#!/usr/bin/env python
# This code is part of the Biopython distribution and governed by its
# license. Please see the LICENSE file that should have been included
# as part of this package.
import unittest
from Bio import pairwise2
class TestPairwiseGlobal(unittest.TestCase):
def test_globalxx_simple(self):
aligns = pairwise2.align.globalxx("GAACT", "GAT")
self.assertEqual(len(aligns), 2)
aligns.sort()
seq1, seq2, score, begin, end = aligns[0]
alignment = pairwise2.format_alignment(seq1, seq2, score, begin, end)
self.assertEqual(alignment, """\
GAACT
|||||
G-A-T
Score=3
""")
seq1, seq2, score, begin, end = aligns[1]
alignment = pairwise2.format_alignment(seq1, seq2, score, begin, end)
self.assertEqual(alignment, """\
GAACT
|||||
GA--T
Score=3
""")
class TestPairwiseLocal(unittest.TestCase):
def test_localxs(self):
aligns = sorted(pairwise2.align.localxs("AxBx", "zABz", -0.1, 0))
seq1, seq2, score, begin, end = aligns[0]
alignment = pairwise2.format_alignment(seq1, seq2, score, begin, end)
self.assertEqual(alignment, """\
-AxBx
|||
zA-Bz
Score=1.9
""")
seq1, seq2, score, begin, end = aligns[1]
alignment = pairwise2.format_alignment(seq1, seq2, score, begin, end)
self.assertEqual(alignment, """\
-AxBx
||||
zA-Bz
Score=1.9
""")
class TestPairwiseOpenPenalty(unittest.TestCase):
def test_match_score_open_penalty1(self):
aligns = pairwise2.align.globalms("AA", "A", 2.0, -1, -0.1, 0)
self.assertEqual(len(aligns), 2)
aligns.sort()
seq1, seq2, score, begin, end = aligns[0]
alignment = pairwise2.format_alignment(seq1, seq2, score, begin, end)
self.assertEqual(alignment, """\
AA
||
-A
Score=1.9
""")
seq1, seq2, score, begin, end = aligns[1]
alignment = pairwise2.format_alignment(seq1, seq2, score, begin, end)
self.assertEqual(alignment, """\
AA
||
A-
Score=1.9
""")
def test_match_score_open_penalty2(self):
aligns = pairwise2.align.globalms("GAA", "GA", 1.5, 0, -0.1, 0)
self.assertEqual(len(aligns), 2)
aligns.sort()
seq1, seq2, score, begin, end = aligns[0]
alignment = pairwise2.format_alignment(seq1, seq2, score, begin, end)
self.assertEqual(alignment, """\
GAA
|||
G-A
Score=2.9
""")
seq1, seq2, score, begin, end = aligns[1]
alignment = pairwise2.format_alignment(seq1, seq2, score, begin, end)
self.assertEqual(alignment, """\
GAA
|||
GA-
Score=2.9
""")
def test_match_score_open_penalty3(self):
aligns = pairwise2.align.globalxs("GAACT", "GAT", -0.1, 0)
self.assertEqual(len(aligns), 1)
seq1, seq2, score, begin, end = aligns[0]
alignment = pairwise2.format_alignment(seq1, seq2, score, begin, end)
self.assertEqual(alignment, """\
GAACT
|||||
GA--T
Score=2.9
""")
def test_match_score_open_penalty4(self):
aligns = pairwise2.align.globalms("GCT", "GATA", 1, -2, -0.1, 0)
self.assertEqual(len(aligns), 1)
seq1, seq2, score, begin, end = aligns[0]
alignment = pairwise2.format_alignment(seq1, seq2, score, begin, end)
self.assertEqual(alignment, """\
GCT-
||||
GATA
Score=-0.1
""")
class TestPairwiseExtendPenalty(unittest.TestCase):
def test_extend_penalty1(self):
aligns = pairwise2.align.globalxs("GACT", "GT", -0.2, -0.5)
self.assertEqual(len(aligns), 1)
seq1, seq2, score, begin, end = aligns[0]
alignment = pairwise2.format_alignment(seq1, seq2, score, begin, end)
self.assertEqual(alignment, """\
GACT
||||
G--T
Score=1.3
""")
def test_extend_penalty2(self):
aligns = pairwise2.align.globalxs("GACT", "GT", -0.2, -1.5)
self.assertEqual(len(aligns), 2)
aligns.sort()
seq1, seq2, score, begin, end = aligns[0]
alignment = pairwise2.format_alignment(seq1, seq2, score, begin, end)
self.assertEqual(alignment, """\
GACT
||||
-G-T
Score=0.6
""")
seq1, seq2, score, begin, end = aligns[1]
alignment = pairwise2.format_alignment(seq1, seq2, score, begin, end)
self.assertEqual(alignment, """\
GACT
||||
G-T-
Score=0.6
""")
class TestPairwisePenalizeExtendWhenOpening(unittest.TestCase):
def test_penalize_extend_when_opening(self):
aligns = pairwise2.align.globalxs("GACT", "GT", -0.2, -1.5, penalize_extend_when_opening=1)
self.assertEqual(len(aligns), 1)
seq1, seq2, score, begin, end = aligns[0]
alignment = pairwise2.format_alignment(seq1, seq2, score, begin, end)
self.assertEqual(alignment, """\
GACT
||||
G--T
Score=-1.2
""")
class TestPairwisePenalizeEndgaps(unittest.TestCase):
def test_penalize_end_gaps(self):
aligns = pairwise2.align.globalxs("GACT", "GT", -0.2, -0.8, penalize_end_gaps=0)
self.assertEqual(len(aligns), 3)
aligns.sort()
seq1, seq2, score, begin, end = aligns[0]
alignment = pairwise2.format_alignment(seq1, seq2, score, begin, end)
self.assertEqual(alignment, """\
GACT
||||
--GT
Score=1
""")
seq1, seq2, score, begin, end = aligns[1]
alignment = pairwise2.format_alignment(seq1, seq2, score, begin, end)
self.assertEqual(alignment, """\
GACT
||||
G--T
Score=1
""")
seq1, seq2, score, begin, end = aligns[2]
alignment = pairwise2.format_alignment(seq1, seq2, score, begin, end)
self.assertEqual(alignment, """\
GACT
||||
GT--
Score=1
""")
class TestPairwiseSeparateGapPenalties(unittest.TestCase):
def test_separate_gap_penalties1(self):
aligns = pairwise2.align.localxd("GAT", "GTCT", -0.3, 0, -0.8, 0)
self.assertEqual(len(aligns), 2)
aligns.sort()
seq1, seq2, score, begin, end = aligns[0]
alignment = pairwise2.format_alignment(seq1, seq2, score, begin, end)
self.assertEqual(alignment, """\
G-AT
||||
GTCT
Score=1.7
""")
seq1, seq2, score, begin, end = aligns[1]
alignment = pairwise2.format_alignment(seq1, seq2, score, begin, end)
self.assertEqual(alignment, """\
GA-T
||||
GTCT
Score=1.7
""")
def test_separate_gap_penalties2(self):
aligns = pairwise2.align.localxd("GAT", "GTCT", -0.5, 0, -0.2, 0)
self.assertEqual(len(aligns), 1)
seq1, seq2, score, begin, end = aligns[0]
alignment = pairwise2.format_alignment(seq1, seq2, score, begin, end)
self.assertEqual(alignment, """\
GAT--
|||
G-TCT
Score=1.8
""")
class TestPairwiseSeparateGapPenaltiesWithExtension(unittest.TestCase):
def test_separate_gap_penalties_with_extension(self):
aligns = pairwise2.align.localxd(list("GAAT"), list("GTCCT"), -0.1, 0, -0.1, -0.1, gap_char=["-"])
self.assertEqual(len(aligns), 3)
aligns.sort()
seq1, seq2, score, begin, end = aligns[0]
alignment = pairwise2.format_alignment(seq1, seq2, score, begin, end)
self.assertEqual(alignment, """\
['G', '-', 'A', 'A', 'T']
|||||
['G', 'T', 'C', 'C', 'T']
Score=1.9
""")
seq1, seq2, score, begin, end = aligns[1]
alignment = pairwise2.format_alignment(seq1, seq2, score, begin, end)
self.assertEqual(alignment, """\
['G', 'A', '-', 'A', 'T']
|||||
['G', 'T', 'C', 'C', 'T']
Score=1.9
""")
seq1, seq2, score, begin, end = aligns[2]
alignment = pairwise2.format_alignment(seq1, seq2, score, begin, end)
self.assertEqual(alignment, """\
['G', 'A', 'A', '-', 'T']
|||||
['G', 'T', 'C', 'C', 'T']
Score=1.9
""")
class TestPairwiseMatchDictionary(unittest.TestCase):
match_dict = {
("A", "A") : 1.5,
("A", "T") : 0.5,
("T", "T") : 1.0
}
def test_match_dictionary1(self):
aligns = pairwise2.align.localds("ATAT", "ATT", self.match_dict, -.5, 0)
self.assertEqual(len(aligns), 2)
aligns.sort()
seq1, seq2, score, begin, end = aligns[0]
alignment = pairwise2.format_alignment(seq1, seq2, score, begin, end)
self.assertEqual(alignment, """\
ATAT
||||
AT-T
Score=3
""")
seq1, seq2, score, begin, end = aligns[1]
alignment = pairwise2.format_alignment(seq1, seq2, score, begin, end)
self.assertEqual(alignment, """\
ATAT
|||
ATT-
Score=3
""")
def test_match_dictionary2(self):
aligns = pairwise2.align.localds("ATAT", "ATT", self.match_dict, -1, 0)
self.assertEqual(len(aligns), 1)
seq1, seq2, score, begin, end = aligns[0]
alignment = pairwise2.format_alignment(seq1, seq2, score, begin, end)
self.assertEqual(alignment, """\
ATAT
|||
ATT-
Score=3
""")
def test_match_dictionary3(self):
aligns = pairwise2.align.localds("ATT", "ATAT", self.match_dict, -1, 0)
self.assertEqual(len(aligns), 1)
seq1, seq2, score, begin, end = aligns[0]
alignment = pairwise2.format_alignment(seq1, seq2, score, begin, end)
self.assertEqual(alignment, """\
ATT-
|||
ATAT
Score=3
""")
class TestPairwiseOneCharacter(unittest.TestCase):
def test_align_one_char1(self):
aligns = pairwise2.align.localxs("abcde", "c", -0.3, -0.1)
self.assertEqual(len(aligns), 1)
seq1, seq2, score, begin, end = aligns[0]
alignment = pairwise2.format_alignment(seq1, seq2, score, begin, end)
self.assertEqual(alignment, """\
abcde
|
--c--
Score=1
""")
def test_align_one_char2(self):
aligns = pairwise2.align.localxs("abcce", "c", -0.3, -0.1)
self.assertEqual(len(aligns), 2)
aligns.sort()
seq1, seq2, score, begin, end = aligns[0]
alignment = pairwise2.format_alignment(seq1, seq2, score, begin, end)
self.assertEqual(alignment, """\
abcce
|
---c-
Score=1
""")
seq1, seq2, score, begin, end = aligns[1]
alignment = pairwise2.format_alignment(seq1, seq2, score, begin, end)
self.assertEqual(alignment, """\
abcce
|
--c--
Score=1
""")
def test_align_one_char3(self):
aligns = pairwise2.align.globalxs("abcde", "c", -0.3, -0.1)
self.assertEqual(len(aligns), 1)
seq1, seq2, score, begin, end = aligns[0]
alignment = pairwise2.format_alignment(seq1, seq2, score, begin, end)
self.assertEqual(alignment, """\
abcde
|||||
--c--
Score=0.2
""")
class TestPersiteGapPenalties(unittest.TestCase):
"""Check gap penalty callbacks use correct gap opening position.
This tests that the gap penalty callbacks are really being used
with the correct gap opening position.
"""
def test_gap_here_only_1(self):
seq1 = "AAAABBBAAAACCCCCCCCCCCCCCAAAABBBAAAA"
seq2 = "AABBBAAAACCCCAAAABBBAA"
breaks = [0, 11, len(seq2)]
# Very expensive to open a gap in seq1:
nogaps = lambda x, y: -2000 - y
# Very expensive to open a gap in seq2 unless it is in one of the allowed positions
specificgaps = lambda x, y: (-2 -y) if x in breaks else (-2000 - y)
alignments = pairwise2.align.globalmc(seq1, seq2, 1, -1, nogaps, specificgaps)
self.assertEqual(len(alignments), 1)
formatted = pairwise2.format_alignment(*alignments[0])
self.assertEqual(formatted, """\
AAAABBBAAAACCCCCCCCCCCCCCAAAABBBAAAA
||||||||||||||||||||||||||||||||||||
--AABBBAAAACC----------CCAAAABBBAA--
Score=2
""")
def test_gap_here_only_2(self):
"""Force a bad alignment.
Forces a bad alignment by having a very expensive gap penalty
where one would normally expect a gap, and a cheap gap penalty
in another place.
"""
seq1 = "AAAABBBAAAACCCCCCCCCCCCCCAAAABBBAAAA"
seq2 = "AABBBAAAACCCCAAAABBBAA"
breaks = [0, 3, len(seq2)]
#Very expensive to open a gap in seq1:
nogaps = lambda x, y: -2000 - y
#Very expensive to open a gap in seq2 unless it is in one of the allowed positions:
specificgaps = lambda x, y: (-2 - y) if x in breaks else (-2000 - y)
alignments = pairwise2.align.globalmc(seq1, seq2, 1, -1, nogaps, specificgaps)
self.assertEqual(len(alignments), 1)
formatted = pairwise2.format_alignment(*alignments[0])
self.assertEqual(formatted, """\
AAAABBBAAAACCCCCCCCCCCCCCAAAABBBAAAA
||||||||||||||||||||||||||||||||||||
--AAB----------BBAAAACCCCAAAABBBAA--
Score=-10
""")
if __name__ == '__main__':
runner = unittest.TextTestRunner(verbosity = 2)
unittest.main(testRunner=runner)
|
