def test_goto_assignment1(self):
"""
test_goto_assignment1 fullfils A1.
It first tests the output.
Then it writes the output to the file 'results/assignment1/2_2.txt'.
"""
tests = [
(read_fasta_file('data/test1_1.fasta'),
read_fasta_file('data/test1_2.fasta'), -3, -1, None, (
10,
-10,
'AATCCGCTAGAAACCCTTAG',
'_ATC______TTACCTTCAT',
' *** ||***|*|*|',
), 'results/assignment1_1.txt'),
(
read_fasta_file('data/test2_1.fasta'),
read_fasta_file('data/test2_2.fasta'),
-3,
-1,
None,
(
1,
2,
'ATTCACTAGATTACCTTCACT',
'________GATTACCTTCACT',
' *************',
),
'results/assignment1_2.txt',
),
]
g = gotoh.Gotoh()
gotoh_funcs = [gotoh.gotoh, g.run]
for func in gotoh_funcs:
for t in tests:
score, alignments = func(t[0], t[1], t[2], t[3])
should = t[5]
self.assertEqual(should[0], len(alignments))
self.assertEqual(should[1], score)
self.assertEqual(should[2], ''.join(alignments[0][0]))
self.assertEqual(should[3], ''.join(alignments[0][1]))
self.assertEqual(should[4], ''.join(alignments[0][2]))
f = None
for t in tests:
score, alignments = gotoh.gotoh(t[0], t[1], t[2], t[3])
# open(t[6], "w").close()
f = open(t[6], "w")
score, alignments = gotoh.gotoh(t[0], t[1], t[2], t[3], t[4])
f.write('Score ' + str(score) + ' and ' + str(len(alignments)) +
' optimal alignments. \n')
for a in alignments:
f.write(''.join(a[0]) + '\n')
f.write(''.join(a[2]) + '\n')
f.write(''.join(a[1]) + '\n\n')
f.write('\n\n\n')
f.close()
def test_empty(self):
"""Checks if everything is fine with empty sequences."""
gt = gotoh.Gotoh()
result = gt.run("../T_INPUT/empty_test.fasta",
"../T_INPUT/empty_test.fasta", "../T_INPUT/6eva.txt",
-4, -1, True)
(id_seq1, seq1, id_seq2, seq2, score, alignments) = result
assert id_seq1 == ""
assert id_seq2 == ""
assert seq1 == ""
assert seq2 == ""
assert score == 0
assert alignments == [] # order of elements can be random!
def test_one_empty(self):
"""Checks if everything is fine with one empty sequence."""
gt = gotoh.Gotoh()
result = gt.run("../T_INPUT/empty_test.fasta",
"../T_INPUT/5test_seq2.fasta", "../T_INPUT/6eva.txt",
-4, -1, True)
(id_seq1, seq1, id_seq2, seq2, score, alignments) = result
assert id_seq1 == ""
assert id_seq2 == "Seq2"
assert seq1 == ""
assert seq2 == "TCCGA"
assert score == -9
assert alignments == [["-----",
"TCCGA"]] # order of elements is random!
def test_6(self):
"""Test if run function can be called."""
gt = gotoh.Gotoh()
result = gt.run("../T_INPUT/6test_seq1.fasta",
"../T_INPUT/6test_seq2.fasta", "../T_INPUT/6eva.txt",
-4, -1, True)
(id_seq1, seq1, id_seq2, seq2, score, alignments) = result
assert id_seq1 == "Seq1"
assert id_seq2 == "Seq2"
assert seq1 == "CC"
assert seq2 == "ACCT"
assert score == -7
assert alignments == [['--CC', 'ACCT'],
['CC--',
'ACCT']] # order of elements can be random!
def test_4(self):
"""Test if run function can be called."""
gt = gotoh.Gotoh()
result = gt.run("../T_INPUT/4test_seq1.fasta",
"../T_INPUT/4test_seq2.fasta", "../T_INPUT/4eva.txt",
-3, -1, True)
(id_seq1, seq1, id_seq2, seq2, score, alignments) = result
assert id_seq1 == "Seq1"
assert id_seq2 == "Seq2"
assert seq1 == "TGGA"
assert seq2 == "GG"
assert score == -6
assert alignments == [['TGGA', '--GG'],
['TGGA',
'GG--']] # order of elements can be random!
def test_gotoh_edgecases(self):
"""
test_gotoh_edgecases tests 3 edge cases.
1. Only wrongs.
2. First two gap with (*,0)
3. First two gap with (0,*)
"""
tests = [
([' ', 'A', 'T'], [' ', 'T', 'A'], -3, -1, None, (
1,
-2,
'AT',
'TA',
'||',
)),
([' ', 'A', 'T', 'T', 'A'], [' ', 'T', 'A'], -3, -1, None, (
1,
-3,
'ATTA',
'__TA',
' **',
)),
([' ', 'T', 'A'], [' ', 'A', 'T', 'T', 'A'], -3, -1, None, (
1,
-3,
'__TA',
'ATTA',
' **',
)),
]
for t in tests:
score, alignments = gotoh.gotoh(t[0], t[1], t[2], t[3])
should = t[5]
self.assertEqual(should[0], len(alignments))
self.assertEqual(should[1], score)
self.assertEqual(should[2], ''.join(alignments[0][0]))
self.assertEqual(should[3], ''.join(alignments[0][1]))
self.assertEqual(should[4], ''.join(alignments[0][2]))
g = gotoh.Gotoh()
for t in tests:
score, alignments = g.run(t[0], t[1], t[2], t[3])
should = t[5]
self.assertEqual(should[0], len(alignments))
self.assertEqual(should[1], score)
self.assertEqual(should[2], ''.join(alignments[0][0]))
self.assertEqual(should[3], ''.join(alignments[0][1]))
self.assertEqual(should[4], ''.join(alignments[0][2]))
def test_5(self):
"""Test if run function can be called."""
gt = gotoh.Gotoh()
result = gt.run("../T_INPUT/5test_seq1.fasta",
"../T_INPUT/5test_seq2.fasta", "../T_INPUT/5eva.txt",
-4, -1, True)
(id_seq1, seq1, id_seq2, seq2, score, alignments) = result
assert id_seq1 == "Seq1"
assert id_seq2 == "Seq2"
assert seq1 == "TACGCAGA"
assert seq2 == "TCCGA"
assert score == -3
assert alignments == [['TACGCAGA',
'T---CCGA'], ['TACGCAGA', 'TCC---GA'],
['TACGCAGA',
'TCCG---A']] # order of elements can be random!
def test_instance(self):
"""Check inheritance."""
assert issubclass(gotoh.Gotoh, GotohBase)
assert isinstance(gotoh.Gotoh(), GotohBase)