def test_intersection(self):
'''Intersection should either return None or the correct intersection'''
a = intervals.Interval(5, 10)
b = intervals.Interval(8, 15)
c = intervals.Interval(12, 20)
self.assertEqual(a.intersection(c), None)
self.assertEqual(a.intersection(b), intervals.Interval(8, 10))
def test_length_sum_from_list(self):
'''Test that total length of intervals is summed correctly'''
a = [
intervals.Interval(1, 2),
intervals.Interval(4, 5),
intervals.Interval(10, 19)
]
self.assertEqual(14, intervals.length_sum_from_list(a))
def test_init(self):
'''Throw error if try to construct genome_interval from a non-int, or end<start'''
with self.assertRaises(intervals.Error):
intervals.Interval('a', 1)
with self.assertRaises(intervals.Error):
intervals.Interval(1, 'a')
with self.assertRaises(intervals.Error):
intervals.Interval('a', 'a')
with self.assertRaises(intervals.Error):
intervals.Interval(3, 2)
def test_union_flll_gap(self):
'''union_fill_gap() should ignore intersections and return the maximum range of coords'''
a = intervals.Interval(5, 10)
b = intervals.Interval(8, 15)
c = intervals.Interval(12, 20)
d = intervals.Interval(21, 22)
self.assertEqual(a.union_fill_gap(c), intervals.Interval(5, 20))
self.assertEqual(c.union_fill_gap(a), intervals.Interval(5, 20))
self.assertEqual(a.union_fill_gap(b), intervals.Interval(5, 15))
self.assertEqual(b.union_fill_gap(a), intervals.Interval(5, 15))
self.assertEqual(c.union_fill_gap(d), intervals.Interval(12, 22))
self.assertEqual(d.union_fill_gap(c), intervals.Interval(12, 22))
def _orfs_from_aa_seq(seq):
orfs = []
pos = 0
while pos < len(seq):
next_stop = seq.find('*', pos)
if next_stop == -1:
orfs.append(intervals.Interval(pos, len(seq) - 1))
break
elif next_stop > pos:
orfs.append(intervals.Interval(pos, next_stop))
pos = next_stop + 1
return orfs
def gaps(self, min_length=1):
'''Finds the positions of all gaps in the sequence that are at least min_length long. Returns a list of Intervals. Coords are zero-based'''
gaps = []
regex = re.compile('N+', re.IGNORECASE)
for m in regex.finditer(self.seq):
if m.span()[1] - m.span()[0] + 1 >= min_length:
gaps.append(intervals.Interval(m.span()[0], m.span()[1] - 1))
return gaps
def test_union(self):
'''Union should either return None or the correct union'''
a = intervals.Interval(5, 10)
b = intervals.Interval(8, 15)
c = intervals.Interval(12, 20)
d = intervals.Interval(21, 22)
self.assertEqual(a.union(c), None)
self.assertEqual(c.union(a), None)
self.assertEqual(a.union(b), intervals.Interval(5, 15))
self.assertEqual(b.union(a), intervals.Interval(5, 15))
self.assertEqual(c.union(d), intervals.Interval(12, 22))
self.assertEqual(d.union(c), intervals.Interval(12, 22))
def test_merge_overlapping_in_list(self):
'''merge_overlapping_in_list() merges correctly'''
a = [
intervals.Interval(1, 2),
intervals.Interval(51, 60),
intervals.Interval(10, 20),
intervals.Interval(20, 30),
intervals.Interval(20, 30),
intervals.Interval(29, 50),
intervals.Interval(65, 70)
]
b = [
intervals.Interval(1, 2),
intervals.Interval(10, 60),
intervals.Interval(65, 70)
]
intervals.merge_overlapping_in_list(a)
self.assertSequenceEqual(a, b)
def contig_coords(self):
'''Finds coords of contigs, i.e. everything that's not a gap (N or n). Returns a list of Intervals. Coords are zero-based'''
# contigs are the opposite of gaps, so work out the coords from the gap coords
gaps = self.gaps()
if len(gaps) == 0:
return [intervals.Interval(0, len(self) - 1)]
coords = [0]
for g in gaps:
if g.start == 0:
coords = [g.end + 1]
else:
coords += [g.start - 1, g.end + 1]
if coords[-1] < len(self):
coords.append(len(self) - 1)
return [
intervals.Interval(coords[i], coords[i + 1])
for i in range(0,
len(coords) - 1, 2)
]
def test_intersects(self):
'''Intersection of two intervals should do the right thing'''
a = intervals.Interval(5, 10)
no_intersect = [intervals.Interval(3, 4), intervals.Interval(11, 20)]
intersect = [
intervals.Interval(3, 5),
intervals.Interval(3, 6),
intervals.Interval(9, 12),
intervals.Interval(10, 12),
intervals.Interval(6, 7),
intervals.Interval(1, 20)
]
for i in no_intersect:
self.assertFalse(a.intersects(i),
'shouldn\'t intersect: ' + str(a) + ', ' + str(i))
for i in intersect:
self.assertTrue(a.intersects(i),
'should intersect: ' + str(a) + ', ' + str(i))
def test_orfs_from_aa_seq(self):
'''Test _orfs_from_aa_seq()'''
test_seqs = [
'', '*', '**', 'A', 'A*A*A', 'AB**CDE*AB', '*ABCDE*', '**ABCDE**'
]
correct_coords = [[], [], [], [intervals.Interval(0, 0)],
[
intervals.Interval(0, 1),
intervals.Interval(2, 3),
intervals.Interval(4, 4)
],
[
intervals.Interval(0, 2),
intervals.Interval(4, 7),
intervals.Interval(8, 9)
], [intervals.Interval(1, 6)],
[intervals.Interval(2, 7)]]
for i in range(len(test_seqs)):
orfs = sequences._orfs_from_aa_seq(test_seqs[i])
self.assertListEqual(correct_coords[i], orfs)
def orfs(self, frame=0, revcomp=False):
assert frame in [0, 1, 2]
if revcomp:
self.revcomp()
aa_seq = self.translate(frame=frame).seq.rstrip('X')
if revcomp:
self.revcomp()
orfs = _orfs_from_aa_seq(aa_seq)
for i in range(len(orfs)):
if revcomp:
start = len(self) - (orfs[i].end * 3 + 3) - frame
end = len(self) - (orfs[i].start * 3) - 1 - frame
else:
start = orfs[i].start * 3 + frame
end = orfs[i].end * 3 + 2 + frame
orfs[i] = intervals.Interval(start, end)
return orfs
def test_gaps(self):
'''gaps() should find the gaps in a sequence correctly'''
test_seqs = [
sequences.Fasta('ID', 'ACGT'),
sequences.Fasta('ID', 'NACGT'),
sequences.Fasta('ID', 'NACGTN'),
sequences.Fasta('ID', 'ANNCGT'),
sequences.Fasta('ID', 'NANNCGTNN')
]
correct_gaps = [[], [intervals.Interval(0, 0)],
[intervals.Interval(0, 0),
intervals.Interval(5, 5)], [intervals.Interval(1, 2)],
[
intervals.Interval(0, 0),
intervals.Interval(2, 3),
intervals.Interval(7, 8)
]]
for i in range(len(test_seqs)):
gaps = test_seqs[i].gaps()
self.assertListEqual(correct_gaps[i], gaps)
def test_comparisons(self):
'''<, <=, == should work as expected'''
self.assertTrue(intervals.Interval(1, 2) < intervals.Interval(2, 2))
self.assertTrue(intervals.Interval(1, 2) <= intervals.Interval(2, 2))
self.assertFalse(intervals.Interval(2, 2) <= intervals.Interval(1, 2))
self.assertFalse(intervals.Interval(2, 2) < intervals.Interval(1, 2))
self.assertFalse(intervals.Interval(2, 2) < intervals.Interval(2, 2))
self.assertTrue(intervals.Interval(1, 2) == intervals.Interval(1, 2))
self.assertFalse(intervals.Interval(1, 2) == intervals.Interval(1, 3))
self.assertTrue(intervals.Interval(1, 2) != intervals.Interval(1, 3))
self.assertFalse(intervals.Interval(1, 2) != intervals.Interval(1, 2))
def test_all_orfs(self):
'''Test all_orfs()'''
d = {}
tasks.file_to_dict(os.path.join(data_dir, 'sequences_test_orfs.fa'), d)
seq = d['1']
orfs = seq.all_orfs(min_length=120)
expected = [(intervals.Interval(27, 221), False),
(intervals.Interval(44, 226), False),
(intervals.Interval(48, 170), True),
(intervals.Interval(109, 240), False),
(intervals.Interval(143, 265), True),
(intervals.Interval(227, 421), False),
(intervals.Interval(277, 432), True),
(intervals.Interval(286, 477), False),
(intervals.Interval(288, 518), True),
(intervals.Interval(562, 702), False),
(intervals.Interval(600, 758), False),
(intervals.Interval(605, 817), False),
(intervals.Interval(818, 937), False),
(intervals.Interval(835, 987), False),
(intervals.Interval(864, 998), False)]
self.assertEqual(len(orfs), len(expected))
for i in range(len(orfs)):
print(orfs[i][0], expected[i][0])
self.assertEqual(orfs[i][0], expected[i][0])
self.assertEqual(orfs[i][1], expected[i][1])
def test_orfs(self):
'''Test orfs()'''
test_seqs = [
(sequences.Fasta('ID',
'AAACCCGG'), 0, False, [intervals.Interval(0,
5)]),
(sequences.Fasta('ID', 'AAAACCCGG'), 1, False,
[intervals.Interval(1, 6)]),
(sequences.Fasta('ID', 'AAAAACCCGG'), 2, False,
[intervals.Interval(2, 7)]),
(sequences.Fasta('ID',
'CCGGGTTT'), 0, True, [intervals.Interval(2, 7)]),
(sequences.Fasta('ID',
'CCGGGTTTT'), 1, True, [intervals.Interval(2,
7)]),
(sequences.Fasta('ID', 'CCGGGTTTTT'), 2, True,
[intervals.Interval(2, 7)]),
(sequences.Fasta('ID', 'AAACCCTGA'), 0, False,
[intervals.Interval(0, 8)]),
(sequences.Fasta('ID', 'AAACCCTGATAG'), 0, False,
[intervals.Interval(0, 8)]),
(sequences.Fasta('ID', 'AAACCCTGA'), 1, False,
[intervals.Interval(1, 6)]),
(sequences.Fasta('ID', ''), 0, False, []),
(sequences.Fasta('ID', 'A'), 0, False, []),
(sequences.Fasta('ID', 'AA'), 0, False, []),
(sequences.Fasta('ID',
'AAA'), 0, False, [intervals.Interval(0, 2)]),
(sequences.Fasta('ID',
'AAAAAA'), 0, False, [intervals.Interval(0, 5)]),
(sequences.Fasta('ID', 'AAA'), 1, False, []),
(sequences.Fasta('ID', 'AAA'), 2, False, []),
(sequences.Fasta('ID', 'AAA'), 0, True, [intervals.Interval(0,
2)]),
(sequences.Fasta('ID', 'AAA'), 1, True, []),
(sequences.Fasta('ID', 'AAA'), 2, True, []),
(sequences.Fasta('ID', 'TAA'), 0, False, []),
(sequences.Fasta('ID', 'CTA'), 0, True, [])
]
for t in test_seqs:
orfs = t[0].orfs(frame=t[1], revcomp=t[2])
self.assertListEqual(orfs, t[3])
def test_contig_coords(self):
'''contig_coords() should get the coords of all contigs in a sequence correctly'''
test_seqs = [
sequences.Fasta('ID', 'ACGT'),
sequences.Fasta('ID', 'NACGT'),
sequences.Fasta('ID', 'NNACGT'),
sequences.Fasta('ID', 'ACGTN'),
sequences.Fasta('ID', 'ACGTNN'),
sequences.Fasta('ID', 'NANNCGT'),
sequences.Fasta('ID', 'ACNNNGTNA'),
sequences.Fasta('ID', 'ANNCGTNNAAAAA')
]
correct_coords = [[intervals.Interval(0,
3)], [intervals.Interval(1, 4)],
[intervals.Interval(2,
5)], [intervals.Interval(0, 3)],
[intervals.Interval(0, 3)],
[intervals.Interval(1, 1),
intervals.Interval(4, 6)],
[
intervals.Interval(0, 1),
intervals.Interval(5, 6),
intervals.Interval(8, 8)
],
[
intervals.Interval(0, 0),
intervals.Interval(3, 5),
intervals.Interval(8, 12)
]]
for i in range(len(test_seqs)):
gaps = test_seqs[i].contig_coords()
self.assertListEqual(correct_coords[i], gaps)
def test_len(self):
self.assertEqual(len(intervals.Interval(1, 2)), 2)
self.assertEqual(len(intervals.Interval(1, 1)), 1)
self.assertEqual(len(intervals.Interval(10, 20)), 11)
def test_contains(self):
'''Check that contains() works as expected'''
a = intervals.Interval(5, 10)
not_contained = [
intervals.Interval(1, 2),
intervals.Interval(4, 5),
intervals.Interval(4, 10),
intervals.Interval(4, 11),
intervals.Interval(5, 11),
intervals.Interval(1, 2),
intervals.Interval(9, 11),
intervals.Interval(10, 11),
intervals.Interval(11, 20)
]
contained = [
intervals.Interval(5, 5),
intervals.Interval(5, 10),
intervals.Interval(6, 7),
intervals.Interval(6, 10),
intervals.Interval(10, 10)
]
for i in not_contained:
self.assertFalse(a.contains(i),
'shouldn\'t contain: ' + str(a) + ', ' + str(i))
for i in contained:
self.assertTrue(a.contains(i),
'should contain: ' + str(a) + ', ' + str(i))
def test_remove_contained_in_list(self):
'''test_remove_contained_in_list removes the right elements of list'''
a = [
intervals.Interval(1, 2),
intervals.Interval(4, 4),
intervals.Interval(4, 5),
intervals.Interval(5, 6),
intervals.Interval(7, 9),
intervals.Interval(8, 10),
intervals.Interval(9, 11),
intervals.Interval(20, 25),
intervals.Interval(20, 24),
intervals.Interval(20, 26),
intervals.Interval(30, 38),
intervals.Interval(30, 37),
intervals.Interval(30, 36),
intervals.Interval(30, 35),
intervals.Interval(30, 35),
intervals.Interval(32, 33),
intervals.Interval(38, 50),
intervals.Interval(65, 70),
intervals.Interval(67, 70)
]
b = [
intervals.Interval(1, 2),
intervals.Interval(4, 5),
intervals.Interval(5, 6),
intervals.Interval(7, 9),
intervals.Interval(8, 10),
intervals.Interval(9, 11),
intervals.Interval(20, 26),
intervals.Interval(30, 38),
intervals.Interval(38, 50),
intervals.Interval(65, 70)
]
intervals.remove_contained_in_list(a)
self.assertSequenceEqual(a, b)
def test_intersection(self):
'''intersection() should correctly intersect two lists of intervals'''
a = [
intervals.Interval(1, 2),
intervals.Interval(10, 20),
intervals.Interval(51, 52),
intervals.Interval(54, 55),
intervals.Interval(57, 58)
]
b = [
intervals.Interval(5, 6),
intervals.Interval(9, 11),
intervals.Interval(13, 14),
intervals.Interval(17, 18),
intervals.Interval(20, 25),
intervals.Interval(50, 60)
]
c = [intervals.Interval(100, 200)]
i = [
intervals.Interval(10, 11),
intervals.Interval(13, 14),
intervals.Interval(17, 18),
intervals.Interval(20, 20),
intervals.Interval(51, 52),
intervals.Interval(54, 55),
intervals.Interval(57, 58)
]
self.assertSequenceEqual(intervals.intersection(a, b), i)
self.assertSequenceEqual(intervals.intersection(b, a), i)
self.assertSequenceEqual(intervals.intersection(c, a), [])
self.assertEqual(intervals.intersection([], a), [])
self.assertEqual(intervals.intersection(a, []), [])
