def test_map(self):
"""reversing a map with multiple spans should preserve span relative
order"""
forward = [Span(20, 30), Span(40, 50)]
fmap = Map(spans=forward, parent_length=100)
fmap_reversed = fmap.nucleic_reversed()
reverse = [Span(70, 80, reverse=True), Span(50, 60, reverse=True)]
rmap = Map(spans=reverse, parent_length=100)
for i in range(2):
self.assertEqual(fmap_reversed.spans[i], rmap.spans[i])
def _remap(map):
start = map.start
if start == 0:
new_map = map
new_map.parent_length = map.end
else:
spans = []
for span in map.spans:
if span.lost:
spans.append(span)
else:
span.start = span.start - start
span.end = span.end - start
length = span.end
spans.append(span)
new_map = Map(spans=spans, parent_length=length)
return new_map
def cigar_to_map(cigar_text):
"""convert cigar string into Map"""
assert "I" not in cigar_text
spans, posn = [], 0
for n, c in pattern.findall(cigar_text):
if n:
n = int(n)
else:
n = 1
if c == "M":
spans.append(Span(posn, posn + n))
posn += n
else:
spans.append(LostSpan(n))
map = Map(spans=spans, parent_length=posn)
return map
def test_get_coords(self):
"""get_coordinates should return raw coordinates matching input"""
spans = [(0, 9), (20, 32)]
map = Map(spans, parent_length=100)
coords = map.get_coordinates()
self.assertEqual(coords, spans)
# should work for reversed Maps too
spans = [(32, 20), (9, 0)]
map = Map(spans, parent_length=100)
coords = map.get_coordinates()
self.assertEqual(coords, spans)
def test_spans(self):
# a simple two part map of length 10
map = Map([(0, 5), (5, 10)], parent_length=10)
# try different spans on the above map
for ((start, end), expected) in [
((0, 4), "[0:4]"),
((0, 5), "[0:5]"),
((0, 6), "[0:5, 5:6]"),
((5, 10), "[5:10]"),
((-1, 10), "[-1-, 0:5, 5:10]"),
((5, 11), "[5:10, -1-]"),
((0, 10), "[0:5, 5:10]"),
((10, 0), "[10:5, 5:0]"),
]:
r = repr(Span(start, end, reverse=start > end).remap_with(map))
# print (start, end), r,
if r != expected:
self.fail(repr((r, expected)))
self.assertEqual(str(answer[0]), "TCGAT")
def test_get_by_seq_annotation(self):
aln = make_aligned_seqs(
data={"a": "ATCGAAATCGAT", "b": "ATCGA--TCGAT"}, array_align=False
)
b = aln.get_seq("b")
b.add_annotation(Feature, "test_type", "test_label", [(4, 6)])
answer = aln.get_by_seq_annotation("b", "test_type")[0].to_dict()
self.assertEqual(answer, {"b": "A--T", "a": "AAAT"})
if 0: # old, needs fixes
# Maps
a = Map([(10, 20)], parent_length=100)
for (desc, map, expected) in [
("a ", a, "Map([10:20] on base)"),
("i ", a.inverse(), "Map([-10-, 0:10, -80-] on Map([10:20] on base))"),
("1 ", a[5:], "Map([5:10] on Map([10:20] on base))"),
("1r", a[5:].relative_to(b), "Map([15:20] on base)"),
("2 ", a[:5], "Map([0:5] on Map([10:20] on base))"),
("2r", a[:5].relative_to(b), "Map([10:15] on base)"),
(
"r ",
a.relative_to(a[5:]),
"Map([-5-, 0:5] on Map([5:10] on Map([10:20] on base)))",
),
(
"r ",