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#!/usr/bin/env python
import unittest
from cogent3 import DNA, make_aligned_seqs
from cogent3.core.annotation import Feature, _Feature
from cogent3.core.location import Map, Span
__author__ = "Peter Maxwell"
__copyright__ = "Copyright 2007-2022, The Cogent Project"
__credits__ = ["Peter Maxwell", "Gavin Huttley", "Rob Knight", "Matthew Wakefield"]
__license__ = "BSD-3"
__version__ = "2023.2.12a1"
__maintainer__ = "Gavin Huttley"
__email__ = "gavin.huttley@anu.edu.au"
__status__ = "Production"
def SimpleAnnotation(parent, locations, name):
return Feature(parent, "", name, locations)
def annotate(parent, start, end, name):
annot = parent.add_annotation(SimpleAnnotation, locations=[(start, end)], name=name)
return annot
def structure(a, depth=0):
annots = [structure(annot, depth + 1) for annot in a.annotations]
if not isinstance(a, _Feature):
return ("seq", len(a), annots)
elif annots:
return (a.name, repr(a.map), annots)
else:
return (a.name, repr(a.map))
class MapTest(unittest.TestCase):
"""Testing annotation of and by maps"""
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)))
def test_maps_on_maps(self):
seq = DNA.make_seq("ATCGATCGAT" * 5, name="base")
feat1 = annotate(seq, 10, 20, "fake")
annotate(feat1, 3, 5, "fake2")
annotate(seq, 1, 3, "left")
seq2 = seq[5:]
self.assertEqual(
structure(seq),
(
"seq",
50,
[("fake", "[10:20]/50", [("fake2", "[3:5]/10")]), ("left", "[1:3]/50")],
),
)
self.assertEqual(
structure(seq2),
("seq", 45, [("fake", "[5:15]/45", [("fake2", "[3:5]/10")])]),
)
def test_get_by_annotation(self):
seq = DNA.make_seq("ATCGATCGAT" * 5, name="base")
seq.add_annotation(Feature, "test_type", "test_label", [(5, 10)])
seq.add_annotation(Feature, "test_type", "test_label2", [(15, 18)])
answer = list(seq.get_by_annotation("test_type"))
self.assertEqual(len(answer), 2)
self.assertEqual(str(answer[0]), "TCGAT")
self.assertEqual(str(answer[1]), "TCG")
answer = list(seq.get_by_annotation("test_type", "test_label"))
self.assertEqual(len(answer), 1)
self.assertEqual(str(answer[0]), "TCGAT")
# test ignoring of a partial annotation
sliced_seq = seq[:17]
answer = list(sliced_seq.get_by_annotation("test_type", ignore_partial=True))
self.assertEqual(len(answer), 1)
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 ",
a[2:4].relative_to(a[2:6]),
"Map([0:2] on Map([2:6] on Map([10:20] on base)))",
),
(
"r ",
a[2:4].relative_to(a[2:6][0:3]),
"Map([0:2] on Map([0:3] on Map([2:6] on Map([10:20] on base))))",
),
]:
print(desc, repr(map), end=" ")
if repr(map) == expected:
print()
else:
print(" <--- ", expected)
bad = True
if __name__ == "__main__":
unittest.main()
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