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import unittest
from cogent3 import DNA, make_aligned_seqs
from cogent3.core.location import FeatureMap, Span
class MapTest(unittest.TestCase):
"""Testing annotation of and by maps"""
def test_spans(self):
# a simple two part map of length 10
map = FeatureMap.from_locations(locations=[(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))
if r != expected:
self.fail(repr((r, expected)))
def test_get_by_annotation(self):
seq = DNA.make_seq("ATCGATCGAT" * 5, name="base")
seq.add_feature(biotype="test_type", name="test_label", spans=[(5, 10)])
seq.add_feature(biotype="test_type", name="test_label2", spans=[(15, 18)])
answer = list(seq.get_features(biotype="test_type"))
self.assertEqual(len(answer), 2)
self.assertEqual(str(seq[answer[0]]), "TCGAT")
self.assertEqual(str(seq[answer[1]]), "TCG")
answer = list(seq.get_features(biotype="test_type", name="test_label"))
self.assertEqual(len(answer), 1)
self.assertEqual(str(seq[answer[0]]), "TCGAT")
# test ignoring of a partial annotation
sliced_seq = seq[:17]
answer = list(sliced_seq.get_features(biotype="test_type", allow_partial=False))
self.assertEqual(len(answer), 1)
self.assertEqual(str(sliced_seq[answer[0]]), "TCGAT")
def test_get_by_seq_annotation_allow_gaps():
aln = make_aligned_seqs(
data={"a": "ATCGAAATCGAT", "b": "ATCGA--TCGAT"}, array_align=False
)
# original version was putting annotation directly on seq
f = aln.add_feature(
seqid="b",
biotype="test_type",
name="test_label",
spans=[(4, 6)],
on_alignment=False,
)
# in the original get_by_seq_annotations(), inside the method it
# used self[feature.map.start : feature.map.end],
# so what was returned was an alignment slice compared to below,
# which is only non-gap positions of "b"
# when we set allow_gaps, we get gaps in an alignment
f = list(aln.get_features(seqid="b", biotype="test_type"))[0]
got = f.get_slice(allow_gaps=True).to_dict()
assert got == {"b": "A--T", "a": "AAAT"}
# otherwise we only get the exact positions represented
got = f.get_slice(allow_gaps=False).to_dict()
assert got == {"b": "AT", "a": "AT"}
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