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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, as_map
from cogent3.core.sequence import DnaSequence, RnaSequence
__author__ = "Gavin Huttley"
__copyright__ = "Copyright 2007-2022, The Cogent Project"
__credits__ = ["Gavin Huttley"]
__license__ = "BSD-3"
__version__ = "2023.2.12a1"
__maintainer__ = "Gavin Huttley"
__email__ = "gavin.huttley@anu.edu.au"
__status__ = "Production"
def makeSampleSequence(with_gaps=False):
raw_seq = "AACCCAAAATTTTTTGGGGGGGGGGCCCC"
cds = (15, 25)
utr = (12, 15)
if with_gaps:
raw_seq = raw_seq[:5] + "-----" + raw_seq[10:-2] + "--"
seq = DNA.make_seq(raw_seq)
seq.add_annotation(Feature, "CDS", "CDS", [cds])
seq.add_annotation(Feature, "5'UTR", "5' UTR", [utr])
return seq
def makeSampleAlignment():
seq1 = makeSampleSequence()
seq2 = makeSampleSequence(with_gaps=True)
seqs = {"FAKE01": seq1, "FAKE02": seq2}
aln = make_aligned_seqs(data=seqs, array_align=False)
aln.add_annotation(Feature, "misc_feature", "misc", [(12, 25)])
aln.add_annotation(Feature, "CDS", "blue", [(15, 25)])
aln.add_annotation(Feature, "5'UTR", "red", [(2, 4)])
aln.add_annotation(Feature, "LTR", "fake", [(2, 15)])
return aln
class TestAnnotations(unittest.TestCase):
def setUp(self):
self.seq = makeSampleSequence()
self.aln = makeSampleAlignment()
def test_inherit_feature(self):
"""should be able to subclass and extend _Feature"""
class NewFeat(_Feature):
def __init__(self, *args, **kwargs):
super(NewFeat, self).__init__(*args, **kwargs)
def newMethod(self):
if len(self.map.spans) > 1:
as_one = self.as_one_span() # should create new instance of NewFeat
return as_one.newMethod()
return True
seq = DNA.make_seq("ACGTACGTACGT")
f = seq.add_annotation(
NewFeat, as_map([(1, 3), (5, 7)], len(seq)), type="gene", name="abcd"
)
self.assertEqual(type(f.as_one_span()), NewFeat)
self.assertEqual(type(f.get_shadow()), NewFeat)
f2 = seq.add_annotation(
NewFeat, as_map([(3, 5)], len(seq)), type="gene", name="def"
)
self.assertEqual(
type(seq.get_region_covering_all([f, f2], feature_class=NewFeat)), NewFeat
)
# now use the new method
f.newMethod()
def test_slice_seq_with_annotations(self):
newseq = self.seq[:5] + self.seq[10:]
for annot_type in ["CDS", "5'UTR"]:
orig = str(list(self.seq.get_by_annotation(annot_type))[0])
new = str(list(newseq.get_by_annotation(annot_type))[0])
assert orig == new, (annot_type, orig, new)
def test_aln_annotations(self):
"""test that annotations to alignment and its' sequences"""
aln_expecteds = {
"misc_feature": {"FAKE01": "TTTGGGGGGGGGG", "FAKE02": "TTTGGGGGGGGGG"},
"CDS": {"FAKE01": "GGGGGGGGGG", "FAKE02": "GGGGGGGGGG"},
"5'UTR": {"FAKE01": "CC", "FAKE02": "CC"},
"LTR": {"FAKE01": "CCCAAAATTTTTT", "FAKE02": "CCC-----TTTTT"},
}
seq_expecteds = {
"CDS": {"FAKE01": "GGGGGGGGGG", "FAKE02": "GGGGGGGGGG"},
"5'UTR": {"FAKE01": "TTT", "FAKE02": "TTT"},
}
for annot_type in ["misc_feature", "CDS", "5'UTR", "LTR"]:
observed = list(self.aln.get_by_annotation(annot_type))[0].to_dict()
expected = aln_expecteds[annot_type]
assert observed == expected, (annot_type, expected, observed)
if annot_type in ["misc_feature", "LTR"]:
continue # because seqs haven't been annotated with it
for name in self.aln.names:
observed = list(
self.aln.named_seqs[name].data.get_by_annotation(annot_type)
)[0]
observed = str(observed)
expected = seq_expecteds[annot_type][name]
assert str(observed) == expected, (annot_type, name, expected, observed)
def test_slice_aln_with_annotations(self):
"""test that annotations of sequences and alignments survive alignment
slicing."""
aln_expecteds = {
"misc_feature": {"FAKE01": "TTTGGGGGGGGGG", "FAKE02": "TTTGGGGGGGGGG"},
"CDS": {"FAKE01": "GGGGGGGGGG", "FAKE02": "GGGGGGGGGG"},
"5'UTR": {"FAKE01": "CC", "FAKE02": "CC"},
"LTR": {"FAKE01": "CCCTTTTT", "FAKE02": "CCCTTTTT"},
}
newaln = self.aln[:5] + self.aln[10:]
feature_list = newaln.get_annotations_matching("LTR")
for annot_type in ["LTR", "misc_feature", "CDS", "5'UTR"]:
feature_list = newaln.get_annotations_matching(annot_type)
new = newaln.get_region_covering_all(feature_list).get_slice().to_dict()
expected = aln_expecteds[annot_type]
assert expected == new, (annot_type, expected, new)
if annot_type in ["misc_feature", "LTR"]:
continue # because seqs haven't been annotated with it
for name in self.aln.names:
orig = str(
list(self.aln.get_annotations_from_seq(name, annot_type))[
0
].get_slice()
)
new = str(
list(newaln.get_annotations_from_seq(name, annot_type))[
0
].get_slice()
)
assert orig == new, (name, annot_type, orig, new)
def test_feature_projection(self):
expecteds = {"FAKE01": "CCCAAAATTTTTT", "FAKE02": "CCC-----TTTTT"}
aln_ltr = self.aln.get_annotations_matching("LTR")[0]
for seq_name in ["FAKE01", "FAKE02"]:
expected = expecteds[seq_name]
seq_ltr = self.aln.project_annotation(seq_name, aln_ltr)
if "-" in expected:
self.assertRaises(ValueError, seq_ltr.get_slice)
seq_ltr = seq_ltr.without_lost_spans()
expected = expected.replace("-", "")
self.assertEqual(seq_ltr.get_slice(), expected)
def test_feature_copy_annotations_to(self):
"""test correct copy of annotations"""
orig = DnaSequence("TTTTTTTTTTAAAA", name="Orig")
annot = orig.add_annotation(Feature, "exon", "fred", [(0, 14)])
seq = RnaSequence("UUUUUUUUUUAAAA", name="Test")
got = annot.copy_annotations_to(seq)
self.assertEqual(len(orig.annotations), len(got.annotations))
for src, dest in zip(orig.annotations, got.annotations):
self.assertEqual(src.get_coordinates(), dest.get_coordinates())
self.assertIsInstance(src, dest.__class__)
self.assertIs(dest.parent, seq)
with self.assertRaises(AssertionError):
_ = annot.copy_annotations_to(seq[:-2])
def test_reverse_complement(self):
"""test correct translation of annotations on reverse complement."""
aln_expecteds = {
"misc_feature": {"FAKE01": "TTTGGGGGGGGGG", "FAKE02": "TTTGGGGGGGGGG"},
"CDS": {"FAKE01": "GGGGGGGGGG", "FAKE02": "GGGGGGGGGG"},
"5'UTR": {"FAKE01": "CC", "FAKE02": "CC"},
"LTR": {"FAKE01": "CCCAAAATTTTTT", "FAKE02": "CCC-----TTTTT"},
}
seq_expecteds = {
"CDS": {"FAKE01": "GGGGGGGGGG", "FAKE02": "GGGGGGGGGG"},
"5'UTR": {"FAKE01": "TTT", "FAKE02": "TTT"},
}
rc = self.aln.rc()
# rc'ing an Alignment or Sequence rc's their annotations too. This means
# slicing returns the same sequence as the non-rc'd alignment/seq
for annot_type in ["misc_feature", "CDS", "5'UTR", "LTR"]:
observed = list(self.aln.get_by_annotation(annot_type))[0].to_dict()
expected = aln_expecteds[annot_type]
assert observed == expected, ("+", annot_type, expected, observed)
observed = list(rc.get_by_annotation(annot_type))[0].to_dict()
expected = aln_expecteds[annot_type]
assert observed == expected, ("-", annot_type, expected, observed)
if annot_type in ["misc_feature", "LTR"]:
continue # because seqs haven't been annotated with it
for name in self.aln.names:
observed = list(
self.aln.named_seqs[name].data.get_by_annotation(annot_type)
)[0]
observed = str(observed)
expected = seq_expecteds[annot_type][name]
assert str(observed) == expected, (
"+",
annot_type,
name,
expected,
observed,
)
observed = list(rc.named_seqs[name].data.get_by_annotation(annot_type))[
0
]
observed = str(observed)
expected = seq_expecteds[annot_type][name]
assert str(observed) == expected, (
"-",
annot_type,
name,
expected,
observed,
)
class TestMapSpans(unittest.TestCase):
"""Test attributes of Map & Spans classes critical to annotation
manipulation."""
def test_span(self):
forward = Span(20, 30)
reverse = Span(70, 80, reverse=True)
assert forward.reversed_relative_to(100) == reverse
assert reverse.reversed_relative_to(100) == forward
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])
if __name__ == "__main__":
unittest.main()
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