1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
|
import unittest
from cogent3 import DNA, make_aligned_seqs
from cogent3.core.annotation_db import GffAnnotationDb
from cogent3.parse.cigar import (
CigarParser,
aligned_from_cigar,
cigar_to_map,
map_to_cigar,
slice_cigar,
)
class TestCigar(unittest.TestCase):
def setUp(self):
self.cigar_text = "3D2M3D6MDM2D3MD"
self.aln_seq = DNA.make_seq("---AA---GCTTAG-A--CCT-")
self.aln_seq1 = DNA.make_seq("CCAAAAAA---TAGT-GGC--G")
self.map, self.seq = self.aln_seq.parse_out_gaps()
self.map1, self.seq1 = self.aln_seq1.parse_out_gaps()
self.slices = [(1, 4), (0, 8), (7, 12), (0, 1), (3, 5)]
self.aln = make_aligned_seqs(
{"FAKE01": self.aln_seq, "FAKE02": self.aln_seq1}, array_align=False
)
self.cigars = {"FAKE01": self.cigar_text, "FAKE02": map_to_cigar(self.map1)}
self.seqs = {"FAKE01": str(self.seq), "FAKE02": str(self.seq1)}
def test_map_to_cigar(self):
"""convert a Map to cigar string"""
assert map_to_cigar(self.map) == self.cigar_text
def test_cigar_to_map(self):
"""test generating a Map from cigar"""
map = cigar_to_map(self.cigar_text)
assert str(map) == str(self.map)
def test_aligned_from_cigar(self):
"""test generating aligned seq from cigar"""
aligned_seq = aligned_from_cigar(self.cigar_text, self.seq)
assert aligned_seq == self.aln_seq
def test_slice_cigar(self):
"""test slicing cigars"""
for start, end in self.slices:
# test by_align = True
map1, loc1 = slice_cigar(self.cigar_text, start, end)
ori1 = self.aln_seq[start:end]
if loc1:
slicealn1 = self.seq[loc1[0] : loc1[1]].gapped_by_map(map1)
assert ori1 == slicealn1
else:
assert len(map1) == len(ori1)
# test by_align = False
map2, loc2 = slice_cigar(self.cigar_text, start, end, by_align=False)
slicealn2 = self.seq[start:end].gapped_by_map(map2)
ori2 = self.aln_seq[loc2[0] : loc2[1]]
assert slicealn2 == ori2
def test_CigarParser(self):
"""test without slice"""
aln = CigarParser(self.seqs, self.cigars)
aln = aln.to_type(array_align=False)
assert aln == self.aln
# test slice
db = GffAnnotationDb()
aln.annotation_db = db
i = 1
for start, end in self.slices:
db.add_feature(
seqid="FAKE01", biotype=f"annot{i}", name="annot", spans=[(start, end)]
)
annot = list(aln.get_features(biotype=f"annot{i}"))
annot = annot[0].union(annot[1:])
slice_aln = annot.as_one_span().get_slice()
i += 1
cmp_aln = CigarParser(
self.seqs,
self.cigars,
sliced=True,
ref_seqname="FAKE01",
start=start,
end=end,
)
assert cmp_aln.to_dict() == slice_aln.to_dict(), (start, end)
if __name__ == "__main__":
unittest.main()
|
