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#!/usr/bin/env python
import unittest
from cogent3 import DNA, make_aligned_seqs
from cogent3.parse.cigar import (
CigarParser,
aligned_from_cigar,
cigar_to_map,
map_to_cigar,
slice_cigar,
)
__author__ = "Hua Ying"
__copyright__ = "Copyright 2007-2022, The Cogent Project"
__credits__ = ["Hua Ying", "Gavin Huttley"]
__license__ = "BSD-3"
__version__ = "2023.2.12a1"
__maintainer__ = "Hua Ying"
__email__ = "hua.ying@anu.edu.au"
__status__ = "Production"
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 map1.length == 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
i = 1
for start, end in self.slices:
self.aln.get_seq("FAKE01").add_feature(
"annot%d" % i, "annot", [(start, end)]
)
annot = self.aln.get_annotations_from_any_seq("annot%d" % i)
slice_aln = aln.get_region_covering_all(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 == slice_aln
if __name__ == "__main__":
unittest.main()
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