def test_region_subject_to_query_00(self):
a = AlignedPair(
("a", "ABCDEFG"),
("b", "---KLMN"),
)
r = AlignedRegion.from_subject(a, 0, 2)
self.assertEqual(r.in_alignment(), (3, 5)) # KL
self.assertEqual(r.in_subject(), (0, 2)) # KL
self.assertEqual(r.in_query(), (3, 5)) # DE
r = AlignedRegion.from_subject(a, 0, 0)
self.assertEqual(r.in_alignment(), (3, 3)) # --- | KLMN
self.assertEqual(r.in_subject(), (0, 0)) # empty sequence
self.assertEqual(r.in_query(), (3, 3)) # ABC | DEFG
def test_from_subject_region_crazy(self):
a = AlignedPair(
("a", "-A-BC-EF---"),
("b", "--HI-JK-LMN"))
r = AlignedRegion.from_subject(a, 0, 3)
self.assertEqual(r.start_idx, 2)
self.assertEqual(r.end_idx, 6)
def test_from_subject_with_endgaps(self):
a = AlignedPair(
("a", "--ABC-EF---"),
("b", "HIJKLMNOPQR"))
r = AlignedRegion.from_subject(a, 1, 7)
self.assertEqual(r.start_idx, 1)
self.assertEqual(r.end_idx, 7)
def test_from_subject_no_endgaps(self):
a = AlignedPair(
("a", "ABCDEF"),
("b", "HIJKLM"))
r = AlignedRegion.from_subject(a, 2, 5)
self.assertEqual(r.start_idx, 2)
self.assertEqual(r.end_idx, 5)
def find_in_seqs(self, seqs):
if seqs.all_matched():
return
# Create the file paths
subject_fp = self._make_fp("subject_{0}.fa".format(self.suffix))
query_fp = self._make_fp("query_{0}.fa".format(self.suffix))
result_fp = self._make_fp("query_{0}.txt".format(self.suffix))
# Search
with open(subject_fp, "w") as f:
write_fasta(f, seqs.get_matched_offset0())
ba = VsearchAligner(subject_fp)
search_args = {
"min_id": round(self.min_pct_id / 100, 2),
"top_hits_only": None}
if self.cores > 0:
search_args["threads"] = self.cores
hits = ba.search(
seqs.get_unmatched_recs(), input_fp=query_fp, output_fp=result_fp,
**search_args)
# Refine
bext = HitExtender(seqs.get_unmatched_recs(), seqs.get_matched_offset0())
for hit in hits:
alignment = bext.extend_hit(hit)
subject_match = seqs.matches[alignment.subject_id]
aligned_region = AlignedRegion.from_subject(
alignment, subject_match.start, subject_match.end)
query_start_idx, query_end_idx = aligned_region.in_query()
query_offset = aligned_region.query_offset()
matchobj = PrimerMatch(
query_start_idx, query_end_idx, query_offset, "Alignment")
yield alignment.query_id, matchobj
def test_region_subject_to_query_crazy_alignment(self):
a = AlignedPair(
("a", "-A-BC-EF---"),
("b", "--HI-JK-LMN"))
r = AlignedRegion.from_subject(a, 0, 3)
self.assertEqual(r.in_subject(), (0, 3)) # HIJ
self.assertEqual(r.in_alignment(), (2, 6)) # HI-J
self.assertEqual(r.in_query(), (1, 3)) # BC in HIJ
r = AlignedRegion.from_subject(a, 1, 4)
self.assertEqual(r.in_subject(), (1, 4)) # IJK
self.assertEqual(r.in_alignment(), (3, 7)) # I-JK
self.assertEqual(r.in_query(), (1, 4)) # BCE in IJK
r = AlignedRegion.from_subject(a)
self.assertEqual(r.in_subject(), (0, 7)) # whole sequence, HIJKLMN
self.assertEqual(r.in_alignment(), (2, 11)) # HI-JK-LMN
self.assertEqual(r.in_query(), (1, 5)) # BCEF in subject
def test_region_subject_to_query_with_endgaps(self):
a = AlignedPair(
("a", "--ABC-EF---"),
("b", "HIJKLMNOPQR"))
r = AlignedRegion.from_subject(a, 0, 3)
self.assertEqual(r.in_subject(), (0, 3)) # HIJ
self.assertEqual(r.in_alignment(), (0, 3))
self.assertEqual(r.in_query(), (0, 1)) # A in HIJ
r = AlignedRegion.from_subject(a, 1, 6)
self.assertEqual(r.in_subject(), (1, 6)) # IJKLM
self.assertEqual(r.in_alignment(), (1, 6))
self.assertEqual(r.in_query(), (0, 3)) # ABC in IJKLM
r = AlignedRegion.from_subject(a)
self.assertEqual(r.in_subject(), (0, 11)) # whole sequence
self.assertEqual(r.in_alignment(), (0, 11))
self.assertEqual(r.in_query(), (0, 5)) # ABCEF in subject
def test_region_subject_to_query_no_endgaps(self):
a = AlignedPair(
("a", "ABCDEF"),
("b", "HIJKLM"))
# In an alignment with no gaps, the query sequence coordinates should
# always match the subject sequence coordinates
r = AlignedRegion.from_subject(a, 0, 3)
self.assertEqual(r.in_alignment(), (0, 3))
rq = AlignedRegion.from_query(a, 0, 3)
self.assertEqual(r.in_alignment(), (0, 3))
r = AlignedRegion.from_subject(a, 1, 5)
self.assertEqual(r.in_alignment(), (1, 5))
rq = AlignedRegion.from_query(a, 1, 5)
self.assertEqual(r.in_alignment(), (1, 5))
r = AlignedRegion.from_subject(a)
self.assertEqual(r.in_alignment(), (0, 6))
rq = AlignedRegion.from_query(a)
self.assertEqual(r.in_alignment(), (0, 6))