def alignments_rc_subject(self, seqs):
subjects, query = seqs
subjects[0]["bases"] = reverse_complement(subjects[0]["bases"])
j = JSONBlast(subjects, query, span_origin=False)
j.blastn()
results = j.get_perfect()
return results
def alignments_span_origin_true_query_not_circular(self, seqs):
subjects, query = seqs
query["circular"] = False
j = JSONBlast(subjects, query, span_origin=False)
j.blastn()
results = j.get_perfect()
return results
def test_perfect_matches(self, here):
with open(os.path.join(here, "data/test_data/primer.json"), "r") as f:
subjects = json.load(f)
with open(os.path.join(here, "data/test_data/query.json"), "r") as f:
query = json.load(f)
j = JSONBlast(subjects, query)
j.blastn_short()
alignments = j.get_perfect()
print(len(alignments))
def long_seqs_alignment(self, long_seqs):
subjects, query = long_seqs
j = JSONBlast(
subjects,
query,
span_origin=True,
config=dict(gapopen=3, gapextend=3, penalty=-5, reward=1),
)
j.blastn()
results = j.get_perfect()
return results
def alignments(self, seqs):
subjects, query = seqs
j = JSONBlast(subjects, query, span_origin=False)
j.blastn()
results = j.get_perfect()
return results
