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