def test_with_site_outside_cds(self):
dna_seq = Seq("GAGATCCGGTCCATATCTTATTCAACGCAAGAATTCAT",
unambiguous_dna)
new_seq = recode_site_from_cds(dna_seq, self.EcoRI, self.codon_sampler,
self.cds_start, self.cds_end)
assert new_seq.find(self.EcoRI) >= 0
assert new_seq == dna_seq
def test_bad_cds_with_site(self):
# NOTE: CDS is different in this test
cds_start = 10
cds_end = 27
dna_seq = Seq("GAGATCCGGAATTCATCTTATTCAACGAAGTTGTTAT")
with raises(PepsynError):
new_seq = recode_site_from_cds(dna_seq, self.EcoRI,
self.codon_sampler, cds_start,
cds_end)
def test_with_site_on_left_boundary(self):
dna_seq = Seq("GAGATCCGGTCCATATCTTATTCGAATTCAGTTGTTAT")
new_seq = recode_site_from_cds(dna_seq, self.EcoRI, self.codon_sampler,
self.cds_start, self.cds_end)
orig_trans = dna_seq[self.cds_start:self.cds_end].translate(
table=self.codon_sampler.table)
new_trans = new_seq[self.cds_start:self.cds_end].translate(
table=self.codon_sampler.table)
assert new_seq.find(self.EcoRI) == -1
assert new_seq != dna_seq
assert len(new_seq) == len(dna_seq)
assert new_seq[:self.cds_start] == dna_seq[:self.cds_start]
assert new_seq[self.cds_end:] == dna_seq[self.cds_end:]
assert new_trans == orig_trans
def test_no_site(self):
dna_seq = Seq("GAGATCCGGTCCATATCTTATTCAACGCAAGTTGTTAT")
new_seq = recode_site_from_cds(dna_seq, self.EcoRI, self.codon_sampler,
self.cds_start, self.cds_end)
assert new_seq.find(self.EcoRI) == -1
assert new_seq == dna_seq