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