def xtest_daniels_promoter(self): fasta_path = os.path.join(TEST_DATA, 'prVvbHLH35v2.fa') seqrec = SeqIO.read(fasta_path, 'fasta') dom_seq = domesticate(seqrec, '01-02-03-11-12 (PROM+UTR+ATG)', 'GGAG', 'AATG')[1] print len(dom_seq), seqrec.seq.upper() print len(dom_seq), dom_seq.seq assert ('GGAG', 'AATG') == get_prefix_and_suffix(dom_seq.seq, 'BsaI')
def test_get_prefix_and_suffix(self): 'it tests get a suffix and prefix test' gb_path = os.path.join(TEST_DATA, 'pAn11_uniq.gb') seq = SeqIO.read(gb_path, 'gb') seq = seq.seq assert ('AATG', 'GCTT') == get_prefix_and_suffix(seq, 'BsaI') fasta_path = os.path.join(TEST_DATA, 'seq.fasta') seq = SeqIO.read(fasta_path, 'fasta') seq = seq.seq assert ('TGGA', 'AATG') == get_prefix_and_suffix(seq, 'BsaI') # no rec_sites fasta_path = os.path.join(TEST_DATA, 'seq2.fasta') seq = SeqIO.read(fasta_path, 'fasta') seq = seq.seq assert (None, None) == get_prefix_and_suffix(seq, 'BsaI') # no rec_sites fasta_path = os.path.join(TEST_DATA, 'seq_with_intron.fasta') seqrec = SeqIO.read(fasta_path, 'fasta') dom_seq = domesticate(seqrec, None, 'CCAT', 'AATG')[1] assert ('CCAT', 'AATG') == get_prefix_and_suffix(dom_seq.seq, 'BsaI')