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')
