def worker(motif):
if self.skip_exact:
return 0
try:
return self.spatt.get_exact_prob(
seq=self.seed.mirna_seq,
motif=utils.clean_seq(motif, self.alphabet),
nobs=self.seed.target_seq.count(motif),
length_seq=self.seed.len_target_seq,
alphabet=self.alphabet,
transitions=self.transitions,
markov_order=self.markov_order,
direction='o'
)
except AttributeError:
return 0
def test_clean_seq(self):
dirty = "ATGCPRASHANTAUGC"
clean = "AGCAAAUGC"
alpha = "AUGC"
self.assertEqual(utils.clean_seq(dirty, alpha), clean)
