def test_reverse_complement(self):
self.assertEqual(
utils.reverse_complement("AUGGCCAUUGUAA"),
"UACCGGUAACAUU"[::-1]
)
self.assertEqual(
utils.reverse_complement("ATGGCCATTGTAA"),
"TACCGGTAACATT"[::-1]
)
def find_potential_targets_with_seed(self):
"""
Searches for seed(s) in the target sequence.
Args:
"""
# Reset
out = {
'end_sites': [],
'seed_lengths': [],
'nb_mismatches_except_gu_wobbles': [],
'nb_gu_wobbles': [],
'pairings': [],
}
# Compute
target_seq_rc = utils.reverse_complement(self.target_seq)
# Sliding window (step size 1 of course) on the target sequence with all
# possible target site. Nucleotide(s) before mirna_start_pairing has to
# be paired and we stop before the target site is shorter than
# min_target_length (=>sites length equal to min_target_length are
# included) i is 0-based
upper = self.mirna_start_pairing - 1
lower = self.len_target_seq - self.min_target_length + 1
for i in range(upper, lower):
# We start with the longest seed and stop as soon as we find one
for seed_length in self.allowed_lengths[::-1]:
target_subseq = target_seq_rc[i: i + seed_length]
p = find_pairings(target_subseq, self.mirna_seq,
self.mirna_start_pairing - 1, True)
nb_mismatches_except_gu_wobbles = p[0]
nb_gu_wobbles = p[1]
pairing = p[2]
t_o = (nb_mismatches_except_gu_wobbles <=
self.allowed_mismatches[seed_length])
t_t = nb_gu_wobbles <= self.allowed_gu_wobbles[seed_length]
if t_o and t_t:
# end_site is 1-based and is the end of the target site on
# the real (=not the reverse-complemented) target sequence
end_site = (self.len_target_seq - i +
self.mirna_start_pairing - 1)
out['end_sites'].append(end_site)
out['seed_lengths'].append(seed_length)
out['nb_mismatches_except_gu_wobbles'].append(
nb_mismatches_except_gu_wobbles)
out['nb_gu_wobbles'].append(nb_gu_wobbles)
out['pairings'].append(pairing)
if self.take_best:
break
self.__dict__.update(out)
return out
