def _match(insert_match, offset, insert_match_size, prob):
if offset < self.min_adapter_overlap:
# The reads are mostly overlapping, to the point where
# there's not enough overhang to do a confident adapter
# match. We return just the insert match to signal that
# error correction can be done even though no adapter
# trimming is required.
return (insert_match, None, None)
# TODO: this is very sensitive to the exact correct choice of adapter.
# For example, if you specifiy GATCGGAA... and the correct adapter is
# AGATCGGAA..., the prefixes will not match exactly and the alignment
# will fail. We need to use a comparison that is a bit more forgiving.
a1_match = compare_prefixes(seq1[insert_match_size:], self.adapter1)
a2_match = compare_prefixes(seq2[insert_match_size:], self.adapter2)
adapter_len = min(offset, self.adapter1_len, self.adapter2_len)
max_adapter_mismatches = round(adapter_len * self.max_adapter_mismatch_frac)
if a1_match[5] > max_adapter_mismatches and a2_match[5] > max_adapter_mismatches:
return None
a1_prob = self.match_probability(a1_match[4], adapter_len)
a2_prob = self.match_probability(a2_match[4], adapter_len)
if (adapter_len > self.adapter_check_cutoff) and ((a1_prob * a2_prob) > self.adapter_max_rmp):
return None
adapter_len1 = min(self.adapter1_len, l1 - insert_match_size)
adapter_len2 = min(self.adapter2_len, l2 - insert_match_size)
best_adapter_matches, best_adapter_mismatches = (a1_match if a1_prob < a2_prob else a2_match)[4:6]
return (
insert_match,
Match(0, adapter_len1, insert_match_size, l1, best_adapter_matches, best_adapter_mismatches),
Match(0, adapter_len2, insert_match_size, l2, best_adapter_matches, best_adapter_mismatches)
)
def compare_suffixes(s1, s2, wildcard_ref=False, wildcard_query=False):
"""
Find out whether one string is the suffix of the other one, allowing
mismatches. Used to find an anchored 3' adapter when no indels are allowed.
"""
s1 = s1[::-1]
s2 = s2[::-1]
_, length, _, _, matches, errors = compare_prefixes(s1, s2, wildcard_ref, wildcard_query)
return (len(s1) - length, len(s1), len(s2) - length, len(s2), matches, errors)
def compare_suffixes(s1, s2, wildcard_ref=False, wildcard_query=False):
"""
Find out whether one string is the suffix of the other one, allowing
mismatches. Used to find an anchored 3' adapter when no indels are allowed.
"""
s1 = s1[::-1]
s2 = s2[::-1]
_, length, _, _, matches, errors = compare_prefixes(
s1, s2, wildcard_ref, wildcard_query)
return (len(s1) - length, len(s1), len(s2) - length, len(s2), matches,
errors)
def _match(insert_match, offset, insert_match_size, prob):
if offset < self.min_adapter_overlap:
# The reads are mostly overlapping, to the point where
# there's not enough overhang to do a confident adapter
# match. We return just the insert match to signal that
# error correction can be done even though no adapter
# trimming is required.
return (insert_match, None, None)
# TODO: this is very sensitive to the exact correct choice of adapter.
# For example, if you specifiy GATCGGAA... and the correct adapter is
# AGATCGGAA..., the prefixes will not match exactly and the alignment
# will fail. We need to use a comparison that is a bit more forgiving.
a1_match = compare_prefixes(seq1[insert_match_size:],
self.adapter1)
a2_match = compare_prefixes(seq2[insert_match_size:],
self.adapter2)
adapter_len = min(offset, self.adapter1_len, self.adapter2_len)
max_adapter_mismatches = round(adapter_len *
self.max_adapter_mismatch_frac)
if a1_match[5] > max_adapter_mismatches and a2_match[
5] > max_adapter_mismatches:
return None
a1_prob = self.match_probability(a1_match[4], adapter_len)
a2_prob = self.match_probability(a2_match[4], adapter_len)
if (adapter_len > self.adapter_check_cutoff) and (
(a1_prob * a2_prob) > self.adapter_max_rmp):
return None
adapter_len1 = min(self.adapter1_len, l1 - insert_match_size)
adapter_len2 = min(self.adapter2_len, l2 - insert_match_size)
best_adapter_matches, best_adapter_mismatches = (
a1_match if a1_prob < a2_prob else a2_match)[4:6]
return (insert_match,
Match(0, adapter_len1, insert_match_size, l1,
best_adapter_matches, best_adapter_mismatches),
Match(0, adapter_len2, insert_match_size, l2,
best_adapter_matches, best_adapter_mismatches))
