def define_adapter_presence_substitutions_only(self, adapter, max_substitutions):
"""Sets the adapter_absent attribute according to whether a match is found with a number of substitutions
less or equal to
edit_threshold.
:rtype : None
Args:
self, adapter, edit_threshold
Returns:
None
Args:
self, adapter, max_substitutions
Returns:
None
"""
# Solves the straightforward case where the adapter is exactly present in the read
if adapter in self.sequence_line:
self.adapter_present = True
return
# Otherwise, look for an approximate match of the adapter, less than max_substitutions different
# First do a preliminary (hopefully faster) check whether the adapter is present as an approximate match in
# the read sequence within a Levenshtein distance equal to the allowed number of substitutions
# Two sequences less than N substitutions apart are automatically less than a N edits apart (the reciprocal
# is not true). If the Levenshtein code is faster, then it will save a lot of time pre-filtering adapters
# within the Levenshtein distance, which are much more likely to contain adapters. The slower code checking
# the mismatch distance will then be called on these pre-filtered reads to confirm whether it is an actual
# substituted match or if the Levensthein match involved insertions and deletions
# If 1 or more approximate matches of the adapter were found within a Levenshtein distance of max_substitutions
if len(fuzzysearch.find_near_matches(adapter, self.sequence_line, max_substitutions)):
# scan the read sequence for a potential substituted match
# for each subsequence of the sequence_line of length identical to the adapter (last starting position is
# length of the adapter before the end of the read)
for index in range(len(self.sequence_line) - len(adapter) + 1):
# check if the adapter is less than max_substitutions away from the subsequence
result = ApproxMatch.approx_substitute(adapter, self.sequence_line[index:index + len(adapter)],
max_substitutions)
# If a match was found (result is TRUE)
if result:
# set the adapter presence to True (and stop the function here)
self.adapter_present = True
return
def assign_to_unique_sample(self, sequenced_barcode):
"""Resolves the barcode to a unique sample, or returns False if the barcode is ambiguous.
Args:
self, sequenced_barcode
Returns:
The name of the sample matched to the barcode, or False if the barcode was ambiguous.
"""
# Temporary list to store the expected barcodes which approximately match the sequenced barcode
matches = []
# For each expected barcode
for expected in list(self.expected.keys()):
# check if the sequenced barcode is an approximate match to each of them
if ApproxMatch.approx_substitute(expected, sequenced_barcode, 1):
matches.append(expected)
# If the sequenced barcode is an approximate match of a unique expected barcode
if len(matches) == 1:
# return the corresponding sample name
return self.expected[matches[0]]
# If the sequenced barcode is an approximate match of more than one expected barcode, or not a match at all
else:
# return False
return False
