def _do_check(self, seq):
min_ = self.min
max_ = self.max
length = uppercase_length(get_str_seq(seq)) if self.ignore_masked else get_length(seq)
passed = True
if min_ is not None and length < min_:
passed = False
if max_ is not None and length > max_:
passed = False
return passed
def _do_check(self, seq):
min_ = self.min
max_ = self.max
length = uppercase_length(get_str_seq(seq)) if self.ignore_masked else get_length(seq)
passed = True
if min_ is not None and length < min_:
passed = False
if max_ is not None and length > max_:
passed = False
return passed
def __call__(self, seqrecords):
'It filters out the short seqrecords.'
stats = self._stats
threshold = self.threshold
reverse = self.reverse
ignore_masked = self.ignore_masked
stats[PROCESSED_PACKETS] += 1
processed_seqs = []
for seqrecord in seqrecords:
stats[PROCESSED_SEQS] += 1
seq = str(seqrecord.seq)
length = uppercase_length(seq) if ignore_masked else len(seq)
passed = True if length >= threshold else False
if reverse:
passed = not(passed)
if passed:
processed_seqs.append(seqrecord)
stats[YIELDED_SEQS] += 1
return processed_seqs
def test_uppercase_length(self):
"It counts the number of uppercase letters in a string"
assert uppercase_length("aCTaGGt") == 4
assert uppercase_length("acagt") == 0
def test_uppercase_length(self):
'It counts the number of uppercase letters in a string'
assert uppercase_length('aCTaGGt') == 4
assert uppercase_length('acagt') == 0
def test_uppercase_length(self):
'It counts the number of uppercase letters in a string'
assert uppercase_length('aCTaGGt') == 4
assert uppercase_length('acagt') == 0
