def test_nextseq_trim(): s = Sequence('n', '', '') assert nextseq_trim_index(s, cutoff=22) == 0 s = Sequence( 'n', 'TCTCGTATGCCGTCTTATGCTTGAAAAAAAAAAGGGGGGGGGGGGGGGGGNNNNNNNNNNNGGNGG', 'AA//EAEE//A6///E//A//EA/EEEEEEAEA//EEEEEEEEEEEEEEE###########EE#EA') assert nextseq_trim_index(s, cutoff=22) == 33
def test_nextseq_trim(): s = Sequence('n', '', '') assert nextseq_trim_index(s, cutoff=22) == 0 s = Sequence('n', 'TCTCGTATGCCGTCTTATGCTTGAAAAAAAAAAGGGGGGGGGGGGGGGGGNNNNNNNNNNNGGNGG', 'AA//EAEE//A6///E//A//EA/EEEEEEAEA//EEEEEEEEEEEEEEE###########EE#EA' ) assert nextseq_trim_index(s, cutoff=22) == 33
def __call__(self, read): if len(read) == 0: return read stop = nextseq_trim_index(read, self.cutoff, self.base) return self.subseq(read, end=stop)