Python nextseq_trim_index Examples

Example #1

File: testqualtrim.py Project: jgibson2/cutadapt-vbim

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

Example #2

File: test_qualtrim.py Project: marcelm/cutadapt

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

Example #3

File: modifiers.py Project: rubysheng/cutadapt

	def __call__(self, read, matches):
		stop = nextseq_trim_index(read, self.cutoff, self.base)
		self.trimmed_bases += len(read) - stop
		return read[:stop]

Example #4

File: modifiers.py Project: VDBWRAIR/cutadapt

	def __call__(self, read):
		stop = nextseq_trim_index(read, self.cutoff, self.base)
		self.trimmed_bases += len(read) - stop
		return read[:stop]