Python nextseq_trim_index Exemples

Exemple #1

Fichier : testqualtrim.py Projet : 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

Exemple #2

Fichier : test_qualtrim.py Projet : 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

Exemple #3

Fichier : modifiers.py Projet : 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]

Exemple #4

Fichier : modifiers.py Projet : VDBWRAIR/cutadapt

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