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# coding: utf-8
from __future__ import print_function, division, absolute_import
from cutadapt.seqio import Sequence
from cutadapt.modifiers import (UnconditionalCutter, NEndTrimmer, QualityTrimmer,
Shortener)
def test_unconditional_cutter():
uc = UnconditionalCutter(length=5)
s = 'abcdefg'
assert UnconditionalCutter(length=2)(s) == 'cdefg'
assert UnconditionalCutter(length=-2)(s) == 'abcde'
assert UnconditionalCutter(length=100)(s) == ''
assert UnconditionalCutter(length=-100)(s) == ''
def test_nend_trimmer():
trimmer = NEndTrimmer()
seqs = ['NNNNAAACCTTGGNNN', 'NNNNAAACNNNCTTGGNNN', 'NNNNNN']
trims = ['AAACCTTGG', 'AAACNNNCTTGG', '']
for seq, trimmed in zip(seqs, trims):
_seq = Sequence('read1', seq, qualities='#'*len(seq))
_trimmed = Sequence('read1', trimmed, qualities='#'*len(trimmed))
assert trimmer(_seq) == _trimmed
def test_quality_trimmer():
read = Sequence('read1', 'ACGTTTACGTA', '##456789###')
qt = QualityTrimmer(10, 10, 33)
assert qt(read) == Sequence('read1', 'GTTTAC', '456789')
qt = QualityTrimmer(0, 10, 33)
assert qt(read) == Sequence('read1', 'ACGTTTAC', '##456789')
qt = QualityTrimmer(10, 0, 33)
assert qt(read) == Sequence('read1', 'GTTTACGTA', '456789###')
def test_shortener():
read = Sequence('read1', 'ACGTTTACGTA', '##456789###')
shortener = Shortener(0)
assert shortener(read) == Sequence('read1', '', '')
shortener = Shortener(1)
assert shortener(read) == Sequence('read1', 'A', '#')
shortener = Shortener(5)
assert shortener(read) == Sequence('read1', 'ACGTT', '##456')
shortener = Shortener(100)
assert shortener(read) == read
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