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# coding: utf-8
from __future__ import print_function, division, absolute_import
from cutadapt.seqio import ColorspaceSequence, Sequence
from cutadapt.adapters import Adapter, ColorspaceAdapter, PREFIX, BACK
from cutadapt.scripts.cutadapt import AdapterCutter
def test_cs_5p():
read = ColorspaceSequence("name", "0123", "DEFG", "T")
adapter = ColorspaceAdapter("CG", PREFIX, 0.1)
cutter = AdapterCutter([adapter])
trimmed_read = cutter(read)
# no assertion here, just make sure the above code runs without
# an exception
def test_statistics():
read = Sequence('name', 'AAAACCCCAAAA')
adapters = [Adapter('CCCC', BACK, 0.1)]
cutter = AdapterCutter(adapters, times=3)
trimmed_read = cutter(read)
# TODO make this a lot simpler
trimmed_bp = 0
for adapter in adapters:
for d in (adapter.lengths_front, adapter.lengths_back):
trimmed_bp += sum(seqlen * count for (seqlen, count) in d.items())
assert trimmed_bp <= len(read), trimmed_bp
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