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"""
Tests write output (should it return True or False or write)
"""
import pytest
from dnaio import SequenceRecord
from cutadapt.predicates import TooManyN, TooHighAverageErrorRate
from cutadapt.steps import PairedEndFilter
@pytest.mark.parametrize(
"seq,count,expected",
[
("AAA", 0, False),
("AAA", 1, False),
("AAACCTTGGN", 1, False),
("AAACNNNCTTGGN", 0.5, False),
("NNNNNN", 1, True),
("ANAAAA", 1 / 6, False),
("ANAAAA", 0, True),
],
)
def test_too_many_n(seq, count, expected):
predicate = TooManyN(count=count)
_seq = SequenceRecord("read1", seq, qualities="#" * len(seq))
assert predicate.test(_seq, []) == expected
@pytest.mark.parametrize(
"seq1,seq2,count,expected",
[
("AAA", "AAA", 0, False),
("AAAN", "AAA", 0, True),
("AAA", "AANA", 0, True),
("ANAA", "AANA", 1, False),
],
)
def test_too_many_n_paired(seq1, seq2, count, expected):
predicate = TooManyN(count=count)
filter_legacy = PairedEndFilter(
predicate, predicate, None, pair_filter_mode="first"
)
filter_any = PairedEndFilter(predicate, predicate, None, pair_filter_mode="any")
read1 = SequenceRecord("read1", seq1, qualities="#" * len(seq1))
read2 = SequenceRecord("read1", seq2, qualities="#" * len(seq2))
assert (filter_legacy(read1, read2, [], []) is None) == predicate.test(read1, [])
# True entire pair if one of the reads fulfills criteria
assert (filter_any(read1, read2, [], []) is None) == expected
def test_invalid_pair_filter_mode():
with pytest.raises(ValueError) as e:
PairedEndFilter(None, None, None, "invalidmode")
assert "pair_filter_mode must be" in e.value.args[0]
@pytest.mark.parametrize(
"quals,rate,expected",
[
# 3 * 0.1 is larger than 0.3 due to floating point rounding.
(chr(43) * 3, 0.1, True),
(chr(43) * 3 + chr(33), 0.1, True), # 3 * 0.1 + 1
(chr(43) * 3 + chr(33), 0.33, False), # 3 * 0.1 + 1
(chr(43) * 3 + chr(33), 0.32, True), # 3 * 0.1 + 1
(chr(126) * 9 + chr(33), 0.1, True), # 9 * 10^-9.3 + 1
],
)
def test_too_high_average_error_rate(quals, rate, expected):
predicate = TooHighAverageErrorRate(rate)
_seq = SequenceRecord("read1", "A" * len(quals), qualities=quals)
assert predicate.test(_seq, []) == expected
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