"""
Tests write output (should it return True or False or write)
"""
import pytest
from dnaio import Sequence

from cutadapt.filters import TooManyN
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):
    # third parameter is True if read should be Trueed
    predicate = TooManyN(count=count)
    _seq = Sequence('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(None, predicate, predicate, pair_filter_mode='first')
    filter_any = PairedEndFilter(None, predicate, predicate, pair_filter_mode='any')
    read1 = Sequence('read1', seq1, qualities='#'*len(seq1))
    read2 = Sequence('read1', seq2, qualities='#'*len(seq2))
    assert filter_legacy(read1, read2, [], []) == predicate.test(read1, [])
    # True entire pair if one of the reads fulfills criteria
    assert filter_any(read1, read2, [], []) == 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]

"""
Tests write output (should it return True or False or write)
"""
import pytest
from dnaio import Sequence

from cutadapt.filters import TooManyN
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):
    # third parameter is True if read should be Trueed
    predicate = TooManyN(count=count)
    _seq = Sequence('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(None, predicate, predicate, pair_filter_mode='first')
    filter_any = PairedEndFilter(None, predicate, predicate, pair_filter_mode='any')
    read1 = Sequence('read1', seq1, qualities='#'*len(seq1))
    read2 = Sequence('read1', seq2, qualities='#'*len(seq2))
    assert filter_legacy(read1, read2, [], []) == predicate.test(read1, [])
    # True entire pair if one of the reads fulfills criteria
    assert filter_any(read1, read2, [], []) == 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]

Tests write output (should it return True or False or write) # third parameter is True if read should be Trueed # True entire pair if one of the reads fulfills criteria