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import pytest
from dnaio import SequenceRecord
from cutadapt.qualtrim import nextseq_trim_index, expected_errors, poly_a_trim_index
def test_nextseq_trim():
s = SequenceRecord("n", "", "")
assert nextseq_trim_index(s, cutoff=22) == 0
s = SequenceRecord(
"n",
"TCTCGTATGCCGTCTTATGCTTGAAAAAAAAAAGGGGGGGGGGGGGGGGGNNNNNNNNNNNGGNGG",
"AA//EAEE//A6///E//A//EA/EEEEEEAEA//EEEEEEEEEEEEEEE###########EE#EA",
)
assert nextseq_trim_index(s, cutoff=22) == 33
@pytest.mark.parametrize(
"sequence,tail",
[
("", ""),
("GGGGGGGGAAAGAAGAAGAAGAAGAAGAAG", ""),
("TTTAGA", ""), # shorter than three nucleotides
("TTTAGAA", ""), # shorter than three nucleotides
("TTTAG", "AAA"),
("TCAAGAAGTCCTTTACCAGCTTTC", "AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA"),
("TCAAGAAGTCCTTTACCAGCTTTC", "AAATAAAAAAAAAAAAAAAAAAAAAAAAAAAAA"),
("GCAGATCACCTT", "AAAAAAAAAAAAAAAAAAAAAAAAAAAATAAA"),
("GCAGATCACCTT", "AAAAAAAAAAAAAAAAAAAAAAAAAAAAT"),
("GCAGATCACCTT", "AAAAAAAAAAAAAAAAAAAAAAAAAAAATCG"),
("GCAGATCACCTAT", "AAAACAAAAAAACAAAAAAAACAAAAAA"),
("TTTT", "AAATAAAA"),
("GGGGGGGGAAAGAAGAAGAAGAAGAAGAAG", "AAA"),
],
)
def test_poly_a_trim_index(sequence, tail):
assert poly_a_trim_index(sequence + tail) == len(sequence)
@pytest.mark.parametrize(
"head,sequence",
[
("", ""),
("", "GGGGGGGGAAAGAAGAAGAAGAAGAAGAAG"),
("", "TGTCCC"),
("", "TTGTCCC"),
("TTT", "GTCCC"),
(
"TTTTTTTTTTTTTTTTTTTTT",
"CAAGAAGTCCCCAGCTTTC",
),
("TTTATTTTTTTTTTTTTTTTTTTTTTTTTTTTT", "CAAGAAGTCCTTTACCAGCTTTC"),
("TTTTTATTTTTTTTTTTTTTTTTTTTTTTTTT", "GCAGATCACCTT"),
("ATTTTTTTTTTTTTTTTTTTTTTTTTTTT", "GCAGATCACCTT"),
("AGCTTTTTTTTTTTTTTTTTTTTTTTTTTTT", "GCAGATCACCTT"),
("TTTTGTTTTTTTGTTTTTTTTGTTTTTT", "GCAGATCACCTAT"),
("TTTATTTT", "AAAA"),
("TTT", "GGGGGGGGAAAGAAGAAGAAGAAGAAGAAG"),
],
)
def test_poly_t_trim_index(head, sequence):
assert poly_a_trim_index(head + sequence, revcomp=True) == len(head)
def test_expected_errors():
def encode_qualities(quals):
return "".join(chr(q + 33) for q in quals)
assert pytest.approx(0.0) == expected_errors("")
assert pytest.approx(0.1) == expected_errors(encode_qualities([10]))
assert pytest.approx(0.01) == expected_errors(encode_qualities([20]))
assert pytest.approx(0.001) == expected_errors(encode_qualities([30]))
assert pytest.approx(0.2) == expected_errors(encode_qualities([10, 10]))
assert pytest.approx(0.11) == expected_errors(encode_qualities([10, 20]))
assert pytest.approx(0.11) == expected_errors(encode_qualities([20, 10]))
assert pytest.approx(0.3) == expected_errors(encode_qualities([10, 10, 10]))
assert pytest.approx(0.111) == expected_errors(encode_qualities([10, 20, 30]))
assert pytest.approx(0.2111) == expected_errors(
encode_qualities([10, 10, 20, 30, 40])
)
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