phytest 1.1.0

编写测试文件

我们想对我们的数据强制执行以下约束：

1. 比对有4个序列

2. 序列长度为 100

3. 序列仅包含字符 A、T、G、C、N 和 -

4. 允许序列仅包含单个碱基缺失

5. 最长的 Ns 是 10

6. 这棵树有 4 个提示

7. 树分叉了

8. 对齐和树具有相同的名称

9. 所有内部分支都长于给定阈值

10. 树中没有异常分支

我们可以在 python 文件中编写这些测试example.py

from phytest import Alignment, Sequence, Tree


def test_alignment_has_4_sequences(alignment: Alignment):
    alignment.assert_length(4)


def test_alignment_has_a_width_of_100(alignment: Alignment):
    alignment.assert_width(100)


def test_sequences_only_contains_the_characters(sequence: Sequence):
    sequence.assert_valid_alphabet(alphabet="ATGCN-")


def test_single_base_deletions(sequence: Sequence):
    sequence.assert_longest_stretch_gaps(max=1)


def test_longest_stretch_of_Ns_is_10(sequence: Sequence):
    sequence.assert_longest_stretch_Ns(max=10)


def test_tree_has_4_tips(tree: Tree):
    tree.assert_number_of_tips(4)


def test_tree_is_bifurcating(tree: Tree):
    tree.assert_is_bifurcating()


def test_aln_tree_match_names(alignment: Alignment, tree: Tree):
    aln_names = [i.name for i in alignment]
    tree.assert_tip_names(aln_names)


def test_all_internal_branches_lengths_above_threshold(tree: Tree, threshold=1e-4):
    tree.assert_internal_branch_lengths(min=threshold)


def test_outlier_branches(tree: Tree):
    # Here we create a custom function to detect outliers
    import statistics

    tips = tree.get_terminals()
    branch_lengths = [t.branch_length for t in tips]
    cut_off = statistics.mean(branch_lengths) + statistics.stdev(branch_lengths)
    for tip in tips:
        assert tip.branch_length < cut_off, f"Outlier tip '{tip.name}' (branch length = {tip.branch_length})!"

运行 Phytest

然后我们可以对我们的数据运行这些测试phytest：

phytest examples/example.py -s examples/data/example.fasta -t examples/data/example.tree

通过添加生成报告--report report.html。

从输出中我们可以看到几个测试失败：

FAILED examples/example.py::test_sequences_only_contains_the_characters[Sequence_B] - AssertionError: Invalid pattern found in 'Sequence_B'!
FAILED examples/example.py::test_single_base_deletions[Sequence_C] - AssertionError: Longest stretch of '-' in 'Sequence_C' > 1!
FAILED examples/example.py::test_longest_stretch_of_Ns_is_10[Sequence_D] - AssertionError: Longest stretch of 'N' in 'Sequence_D' > 10!
FAILED examples/example.py::test_outlier_branches - AssertionError: Outlier tip 'Sequence_A' (branch length = 1.0)!

Results (0.07s):
    15 passed
    4 failed
        - examples/example.py:12 test_sequences_only_contains_the_characters[Sequence_B]
        - examples/example.py:16 test_single_base_deletions[Sequence_C]
        - examples/example.py:20 test_longest_stretch_of_Ns_is_10[Sequence_D]
        - examples/example.py:32 test_outlier_branches

有关更多信息，请参阅文档https://phytest-devs.github.io/phytest。