Moving karyotype to anoph
#702
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I added tests to |
| if not self._inversion_tag_path: | ||
| raise FileNotFoundError( | ||
| "The file containing the inversion tags is missing." | ||
| ) |
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FileNotFoundError isn't quite the right exception class here.
| if not self._inversion_tag_path: | |
| raise FileNotFoundError( | |
| "The file containing the inversion tags is missing." | |
| ) | |
| if self._inversion_tag_path is None: | |
| raise NotImplementedError( | |
| "No inversion tags are available for this data resource." | |
| ) |
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I have been of two minds about this one: on one hand, it is true that we have not generated the tags for Af1 and one could argue that NotImplementedError is a more appropriate error for work that is still to be done; on the other hand, the code itself would (I think) work if the file actually existed and it is thus less an issue of missing code and more an issue of a missing input. Also, I can imagine a situation where someone created tags for an inversion and would want to try to use their local file (it is not currently possible, the path that is used is hard-coded in both Ag3 and Af1) in which case the error would come from the path being incorrect (though, an error message referring to the actual path inputed would be more helpful if we want to offer this option).
tests/integration/test_af1.py
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| if inversion == "X_x": | ||
| with pytest.raises(TypeError): | ||
| af1.karyotype( | ||
| inversion=inversion, sample_sets="AG1000G-GH", sample_query=None | ||
| ) | ||
| else: | ||
| with pytest.raises(FileNotFoundError): | ||
| af1.karyotype( | ||
| inversion=inversion, | ||
| sample_sets="1229-VO-GH-DADZIE-VMF00095", | ||
| sample_query=None, | ||
| ) |
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All inversion parameter values should fail with NotImplementedError I think.
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The other question here is if/how to get unit tests using the simulated data. It could be tricky because the simulated data is not guaranteed to generate data at the tag SNP positions. |
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Thanks @alimanfoo. I made most of the changes you recommended. As for the tests, I created another issue #700 to deal with it independently of this as I agree that it is not trivial. |
Addresses #698.
The move is done and all tests pass locally but more tests need to be added (for funestus, for example).