Moving karyotype to anoph
#702
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I added tests to |
| import allel # type: ignore | ||
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| from numpydoc_decorator import doc | ||
| from ..util import check_types, _karyotype_tags_n_alt |
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If _karyotype_tags_n_alt is only used in this module, perhaps it should be moved here.
| from .karyotype_params import inversion_param | ||
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| class AnophelesKaryotypeData(AnophelesSnpData): |
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| class AnophelesKaryotypeData(AnophelesSnpData): | |
| class AnophelesKaryotypeAnalysis(AnophelesSnpData): |
Nit, suggest slight naming change, then will hopefully also make sense if you later on add in here some functions for calculating inversion allele frequencies.
| # If provided, this analysis version will override the | ||
| # default value provided in the release configuration. |
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| # If provided, this analysis version will override the | |
| # default value provided in the release configuration. |
Cruft.
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| @check_types | ||
| @doc( | ||
| summary="Load tag SNPs for a given inversion in Ag.", |
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| summary="Load tag SNPs for a given inversion in Ag.", | |
| summary="Load tag SNPs for a given inversion.", |
| 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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| @check_types | ||
| @doc( | ||
| summary="Infer karyotype from tag SNPs for a given inversion in Ag.", |
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| summary="Infer karyotype from tag SNPs for a given inversion in Ag.", | |
| summary="Infer karyotype from tag SNPs for a given inversion.", |
| inversion_param: TypeAlias = Annotated[ | ||
| Literal["2La", "2Rb", "2Rc_gam", "2Rc_col", "2Rd", "2Rj"], | ||
| "Name of inversion to infer karyotype for.", | ||
| ] |
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These values will only be valid for Ag. Af would have different possible values. Suggest broadening here to just a string.
| inversion_param: TypeAlias = Annotated[ | |
| Literal["2La", "2Rb", "2Rc_gam", "2Rc_col", "2Rd", "2Rj"], | |
| "Name of inversion to infer karyotype for.", | |
| ] | |
| inversion_param: TypeAlias = Annotated[ | |
| str, | |
| "Name of inversion to infer karyotype for.", | |
| ] |
| 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.
| assert all(df["karyotype_2La"].isin([0, 1, 2])) | ||
| assert all(df["karyotype_2La_mean"].between(0, 2)) | ||
| if inversion == "X_x": | ||
| with pytest.raises(TypeError): |
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Should be a ValueError 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. |
Addresses #698.
The move is done and all tests pass locally but more tests need to be added (for funestus, for example).