VariantUtils and TestVariantUtils #272
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TomDuraisingh
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| # Uncomment this if needed | ||
| # self.health = get_health_page(key=self.creds) |
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I think good to remove at this point
dcicutils/variant_utils.py
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| SEARCH_RARE_VARIANTS_BY_GENE = '/search/?samplegeno.samplegeno_role=proband&type=VariantSample\ | ||
| &variant.csq_gnomadg_af_popmax.from=0&variant.csq_gnomadg_af_popmax.to=0.001\ | ||
| &variant.genes.genes_most_severe_gene.display_title=' |
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I would prefer f-string for multi-line strings ie:
SEARCH_RARE_VARIANTS_BY_GENE = (f'/search/?samplegeno.samplegeno_role=proband&type=VariantSample'
f'&variant.csq_gnomadg_af_popmax.from=0&'
f'variant.csq_gnomadg_af_popmax.to=0.001&'
f'variant.genes.genes_most_severe_gene.display_title=')
dcicutils/variant_utils.py
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| def sort_dict_in_descending_order(unsorted_dict): | ||
| """sorts dictionary in descending value order""" | ||
| sorted_list = sorted(unsorted_dict.items(), key=lambda x: x[1], reverse=True) |
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sort dict how? answer: by value (key=lambda x: x[1]), so better name is sort_dict_by_value_descending, or better yet make the descending fact a default argument that can be changed so you can just have sort_dict_by_value. You can also make this one line by calling dict directly on line 41.
dcicutils/variant_utils.py
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| return dict(sorted_list) | ||
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| def create_dict_of_mutations(self, gene): | ||
| """cretes dictionary of specified gene and 10+ occuring positions with their number of variants""" |
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Whenever you're creating a dict like this with specific structure, add info on the docstring on what the return value actually looks like.
| return {gene: self.sort_dict_in_descending_order({k: v for k, v in mutation_dict.items() if v >= 10})} | ||
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| @staticmethod | ||
| def return_json(file_name): |
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Generally, it is useful to use type annotations ie:
def return_json(file_name: str) -> dict:
...
See here for more info. This applies to all functions in this file.
dcicutils/variant_utils.py
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| def create_url(self, gene): | ||
| """returns a url to the variants at the most commonly mutated position of a gene""" |
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create_url isn't the best name I'd say... What you have in the docstring should probably be reflected in the name. As a general convention, for basic usage the function name should be as self explanatory as possible.
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| def create_url(self, gene): | ||
| """returns a url to the variants at the most commonly mutated position of a gene""" | ||
| d = self.create_dict_from_json_file('10+sorted_msa_genes_and_mutations.json') |
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Hard-coded filename likely not desired
test/test_variant_utils.py
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| expected_result = vu.SEARCH_RARE_VARIANTS_BY_GENE + mock_gene + ('&variant.POS.from={pos}\ | ||
| &variant.POS.to={pos}&sort=-DP') |
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Likely to be much cleaner with f-strings ie:
expected_result = (f'{vu.SEARCH_RARE_VARIANTS_BY_GENE}{mock_gene}'
f'&variant.POS.from={pos}'
f'&variant.POS.to={pos}&sort=-DP')
It's also not clear this is working as desired, seems like you may want pos actually injected and that isn't happening as written I don't think?
| expected_result = vu.SEARCH_RARE_VARIANTS_BY_GENE + mock_gene + ('&variant.POS.from={pos}\ | ||
| &variant.POS.to={pos}&sort=-DP') | ||
| assert result == expected_result | ||
| mock_create_dict_from_json_file.assert_called_once_with('10+sorted_msa_genes_and_mutations.json') |
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Hardcoded file path again - will break tests in the workflows
| mock_create_dict_from_json_file.assert_called_once_with('10+sorted_msa_genes_and_mutations.json') | ||
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| @patch('dcicutils.variant_utils.VariantUtils.return_json') | ||
| def test_create_list_of_als_park_genes(self, mock_return_json): |
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This tests looks very similar to another above... See if you can figure out how to parametrize them together as one
Pull Request Test Coverage Report for Build 5894264393
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Functions that help filter down data from CGAP.