Add new variant search capabilities #73
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susannasiebert
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Overall, this looks good. Would be awesome to have real GRCh38 support (like query coordinate liftover), but I think this PR satisfies the 80/20 rule.
The suggestion to refactor the code is not required for merging this (though it would be nice), but you should autodoc the search_variants_by_allele_registry_id and search_variants_by_name methods under a new docs subsection (maybe By Other Attribute?) under Getting records before we merge it in.
civicpy/civic.py
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| def search_variants_by_allele_registry_id(caid): | ||
| """ | ||
| Search the cache for variants matching the queried Allele Registry ID (CAID) | ||
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| :param String caid: Allele Registry ID to query | ||
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| :return: Returns a list of variant hashes matching the Allele Registry ID | ||
| """ | ||
| variants = get_all_variants() | ||
| return [v for v in variants if v.allele_registry_id == caid] | ||
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| def search_variants_by_name(name): | ||
| """ | ||
| Search the cache for variants matching the queried name | ||
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| :param String name: Variant name to query | ||
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| :return: Returns a list of variant hashes matching the name | ||
| """ | ||
| variants = get_all_variants() | ||
| return [v for v in variants if v.name == name] |
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I think we should use this opportunity to create a generalized search_variants_by_attribute (or, even better, search_class_by_attribute) that mirrors this pattern, with appropriate params passed for the explicit routines. Will be less maintenance down the road.
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This has been implemented
susannasiebert
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@ahwagner I added the documentation for the two new search functions. I also added a catch guard to the bulk coordinate search since it doesn't currently support search by non-GRCh37 builds. |
This PR adds variant search by:
TODO:
Add tests