feat: add list_taxons and list_species_calls utilities to SampleMetadata#1164
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Aadik1ng wants to merge 2 commits intomalariagen:masterfrom
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feat: add list_taxons and list_species_calls utilities to SampleMetadata#1164Aadik1ng wants to merge 2 commits intomalariagen:masterfrom
Aadik1ng wants to merge 2 commits intomalariagen:masterfrom
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@jonbrenas Can you please review this pr? |
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Thanks @Aadik1ng, I am not sure I think there is a duplicated |
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This PR addresses a common user need for simpler taxon and species discovery within sample sets. Currently, discovering which unique taxonomic groups are present in a release requires manually loading all sample metadata and computing unique values.
The new methods
list_taxons()andlist_species_calls()provide a clean, read-only API for this common task, improving the overall user experience for data exploration and preparation.Changes
AnophelesSampleMetadata.list_taxons(): Returns a sorted list of unique taxon names.AnophelesSampleMetadata.list_species_calls(): Returns a sorted list of unique species calls from AIM data (if available).malariagen_data/anoph/sample_metadata.pywith robust implementations that handle missing columns and data types gracefully.Testing
Added new test cases to
tests/anoph/test_sample_metadata.py:test_list_taxonstest_list_species_callsVerified functionality across the full suite of simulated datasets:
ag3af1adir1amin1All 20 newly added test cases passed locally with 100% success.