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ancestral: Accept files to --genes #1353

Merged
merged 7 commits into from
Dec 28, 2023
Merged

ancestral: Accept files to --genes #1353

merged 7 commits into from
Dec 28, 2023

Commits on Dec 28, 2023

  1. read_strains: Split underlying logic into read_entries 

    This can be used in other contexts where newline-delimited entries from
a text file are useful.
    @victorlin
    victorlin committed Dec 28, 2023
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  2. translate: Use read_entries

    @victorlin
    victorlin committed Dec 28, 2023
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  3. translate: Move --gene parsing to a function 

    This allows future re-use.
    @victorlin
    victorlin committed Dec 28, 2023
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  4. ancestral: Use parse_genes_argument 

    Previously, the help text for --genes falsely claimed that it could
accept a file. Now, it can truly claim that.

Move the file parsing functions to utils.
    @victorlin
    victorlin committed Dec 28, 2023
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  5. Add test for ancestral --genes file

    @corneliusroemer @victorlin
    corneliusroemer authored and victorlin committed Dec 28, 2023
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  6. Deprecate read_strains from utils, move to io

    @victorlin
    victorlin committed Dec 28, 2023
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  7. Update changelog

    @victorlin
    victorlin committed Dec 28, 2023
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