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Refactor loading genomics #168

Merged
merged 21 commits into from
Aug 24, 2023
Merged

Refactor loading genomics #168

merged 21 commits into from
Aug 24, 2023

Commits on Aug 23, 2023

  1. remove useless step

    @CunliangGeng
    CunliangGeng committed Aug 23, 2023
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  2. remove completed TODO comment

    @CunliangGeng
    CunliangGeng committed Aug 23, 2023
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  3. remove param bgc_genome_mapping from func map_strain_to_bgc 

    The StrainCollection should contains the bgc id, so genome id is not required.
    @CunliangGeng
    CunliangGeng committed Aug 23, 2023
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  4. add property names to class Strain

    @CunliangGeng
    CunliangGeng committed Aug 23, 2023
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  5. update the logic of method __contains__ in StrainCollection

    @CunliangGeng
    CunliangGeng committed Aug 23, 2023
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  6. add method has_name to class StrainCollection

    @CunliangGeng
    CunliangGeng committed Aug 23, 2023
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  7. update method has_strain in classes

    @CunliangGeng
    CunliangGeng committed Aug 23, 2023
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  8. rename MibigBGCLoader to MibigLoader

    @CunliangGeng
    CunliangGeng committed Aug 23, 2023
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  9. rename method get_bgc_genome_mapping to get_strain_bgc_mapping

    @CunliangGeng
    CunliangGeng committed Aug 23, 2023
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  10. refactor mibig loading related code to _load_mibig method

    @CunliangGeng
    CunliangGeng committed Aug 23, 2023
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  11. remove mibig downloading in class DatasetLoader

    @CunliangGeng
    CunliangGeng committed Aug 23, 2023
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  12. refactor bigscape running code to _run_bigscape

    @CunliangGeng
    CunliangGeng committed Aug 23, 2023
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  13. refactor method _load_genomics

    @CunliangGeng
    CunliangGeng committed Aug 23, 2023
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  14. add TODO comments

    @CunliangGeng
    CunliangGeng committed Aug 23, 2023
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  15. add TODO comment

    @CunliangGeng
    CunliangGeng committed Aug 23, 2023
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  16. change StrainCollection._strain_dict_name dict value type to list 

    - Updated methods `add`, `remove` and `lookup` accordingly
- Updated and added unit tests for updated methods
    @CunliangGeng
    CunliangGeng committed Aug 23, 2023
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  17. update references of method StrainCollection.lookup

    @CunliangGeng
    CunliangGeng committed Aug 23, 2023
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Commits on Aug 24, 2023

  1. change KeyError to ValueError in StrainCollection.lookup method

    @CunliangGeng
    CunliangGeng committed Aug 24, 2023
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  2. add ValueError to StrainCollection.remove method

    @CunliangGeng
    CunliangGeng committed Aug 24, 2023
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  3. change KeyError to ValueError for function map_strain_to_bgc

    @CunliangGeng
    CunliangGeng committed Aug 24, 2023
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  4. update docstring for function map_strain_to_bgc

    @CunliangGeng
    CunliangGeng committed Aug 24, 2023
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