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Update prp to handle mykrobe csv format #13

Merged
merged 29 commits into from
Jan 4, 2024
Merged

Update prp to handle mykrobe csv format #13

merged 29 commits into from
Jan 4, 2024

Commits on Dec 27, 2023

  1. Update parse_mykrobe_amr_pred to handle mykrobe csv format

    @ryanjameskennedy
    ryanjameskennedy committed Dec 27, 2023
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Commits on Dec 28, 2023

  1. Fix mykrobe variant parser

    @ryanjameskennedy
    ryanjameskennedy committed Dec 28, 2023
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  2. Fix mykrobe phenotype model

    @ryanjameskennedy
    ryanjameskennedy committed Dec 28, 2023
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  3. Fix read_csv in cli

    @ryanjameskennedy
    ryanjameskennedy committed Dec 28, 2023
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  4. Update CHANGELOG.md

    @ryanjameskennedy
    ryanjameskennedy committed Dec 28, 2023
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Commits on Dec 29, 2023

  1. Fix PhenotypeInfo for tbprofiler

    @ryanjameskennedy
    ryanjameskennedy committed Dec 29, 2023
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  2. Set ref_aa & alt_aa to optional

    @ryanjameskennedy
    ryanjameskennedy committed Dec 29, 2023
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  3. Set coverage in LineageInformation to optional

    @ryanjameskennedy
    ryanjameskennedy committed Dec 29, 2023
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  4. Fix mykrobe lineage csv parser

    @ryanjameskennedy
    ryanjameskennedy committed Dec 29, 2023
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  5. Add Mtuberculosis test files

    @ryanjameskennedy
    ryanjameskennedy committed Dec 29, 2023
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  6. Update test function to include create_bonsai_input for mtuberculosis

    @ryanjameskennedy
    ryanjameskennedy committed Dec 29, 2023
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  7. Create and add _default_amr_phenotype to tbprofiler & mykrobe

    @ryanjameskennedy
    ryanjameskennedy committed Dec 29, 2023
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  8. Fix test_virulencefinder.py file spelling

    @ryanjameskennedy
    ryanjameskennedy committed Dec 29, 2023
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  9. Add pytest to pylint.yml GA

    @ryanjameskennedy
    ryanjameskennedy committed Dec 29, 2023
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  10. Simple pylint.yml GA fix

    @ryanjameskennedy
    ryanjameskennedy committed Dec 29, 2023
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  11. Pylint fixes

    @ryanjameskennedy
    ryanjameskennedy committed Dec 29, 2023
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  12. More pylint fixes

    @ryanjameskennedy
    ryanjameskennedy committed Dec 29, 2023
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Commits on Jan 2, 2024

  1. Add docstrings to test functions

    @ryanjameskennedy
    ryanjameskennedy committed Jan 2, 2024
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  2. Fix data_path error

    @ryanjameskennedy
    ryanjameskennedy committed Jan 2, 2024
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  3. Fix data_fpath error

    @ryanjameskennedy
    ryanjameskennedy committed Jan 2, 2024
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  4. Update CHANGELOG.md

    @ryanjameskennedy
    ryanjameskennedy committed Jan 2, 2024
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Commits on Jan 3, 2024

  1. Fix parsers

    @ryanjameskennedy
    ryanjameskennedy committed Jan 3, 2024
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  2. Remove genes from VariantBase

    @ryanjameskennedy
    ryanjameskennedy committed Jan 3, 2024
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  3. Remove _parse_mykrobe_amr_genes

    @ryanjameskennedy
    ryanjameskennedy committed Jan 3, 2024
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  4. Review fixes regarding mykrobe variant parser

    @ryanjameskennedy
    ryanjameskennedy committed Jan 3, 2024
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Commits on Jan 4, 2024

  1. Restored unreleased version

    @mhkc
    mhkc committed Jan 4, 2024
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  2. minor refactoring

    @mhkc
    mhkc committed Jan 4, 2024
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  3. Fix conflicts

    @ryanjameskennedy
    ryanjameskennedy committed Jan 4, 2024
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  4. Update models to handle freq, kmer counts & conf

    @ryanjameskennedy
    ryanjameskennedy committed Jan 4, 2024
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