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Include Ensembl Tark API for reference retrieval #21

Merged
merged 26 commits into from
Apr 30, 2024
Merged

Include Ensembl Tark API for reference retrieval #21

merged 26 commits into from
Apr 30, 2024

Commits on Mar 4, 2024

  1. First attempt to use tark api

    Xiaoyun Liu committed Mar 4, 2024
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  2. First attemp to use Tark api

    Xiaoyun Liu committed Mar 4, 2024
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  3. Second attempt to use Tark: add json.parse

    Xiaoyun Liu committed Mar 4, 2024
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Commits on Mar 13, 2024

  1. Retrieve transcript info with version number using Tark

    Xiaoyun Liu committed Mar 13, 2024
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Commits on Mar 26, 2024

  1. Add Tark api in configuration

    Xiaoyun Liu committed Mar 26, 2024
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  2. merge tark during fetching reference

    Xiaoyun Liu committed Mar 26, 2024
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  3. add tark test with json files

    Xiaoyun Liu committed Mar 26, 2024
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  4. fix error when using tark in normalise function

    Xiaoyun Liu committed Mar 26, 2024
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  5. fix retrive order: fetch from tark directly

    Xiaoyun Liu committed Mar 26, 2024
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Commits on Mar 29, 2024

  1. fix bug: retrieve earlier version

    Xiaoyun Liu committed Mar 29, 2024
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Commits on Apr 2, 2024

  1. fix errors in tests

    Xiaoyun Liu committed Apr 2, 2024
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Commits on Apr 5, 2024

  1. Add tests

    Xiaoyun Liu committed Apr 5, 2024
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Commits on Apr 8, 2024

  1. update fetch function and add tests

    Xiaoyun Liu committed Apr 8, 2024
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  2. remove some prints

    Xiaoyun Liu committed Apr 8, 2024
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  3. add monkeypatch retriver

    Xiaoyun Liu committed Apr 8, 2024
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Commits on Apr 16, 2024

  1. re-orgnised parser for ensembl json

    Xiaoyun Liu committed Apr 16, 2024
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Commits on Apr 24, 2024

  1. Add api choice in CLI

    Xiaoyun Liu committed Apr 24, 2024
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  2. Remove a print

    Xiaoyun Liu committed Apr 24, 2024
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Commits on Apr 25, 2024

  1. Add option ensembl_tark and ensembl_rest in CLI

    Xiaoyun Liu committed Apr 25, 2024
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Commits on Apr 29, 2024

  1. Implement retrieve sequence and annotation for model type

    Xiaoyun Liu committed Apr 29, 2024
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  2. Fix sequence retrieval bug, add check and doc string in parse

    Xiaoyun Liu committed Apr 29, 2024
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  3. Fix sequence retrieval bug, add check and doc string in parse

    Xiaoyun Liu committed Apr 29, 2024
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  4. Fix sequence retrieval bug, add check and doc string in parse

    Xiaoyun Liu committed Apr 29, 2024
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  5. Clean up and implement ensembl in reference source

    Xiaoyun Liu committed Apr 29, 2024
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  6. Clean up

    Xiaoyun Liu committed Apr 29, 2024
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Commits on Apr 30, 2024

  1. Clean and refactor

    Xiaoyun Liu committed Apr 30, 2024
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