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Feature/sdev 3256 gene list updates pharma cancer predisp #72

Merged
merged 11 commits into from
Dec 8, 2022
Merged

Feature/sdev 3256 gene list updates pharma cancer predisp #72

merged 11 commits into from
Dec 8, 2022

Commits on Oct 19, 2022

  1. SDEV-3256 - bugfix - get_equivalent_features - ignore versions in gen… 

    …e_names or transcripts for equivalent features. Eg. NM_033360.4 should match 'NM_033360' and 'KRAS'.
    @dustinbleile
    dustinbleile committed Oct 19, 2022
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  2. SDEV-3256 - new feature get_preferred_gene_name

    @dustinbleile
    dustinbleile committed Oct 19, 2022
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  3. SDEV-3256 - add get_cancer_predisposition_info and get_pharmacogenomi… 

    …c_info to genes.py
    @dustinbleile
    dustinbleile committed Oct 19, 2022
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Commits on Oct 27, 2022

  1. Merge branch 'develop' of https://github.com/bcgsc/pori_graphkb_python … 

    …into feature/SDEV-3256_gene_list_updates_pharma_cancer_predisp
    @dustinbleile
    dustinbleile committed Oct 27, 2022
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  2. SDEV-3256 - simplify and improve generalizablity of get_pharmacogenom… 

    …ic_info and get_cancer_predisposition_info.
    @dustinbleile
    dustinbleile committed Oct 27, 2022
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  3. SDEV-3256 - remove unused functions and constant.

    @dustinbleile
    dustinbleile committed Oct 27, 2022
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Commits on Oct 28, 2022

  1. Release v1.8.0 

    New Features:
 - new list in genes.py - get_therapeutic_associated_genes
 - constants.py - expanded with commonly used GKB return properties.
 - GraphKBConnection login on init if given username and password.
 - typing_extensions>=3.7.4.2,<4.4
Improvements:
 - new test - match TERT:c.-124C>T
 - skipped test GERO-299 - test_missense_is_not_nonsense - not yet fixed.  (Intercepted by pori_ipr_python).
 - Refactor - simplify __init__.py - move GraphKBConnection to util.py
 - Refactor - simplify - remove custom VERBOSE logging level.
 - update tests - fix test_known_fusion_single_gene_no_match
    @dustinbleile
    dustinbleile committed Oct 28, 2022
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Commits on Nov 2, 2022

  1. Merge pull request #73 from bcgsc/release/v1.8.0_constants_usablity 

    Release/v1.8.0 constants usablity
    @dustinbleile
    dustinbleile authored Nov 2, 2022
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  2. Merge branch 'master' of https://github.com/bcgsc/pori_graphkb_python … 

    …into feature/SDEV-3256_gene_list_updates_pharma_cancer_predisp
    @dustinbleile
    dustinbleile committed Nov 2, 2022
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Commits on Nov 16, 2022

  1. PR - move CHOMOSOMES and PREFERRED_GENE_SOURCE to constants.py

    @dustinbleile
    dustinbleile committed Nov 16, 2022
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Commits on Dec 2, 2022

  1. PR 72 - style suggestion - simplify get commands.

    @dustinbleile
    dustinbleile committed Dec 2, 2022
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