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@brendanreardon brendanreardon released this 10 Mar 13:35
· 21 commits to main since this release
0.4.5
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This release utilizes the v.2023-02-02 release of the underlying MOAlmanac database. It incorporates changes from three pull requests: changing the underlying MOAlmanac database from TinyDB to JSON (#9), adding a simplified input option to run MOAlmanac (#10), and updating datasources (#11).

Additions:

  • A section called function_toggle has been added to moalmanac/config.ini to enable or disable several features of moalmanac, see here for more details.
  • The script moalmanac/simplified_input.py has been added to allow users to input a tab delimited file of somatic variants, germline variants, copy number alterations, and rearrangements. Supporting functions have been added to moalmanac/annotator.py and moalmanac/features.py and example input data has been added to example_data/ to support this change. See here for more details.

Revisions:

  • The underlying moalmanac database is held in memory using the json python library, rather than TinyDB. See here for more details.
  • moalmanac/reporter.py has been refactored to produce the report based on an object.
  • Flask has been upgraded to 2.0.0 in requirements.txt.
  • Documentation has been updated for description of inputs, example outputs, and method usage.
  • Datasources COSMIC and Cancer Gene Census have been updated to version 97, ACMG secondary findings has been updated to version 3, and OncoTree has been updated.

Bug fixes:

  • Warnings are no longer produced when generating the actionability report.
  • Drugs not present in almanac-gdsc-mappings.json no longer cause errors with execution.
  • The output folder is now properly handled by the R subprocesses.
  • Therapies that have not been matched to preclinical drugs produced an error. moalmanac/investigator.py has been revised to only consider therapies that have already been mapped. This was identified in #11.
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