magenpy 0.1.0

v0.1.0

on Python PyPI

A large scale restructuring of the code base to improve efficiency and usability.

Changed

• Bug fixes across the entire code base.
• Simulator classes have been renamed from GWASimulator to PhenotypeSimulator.
• Moved plotting script to its own separate module.
• Updated some method names / commandline flags to be consistent throughout.

Added

• Basic integration testing with pytest and GitHub workflows.
• Documentation for the entire package using mkdocs.
• Integration testing / automating building with GitHub workflows.
• New implementation of the LD matrix that uses CSR matrix data structures.
  • Quantization / float precision specification when storing LD matrices.
  • Allow user to specify Compressor / Compressor options for Zarr storage.
• New implementation of magenpy_simulate script.
  • Allow users to set random seed.
  • Now accept --prop-causal instead of specifying full mixing proportions.
• Tried to incorporate genome_build into various data structures. This will be useful in the
  future to ensure consistent genome builds across different data types.
• Allow user to pass various metadata to magenpy_ld to save information about dataset
  characteristics.
• New sumstats parsers:
  • Saige sumstats format.
  • plink1.9 sumstats format.
  • GWAS Catalog sumstats format.
• Chained transform function for transforming phenotypes.