pheval_kghg
monarch knowledge graph phenotype<-->disease nodes and edges + hyper geometric tests for phenopacket disease prioritization
Example of how to run using pheval
- Download and upack monarch knowledge graph https://data.monarchinitiative.org/monarch-kg/latest/monarch-kg.tar.gz
- Edit config file located in test_configs so that the path_to_nodes and path_to_edges fields reference the path to the monarch kg nodes and edges files respectively
- pheval run -i test_configs/ -t path/to/phenopackets/ -r "kghgphevalrunner" -o test_output/
Example of how to run just using python executable (or pip installed executable)
- Download and upack monarch knowledge graph https://data.monarchinitiative.org/monarch-kg/latest/monarch-kg.tar.gz
- python src/pheval_kghg/kghg.py -i path/to/phenopacket(s) -o path/to/results/directory -n path/to/monarch-kg_nodes.tsv -e path/to/monarch-kg_edges.tsv
- pheval-kghg rank-associations -i path/to/phenopacket(s) -o path/to/results/directory -n path/to/monarch-kg_nodes.tsv -e path/to/monarch-kg_edges.tsv
Acknowledgements
This cookiecutter project was developed from the monarch-project-template template and will be kept up-to-date using cruft.
1 maintainer
Metadata
1 maintainer
Release files for pheval-kghg 0.0.0
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Total release size: 19.6 kB
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