pheval-kghg 0.0.0

Pheval runner for monarch knowledge graph phenotype-disease nodes and edges + hypergeometric test (kghg) for disease prioritization via pvalue ranking

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.