pheval-semphen 0.0.0

Pheval runner for semsimian + phenio db + MONDO (semphen) for disease prioritization via phenotype similarities

pheval_semphen

semsimian + phenio.db for phenopacket disease prioritization
Example of how to run using pheval

• Download http://data.monarchinitiative.org/monarch-kg/latest/phenio.db.gz
  
• Edit config file located in test_configs so that the path_to_phenio references the path to the file we just downloaded
• pheval run -i test_configs/ -t path/to/phenopackets/ -r "semphenphevalrunner" -o test_output/
  
  

Example of how to run just using python executable

• Download http://data.monarchinitiative.org/monarch-kg/latest/phenio.db.gz
  
• python src/pheval_semphen/semphen.py -i path/to/phenopacket(s) -o path/to/results/directory -p path/to/phenio.db file

Acknowledgements

This cookiecutter project was developed from the monarch-project-template template and will be kept up-to-date using cruft.