This is a fork of BOQA that adds a command line interface and standalone installation.
Requires:
To use a Wikidata-supplemented phenotype annotation file, follow the instructions here.
Installation:
mvn install
jar file will be in target directory
Simple usage by:
cd target
java -jar boqa-0.0.3-SNAPSHOT.jar -hpo {comma-separated HPO IDs} -obo path_to_obo_file -af path_to_association_file
Example usage:
java -jar boqa-0.0.3-SNAPSHOT.jar -hpo "HP:0001263,HP:0100022,HP:0001290,HP:0000522,HP:0002353,HP:0002910" -obo hp.obo -af phenotype_annotation.tab
Help
Run java -jar boqa-0.0.3-SNAPSHOT.jar --help to display all arguments.