HPO Annotation QC
Building the application
hpoannotqc depends on phenol; currently, the latest version of phenol needs to be installed locally, but soon this will all be in maven central.
Running the application
We need to pass the application the location of the hp.obo file as well as the location of the directory with the HPO annotation small files. This repository is currently private available here: https://github.com/monarch-initiative/hpo-annotation-data.
The application will download several required files to a (new) subdirectory called
$ java -jar target/HpoAnnotQc.jar download
Creation of phenotype.hpoa
The following command converts the HPO Annotation files ("small files) into the phenotype_annotation.tab file.
$ java -jar target/HpoAnnotQc.jar big-file -a /path/hpo-annotation-data/rare-diseases/annotated
This command will output the
phenotype.hpoa file as well as a log file
phenotype.hpoa file can be used as input for phenol.