iimpulse / hpoannotqc

HPO Annotation QC

hpoannotqc

HPO Annotation QC

Building the application

hpoannotqc depends on the forked version of opntolib called OLPG available at https://github.com/monarch-initiative/OLPG Install this locally on the machine you are building hpoannotqc on.

$ mvn install

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.

Download

The application will download several required files to a (new) subdirectory called data.

$ java -jar target/HpoAnnotQc.jar download

Creation of the 'big file'

The following command converts the new files in v2files into a new phenotype_annotation2.tab file.

$ java -jar target/HpoAnnotQc.jar big-file -s /path/hpo-annotation-data/rare-diseases/annotated

This command will output the phenotype.hpoa file as well as a log file named hpoannotQC.log.date. The phenotype.hpoa file can be used as input for phenol.