HPO Annotation QC
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
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 data
.
$ java -jar target/HpoAnnotQc.jar download
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.