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monarch-initiative / hpoannotqc

HPO Annotation QC
http://hpo-annotation-qc.readthedocs.io/en/latest/#
MIT License
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hpoannotqc

HPO Annotation QC

This application was developed to do Q/C of the HPO annotation (HPOA) files, the so-called small files. It converts the small files to the "big file" (phenotype.hpoa).

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 available here in a private repository: 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 [--overwrite]

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 named hpoannotQC.log.date. The phenotype.hpoa file can be used as input for phenol.