monarch-initiative/hpoannotqc

Name: hpoannotqc

Owner: Monarch Initiative

Description: HPO Annotation QC

Created: 2018-02-02 22:27:08.0

Updated: 2018-02-03 02:12:39.0

Pushed: 2018-02-04 12:50:33.0

Homepage: null

Size: 1193

Language: Java

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README

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.

n 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

The following two steps convert the old file formats to new V2 small file formats and put the new files into a directory called v2files; the second step converts the new files in v2files into a new phenotype_annotation2.tab file.

va -jar target/HpoAnnotQc.jar convert -h /path/to/hp.obo -a /path/hpo-annotation-data/rare-diseases/annotated
va -jar target/HpoAnnotQc.jar big-file

The runs will fill log files named hpoannotQC.log.date. The files show several things including lines that were changed in the course of the Q/C procedures.