ga4ghphetools

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qc ​

This command is intended to be applied to the entire phenopacket store notebook repository. The goal of the command is to perform some basic quality control measures and report problems.

Usage ​

bash
phetools qc -h
Q/C cohort files

Usage: phetools qc [OPTIONS] --hpo <hpo>

Options:
  -d, --directory <dir>  
  -o, --hpo <hpo>        
  -h, --help             Print help

The -d argument specifies the path to the phenopacket store data which contains the individual gene folders, e.g.,

bash
ls ../phenopacket-store/notebooks
CRELD1                HMGCS2                NRAP
(...)

The -o argument is the path to the hp.json file. Be sure to use the latest version.

Example ​

bash
phetools qc -o ../../data/hpo/hp.json -d ../phenopacket-store/notebooks 
Processed 732 gene directories.
Did not recognize MOI: ModeOfInheritance { hpo_id: "HP:0001427", hpo_label: "Mitochondrial inheritance", citation: "PMID:39468830" }