ga4ghphetools

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Command-Line Application ​

Some features of ga4ghphetools are available as a command-line application called phetools.

Building the app ​

To compile (build) the command-line application, enter the following command

bash
cargo build --release --features cli

The phetools binary is created here: ./target/release/phetools:

bash
./target/release/phetools 
GA4GH Phenopacket Schema Curation Library Demo

Usage: phetools [COMMAND]

Commands:
  excel        Compare two cohorts and export to Excel
  extract      Extract phenopackets from Cohort files
  etl          Test converting an EtlDto to CohortData
  compare      Compare two cohorts and export to Excel
  json         Q/C Cohort JSON file
  remove-term  Remove HPO Term and its annotations from Cohort Data file
  update       Update HPO term ids/labels
  help         Print this message or the help of the given subcommand(s)

Options:
  -h, --help     Print help
  -V, --version  Print version

Alternative, the application can be run without build using the following command

bash
cargo run --features cli --bin phetools

In the rest of the documentation, we will assume that the application is on the path and just show phetools.

Compare ​

Compare two cohorts and export to Excel

ETL ​

Test converting an EtlDto to CohortData (only useful for debugging/development!).

json ​

Q/C Cohort JSON file (only useful for debugging/development!).

remove-term ​

Remove HPO Term and its annotations from Cohort Data file. This can be useful if an HPO term has been added to a Cohort in error.

To see private features in documentation ​

bash
cargo doc --document-private-items --open