phenopackets / pxftools

A command line utility for operating over Phenotype eXchange Format (PXF) files.

CAUTION! THIS REPO HAS BEED RETIRED!

This initial implementation has now been archived - please refer to the phenopacket-schema repository for the current implementation.

PXFtools command line utility

This project provides a command line utility for operating over Phenotype eXchange Format (PXF) files.

Building

Install sbt (Scala Build Tool) on your system. For Mac OS X, it is easily done using Homebrew: brew install sbt. sbt requires a working Java installation, but you do not need to otherwise install Scala.

sbt compile

Development versions of pxftools may depend on the latest snapshot version of the PhenoPackets Java API. You may need to install the latest phenopackets-api into your local Maven repository before building pxftools.

Running

You can download a prepackaged release.

To build the command-line executable, run:

sbt stage

You will find executables for Unix and Windows in target/universal/stage/bin/. These depend on the libraries in target/universal/stage/lib.

Packaging a release

sbt universal:packageZipTarball

The release package will be at target/universal/pxftools-<version>.tgz

Usage output

Usage

 pxftools [options] command [command options]

Options

   --informat=STRING  : Input format. By default both yaml and json will be attempted. Set the input format to one of:
                        yaml
                        json
                        hpo-phenote
   --out=STRING       : Output file. Omit to write to standard out.
   --outformat=STRING : Output format. Set the output format to one of:
                        yaml
                        json
                        turtle

Commands

   convert <infile> : Read in a PXF file and output in the specified format.

   merge <files> ... : Read in multiple PXF files and output as a single merged PXF file in the specified format.