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This initial implementation has now been archived - please refer to the phenopacket-schema repository for the current implementation.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

pxftools's Issues

Handle multiple pubs on line in HPO-phenote files

Occasionally multiple publications are entered, separated by '; '. Example in OMIM-194190.tab.

Concat/merge command

The merge command needs implementation.

Merge command needs to be context-aware for identifiers

Different input files may have different embedded contexts. Identifiers need to be expanded before trying to merge.

auto-unfold and fold of descriptions

An idea from Chris, see https://github.com/owlcollab/owltools/wiki/Annotation-Extension-Folding

Add parser/writer for GAF

Many groups use GAFs for phenotypes as well as GO - e.g. planteome (cc @jhpoelen)

Conversely, pxf is generic enough for GO annotations (which are essentially normal, evolved phenotypes for genes)

It would be useful to read/write from GAFs into the phenopacket datamodel.

There are also a family of similar formats which could follow the same pattern. E.g. PAFs:
phenopackets/phenopacket-format#67

And of course the HPOA (non-phenote) TSVs

Add -h as synonym for --help

-h is common, but pxftools expects --help, which is confusing for the newbie

Command for updating obsolete ontology terms

Should the ontologies be provided on the command line? Obtained automatically somehow?

Summarize command

What are the requirements for summarize?

Compare command

What are the requirements for compare?

Travis build is failing because of snapshot dependency

The project currently depends on a phenopackets-api SNAPSHOT version. Not being available in Maven central, this is causing the Travis build to fail.