quant-converter

README

Quantification Converter for PIXLISE

What this is

Go program that converts quantifications to the PIXLISE protobuf-based binary format.

Folder structure

/converter contains code that can be reused externally to convert CSVs to quants /internal/quant-converter contains the code to build the executable cmd, this just calls on code in /converter.

Setup

Make sure you have the data-formats git submodule set up

Building locally

To build, run: local-build.sh This should generate protobuf serialization code in experiment and quantification, run tests, and build an executable quant-converter

NOTE: Since the generated code is now checked in (so it can be included as a go module in other projects, such as the pixlise go API), the above will regenerate it, but in a Gitlab CI build if the generated files differ, the build script will fail, as it's assumed you have locally done development, tested it, and checked in the generated protobuf serialisation code.

Specifically we're talking about ./experiment/experiment.pb.go and ./quantification/quantification.pb.go.

File Format

Output file format is binary, format defined using Protobuf (https://developers.google.com/protocol-buffers).

More information

There are many parameters that can help convert a dataset if there are columns missing. This was done so the initial test datasets work, however in production we'd expect to have a regular set of columns output from piquant and won't need tweaks.

To see the flags in use, look at the test-data repo: convert-quants.sh converts all the test quant maps.