RDML-Python

A python library to handle RDML files.

Install with pip3

apt install python3 python3-pip

pip3 install rdmlpython

Clone the repository

git clone --recursive https://github.com/RDML-consortium/rdmlpython.git rdmlpython

Setup the environment

Install the dependencies:

sudo apt install python python-pip

pip install lxml numpy

Command line functions

The RDML-Python library offers a command line interface to use core functions. The command line interface is limited and should not replace the Python interface.

Examples:

Display a complete list of command line options:

python3 rdml.py -h

Validate RDML files:

python3 rdml.py -v data.rdml

List all experiments of a RDML file:

python3 rdml.py -le data.rdml

List all runs of the experiment 'exp_1' RDML file:

python3 rdml.py -e exp_1 -lr data.rdml

Run LinRegPCR:

python3 rdml.py -lrp data.rdml --pcrEfficiencyExl 0.05 --excludeNoPlateau --excludeEfficiency "mean" -o out_data.rdml --saveResults temp_1_out_results.tsv --timeRun

Run MeltCurveAnalysis:

python3 rdml.py -mca data.rdml -e "Experiment 1" -r "Run 1" --mcaNormMethod "combined" --mcaFluorSource "normalised" --mcaPeakCutoff 0.0 --saveDerivative out_deriv --saveResults out_results.tsv