A python library to handle RDML files.
apt install python3 python3-pip
pip3 install rdmlpython
git clone --recursive https://github.com/RDML-consortium/rdmlpython.git rdmlpython
Install the dependencies:
sudo apt install python python-pip
pip install lxml numpy
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