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rcx-tk package provides tools to process the metadata or alkane files.
On the input, the user is expected to supply a path to the metadata/alkane file in tsv/csv/xls/xlsx file. The file is then converted to a dataframe which is further processed. The main steps are:
- columns rearrangement
- validation of the file names
- validation that the
injectionNumbercolumn is of integer type - derivation of new metadata:
sampleName,sequenceIdentifier,sampleIdentifierandlocalOrder
Finally, the processed dataframe is saved into user-defined location.
To install rcx_tk from GitHub repository, do:
git clone git@github.com:RECETOX/rcx-tk.git
cd rcx-tk
poetry installThe main functions are process_metadata_file and process_alkane_ri_file.
The tool can be run also using command-line interface, either by the python3 or poetry:
python3 -m rcx_tk --method='' <path-to-input-data> <path-to-output-data>poetry run rcx_tk --method='' <file-path-to-input-data> <file-path-to-output-data>The project is documented here.
If you want to contribute to the development of rcx_tk, have a look at the contribution guidelines.
This package was created with Cookiecutter and the NLeSC/python-template.