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How to use rcx_tk

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 injectionNumber column is of integer type
• derivation of new metadata: sampleName, sequenceIdentifier, sampleIdentifier and localOrder

Finally, the processed dataframe is saved into user-defined location.

Installation

To install rcx_tk from GitHub repository, do:

git clone git@github.com:RECETOX/rcx-tk.git
cd rcx-tk
poetry install

The main functions are process_metadata_file and process_alkane_ri_file.

The tool can be run using subcommands in the command-line interface, either by python3 or poetry:

python3 -m rcx_tk sequence <path-to-input-data> <path-to-output-data>
python3 -m rcx_tk alkanes <path-to-input-data> <path-to-output-data>
python3 -m rcx_tk msdial <path-to-input-data> <path-to-output-data> [mz_tol_ppm]

poetry run rcx_tk sequence <file-path-to-input-data> <file-path-to-output-data>
poetry run rcx_tk alkanes <file-path-to-input-data> <file-path-to-output-data>
poetry run rcx_tk msdial <file-path-to-input-data> <file-path-to-output-data> [mz_tol_ppm]

Documentation

The project is documented here.

Contributing

If you want to contribute to the development of rcx_tk, have a look at the contribution guidelines.

Credits

This package was created with Cookiecutter and the NLeSC/python-template.