robertaboukhalil / oct4th

CLI for converting CSV/TSV files to Excel spreadsheets without mangling gene names

oct4th

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CLI tool to convert CSV/TSV files to Excel spreadsheets, while not converting gene names (e.g. OCT4, DEC1) into dates in the process.

For converting small files, you can use the Oct4th web application.

To learn more about this issue, check out this article.

Installation

pip3 install -U oct4th

Usage

As a CLI:

# Convert a CSV file to XLSX
oct4th --input ./data/test.csv --output ./data/test.xlsx

From Python:

import oct4th

# Convert a CSV file to XLSX
oct4th.csv_to_xlsx(file_in="./data/test.csv", file_out="./data/test.xlsx")

Developing

python3 -m venv ve
. ve/bin/activate
pip install setuptools wheel twine pytest xlsxwriter pandas xlrd

Run Tests

PYTHONPATH=. pytest ./tests/

Deploy

# Clean up and rebuild
. ve/bin/activate
rm -rf ./build/ ./dist/
python3 setup.py sdist bdist_wheel

# Check before deploying
twine check dist/*

# Upload to testpypi
python3 -m twine upload --repository testpypi dist/*

# Test install
deactivate; pip3 install -U -i https://test.pypi.org/simple/ oct4th==1.0.0b9

# Deploy to pypi
# python3 -m twine upload --repository pypi dist/*

oct4th's Issues

Can we save the converted table into CSV format?

Dear development team,

Thank you for developing such a wonderful tool!
I was surprised by its conciseness and convenience in addressing long-term issues in bioinformatics.

I've observed that the tool currently supports output only in Excel format.
While this remains convenient, are there any plans to include the option to save the output in CSV or other table formats?
Introducing such flexibility would greatly enhance the tool's usability for diverse applications! :)

Thanks in advance,
Seoyeon