xlsxreport 0.0.8

Automatic generation of formatted excel reports from MS results

XlsxReport

Introduction

XlsxReport is a Python package for automatically generating formatted excel reports from quantitative mass spectrometry result tables. YAML config files are used to describe the content of a result table and the format of the excel report.

Release

Development is currently in early alpha and the interface is not yet stable.

Install

If you do not already have a Python installation, we recommend installing the Anaconda distribution of Continuum Analytics, which already contains a large number of popular Python packages for Data Science. Alternatively, you can also get Python from the Python homepage. XlsxReport requires Python version 3.9 or higher.

You can use pip to install XlsxReport from the distribution file with the following command:

pip install xlsxreport-X.Y.Z-py3-none-any.whl

To uninstall the XlsxReport package type:

pip uninstall xlsxreport

Installation when using Anaconda

If you are using Anaconda, you will need to install the XlsxReport package into a conda environment. Open the Anaconda navigator, activate the conda environment you want to use, run the "CMD.exe" application to open a terminal, and then use the pip install command as described above.

Setting up the AppData directory

After XlsxReport has been installed the local AppData directory needs to be setup and the default configuration files need to be copied. Running the "xlsxreport_setup" script creates a new XlsxReport folder in the local user data directory, for example "C:/User/user_name/AppData/Local/XlsxReport" on Windows 10, and copies the default config files there.

xlsxreport_setup

Run a script

To generate a simple excel protein report, run the "xlsx_report" script with an input and config file. Here is an example with the default maxquant.yaml config file.

xlsxreport C:/proteinGroups.txt maxquant.yaml

The script "cassiopeia_report" can be used to generate an excel protein report from the Matrix_Export_proteinGroups.txt output of the Cassiopeia R script. In this case it is not necessary to specify a config file, as by default the "cassiopeia.yaml" file will be used.

cassiopeia_report C:/Matrix_Export_proteinGroups.txt