A utility for creation of pepXML files from Python objects and TandemXML files.
pyteomics.pepxmltk - a pepXML writer and Tandem2XML converter
pyteomics.pepxmltk is a module based on the [pyteomics](https://pyteomics.readthedocs.io/) package that allows creation of [pepXML](http://tools.proteomecenter.org/wiki/index.php?title=Formats:pepXML) files from Python objects of a certain structure. The structure corresponds to tokens generated by the pyteomics TandemXML parser.
This package provides a module that can be used for writing pepXML files from your Python code, as well as a command-line script for conversion, merging or filtering of X!Tandem files to pepXML. Unlike its analog from Trans-Proteomic Pipeline (TPP), the script is capable of handling non-standard enzymes.
The package contains two scripts: pepxmltk.py and runtandem. pepxmltk.py does conversion from X!Tandem XML to pepXML, or from pepXML to pepXML, while optionally combining multiple files and performing FDR filtering. runtandem is a CLI wrapper that simplifies the repetitive actions of creating taxonomy.xml, running X!Tandem, and converting the result to pepXML.
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