pyteomics.pepxmltk is a module based on the pyteomics package that allows creation of 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.
- pyteomics
- numpy
- lxml
- jinja2
- PyPI: https://pypi.org/project/pyteomics.pepxmltk/
- BitBucket repo & issue tracker: https://bitbucket.org/markmipt/pyteomics.pepxmltk
- Mailing list: pyteomics@googlegroups.com