Skip to main content

A utility for creation of pepXML files from Python objects and TandemXML files.

Project description

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.

Dependencies

  • pyteomics

  • numpy

  • lxml

  • jinja2

Project details


Download files

Download the file for your platform. If you're not sure which to choose, learn more about installing packages.

Source Distribution

pyteomics.pepxmltk-0.3.3.tar.gz (14.7 kB view hashes)

Uploaded source

Built Distribution

pyteomics.pepxmltk-0.3.3-py2.py3-none-any.whl (15.3 kB view hashes)

Uploaded py2 py3

Supported by

AWS AWS Cloud computing Datadog Datadog Monitoring Facebook / Instagram Facebook / Instagram PSF Sponsor Fastly Fastly CDN Google Google Object Storage and Download Analytics Huawei Huawei PSF Sponsor Microsoft Microsoft PSF Sponsor NVIDIA NVIDIA PSF Sponsor Pingdom Pingdom Monitoring Salesforce Salesforce PSF Sponsor Sentry Sentry Error logging StatusPage StatusPage Status page