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Spectrum IO

Spectrum IO is a package primarily developed for usage within oktoberfest (https://github.com/wilhelm-lab/oktoberfest). It handles file conversions and input / output operations for oktoberfest.

Installation

Prerequisites

If you want to convert raw files to mzml, make sure you have ThermoRawFileParser (https://github.com/compomics/ThermoRawFileParser) installed.

If you are on linux or MacOS, make sure mono (https://www.mono-project.com/) is installed (for ThermoRawFileParser).

Using pip

pip install oktoberfest

Features

  • Read search results from different search engines (Mascot, MaxQuant, MSFragger, MS Amanda) and transform them to the internal format used by oktoberfest
  • Read thermo raw files and convert them to mzml, required by oktoberfest
  • Read a fasta file and digest with various configurations (protease, missed cleavages, length of peptides, fragmentation, ...) for spectral library generation
  • Create spectral libraries from peptide lists and output as dlib, msp or spectronaut(csv) format
  • read and write data created as part of oktoberfest in hdf5 libraries

Documentation

Please refer to https://spectrum-io.readthedocs.io for further documentation.

License

The project is licensed under the MIT license.