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mokapot v0.7.0
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@wfondrie wfondrie released this 20 Mar 03:02
v0.7.0
0ab1ac4
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Learn about vigilant mode.

This release adds significantly more functionality, a small speedup, and expands the documentation 🎉

Added

  • Support for downstream peptide and protein quantitation with
    FlashLFQ. This is accomplished
    through the mokapot.to_flashlfq() function or the to_flashlfq() method of
    LinearConfidence objects. Note that to support the FlashLFQ format, you'll
    need to specify additional columns in read_pin() or use a PepXML input file
    (read_pepxml()).
  • Added a top-level function for exporting confident PSMs, peptides, and
    proteins from one or more LinearConfidence objects as a tab-delimited file:
    mokapot.to_txt().
  • Added a top-level function for reading FASTA files for protein-level
    confidence estimates: mokapot.read_fasta().
  • Tests accompanying the support for the features above.
  • Added a "mokapot cookbook" to the documentation with helpful code snippets.

Changed

  • Corresponding with support for new formats, the mokapot.read_pin() function
    and the LinearPsmDataset constructor now have many new optional parameters.
    These specify the columns containing the metadata needed to write the added
    formats.
  • Starting mokapot should be slightly faster for Python >= 3.8. We were able to
    eliminate the runtime call to setuptools, because of the recent addition of
    importlib.metadata to the standard library, saving a few hundred
    milliseconds.
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