Add reader for Proteome Discoverer MSF files; other changes/fixes/additions - Githubissues

compomics / psm_utils

Common utilities for parsing and handling peptide-spectrum matches and search engine results in Python

https://psm-utils.readthedocs.io

Apache License 2.0

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Add reader for Proteome Discoverer MSF files; other changes/fixes/additions #44

Closed RalfG closed 1 year ago

RalfG commented 1 year ago

Added

io: Added support for Proteome Discoverer MSF files
Peptidoform: Added support for initialization from a pyteomics.proforma.ProForma object
PSMList: Added append and extend methods.
io.mzid: Add support for user to define custom score key
io.mzid: Add Proteome Discoverer Delta Score to known scores (with spaces, no colons)
io.mzid: Allow inconsistent presence of score in PSMs in a single mzid file

Changed

PSM: Values of the rescoring_features dictionary are now coerced to floats
Make io reader read_file method inheritable (code cleanup)
Increase max line length to 99 (code formatting)

Fixed

io.Percolator.PercolatorTabWriter: Allow rescoring features that are not in feature_names (extrasaction is now specified in DictWriter)
Fix issue where psm_list["protein_list"] resulted in a Numpy error due to the inconsistent shape of the lists.