Read and write idXML files using pyopenms

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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Read and write idXML files using pyopenms #52

Closed jonasscheid closed 10 months ago

jonasscheid commented 11 months ago

Added

io.idxml: Write support for idXML files, including merging an existing idXML with a PSMList 🎉
Docs: Add intersphinx links to other package documentation pages.

Changed

io.idxml: Use pyOpenMS instead of Pyteomics for reading idXML (~5x faster⚡)
Fixed Black formatting throughout project

jonasscheid commented 11 months ago

Black reformatting mostly responsible for the number of files changed 😁 The PR also includes now tests for reading and writing idXML.

Ready to review @RalfG

ypriverol commented 11 months ago

@jonasscheid thanks for this PR, we have an issue in quantms that depends on this PR. @RalfG we have tested the previous version and it is really not working. Can you help us and give priority to this PR and a new version of ms2rescore for me to test 😜. Thanks in advance.

jonasscheid commented 11 months ago

@ypriverol Can you test if the reader and writer do a proper job for you? Would be good to know before this can be merged