ms2pip
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CompOmics
MS²PIP: Fast and accurate peptide spectrum prediction for multiple fragmentation methods, instruments, and labeling techniques.
This feature request came up in https://github.com/nf-core/mhcquant/issues/317 Currently, the xgboost models are always downloaded to `$HOME/.ms2pip`. In some cases that could lead to permission issues, but the major advantage here...
Fully refactored and drastically more user-friendly version of MS²PIP: - More modular Python API - One consolidated command-line interface with subcommands - Support for all file formats readable by psm_utils...
The ms2_tolerance parameter to MS2PIPFeatureGenerator only supports Da. It would be nice if it supported relative units like ppm as well.
See https://github.com/compomics/ms2pip/actions/runs/7845409300/job/22261596464 ``` Building cp39-macosx_x86_64 wheel CPython 3.9 macOS x86_64 Installing Python cp39... ✓ 34.86s Setting up build environment... ✓ 6.62s Installing build tools... ✓ 3.44s Building wheel... ✓ 301.82s...
- Replace remaining C model files with .xgboost models - Use more accurate mass values - Fix various C compile-time warnings - Format C and Cython code - Fix calculating...
Hey everyone, I have used msgf+ and now have either an mzid and/or a tsv results file. Now I wanted to convert this to a valid peprec file for ms2pip....
This pull request introduces a refactoring of the write functions (msp, mgf, csv, and dlib) in `spectrum_output.py` to utilize a list of `ProcessingResults`
Currently both setup.py and pyproject.toml are used. Building on GH Actions now seems to use pyproject.toml. Before upload to PyPI, we would need to ensure that all package metadata is...
> Hi Ralf, > > I tried the new features today and they seem to work. However, when I set more than one cpu in the config file, the process...
Bibliospec/Skyline output fails when unmodified entries are empty instead of `-` This works: ```csv spec_id,modifications,peptide,charge LSAGVEFLK,-,LSAGVEFLK,2 ``` This does not: ```csv spec_id,modifications,peptide,charge LSAGVEFLK,,LSAGVEFLK,2 ``` (tested on web server)