Comments (3)
One solution would be to move peak processing from Dataset
to Parser
in depthcharge. That way invalid spectra are encountered prior to being added to the index and can immediately be filtered out, rather than when being retrieved from the dataset. As an added advantage, spectrum processing only needs to be done once for each spectrum, when creating the index, rather than repeating it every time the same spectrum is retrieved.
A disadvantage, however, is that when spectrum processing options change, the index would have to be recreated. Nevertheless, I think our spectrum processing based on best practices and we don't really vary it, so for Casanovo at least it should be pretty fixed.
Additionally, it destroys the link between the indexes of the output PSMs and the input spectra. Although this is a broader issue (#70).
@wfondrie What do you think?
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I'm open to this. I also think that the current way of tracking the spectrum index is pretty fragile and not ideal. Instead, that information should be saved in the index itself. Ayse started a PR in depthcharge to solve the spectrum tracking issue, but it was incomplete - I'll see if I can get it updated and integrated.
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#105 will address spectrum index tracking once completed for future reference
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Related Issues (20)
- mzTab validation
- Automate mzTab validation HOT 7
- More information about the train/val/test split HOT 2
- WARNING: Skipped spectra with invalid precursor info HOT 1
- Export casanovo to torchscript/onnx HOT 1
- ValueError: The truth value of an array with more than one element is ambiguous. Use a.any() or a.all() HOT 3
- Make Casanovo produce Skyline compatible output
- 9-Species Benchmark Set: Data Preprocessing Step? HOT 5
- Migrating PeptideMass, PeptideDecoder, and PeptideEncoder from depthcharge v0.2.3 to casanovo HOT 3
- Is there a way to know which spectras are ITMS instead of FTMS? HOT 3
- Numpy release 2.0.0 breaks depthcharge dependency HOT 2
- Use Fourier embeddings
- Add mzTab validator to github actions HOT 1
- Make Casanovo model compatible with torch.compile
- Designate a filename for the "best" model HOT 11
- PyTorch (GPU) not working on Win 11 box HOT 4
- ValueError upon unexpected scan title format HOT 7
- Eliminate the eval command HOT 4
- Greater than or equal to character ≥ causes logging error in end of run report.
- RuntimeError: CUDA error: the launch timed out and was terminated HOT 3
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