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MannLabs / alphapeptdeep

Deep learning framework for proteomics
Apache License 2.0
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Diann #16

Closed jalew188 closed 2 years ago

jalew188 commented 2 years ago

Generate library for DiaNN/Spectronaut. It has been tested with DiaNN and worked well. Except that diann does not support our modification format for localization.

We provide APIs to load fragment intensities from TSV library. But I was wondering that fragments extracted from DIA data are highly interfered and hence not suitable for training.

We can now load modloss ions from MaxQuant msms.txt

jalew188 commented 2 years ago

Hi, codechanges look good. However I couldn't see which code is meant for DIA-NN.

The peptdeep.spec_lib.translate is design for both DiaNN and spectronaut. As diann is the only dia software I have and the name is shorter, so I use 'diann'.

What would help for the notebooks is a little more documentation, even a little header what you'll find in the notebook would help a lot.

Yes, I am working on docstrings before releasing. The key problem for docstrings is because the APIs are rapidly chaning from time to time. I will add docs for stable APIs and now more APIs are very nearly stable.

jalew188 commented 2 years ago

@straussmaximilian A docs PR is coming soon ...