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MannLabs / alphapeptdeep

Deep learning framework for proteomics
Apache License 2.0
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added support for mzml. If redoing transfer_learn with the same files, saves and reloads psm_df and frag_df #95

Closed yangkl96 closed 1 year ago

yangkl96 commented 1 year ago

Tested the reloading method with pepxml/mzml and maxquant msms.txt/mgf

jalew188 commented 1 year ago

Cool @yangkl96 , I will test this week.

jalew188 commented 1 year ago

@yangkl96 Hi kevin, my plan is to move all ms data reader stuffs to AlphaRaw. Therefore, I plan to move this PR to alpharaw. What do you think? See #98

yangkl96 commented 1 year ago

@jalew188 Hi Wen-Feng, that sounds good. Not all my changes have to do with ms data reading; would those non-related changes stay here?

jalew188 commented 1 year ago

Overall changes look nice, I am going to run this code for different tasks, and then give more comments on this PR.

jalew188 commented 1 year ago

@yangkl96 Thank you for these commits. As a suggestion, please make different commits or PRs for different features. It will be easier to merge some key features if they are important for the repo; for others, we can wait for next merge.

yangkl96 commented 1 year ago

You're welcome! Sorry for the difficulties, I'm still learning best practices for GitHub. Are you planning to merge these changes to the main branch soon? I'm a little busy preparing for ASMS, but I can put these commits to different branches and pull requests if it is urgent

jalew188 commented 1 year ago

You're welcome! Sorry for the difficulties, I'm still learning best practices for GitHub. Are you planning to merge these changes to the main branch soon? I'm a little busy preparing for ASMS, but I can put these commits to different branches and pull requests if it is urgent

No hurries. We can merge before the release of v1.1.0

yangkl96 commented 1 year ago

I am currently moving these commits to separate PRs

jalew188 commented 1 year ago

104 merged, close this PR