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MannLabs / alphapeptdeep

Deep learning framework for proteomics
Apache License 2.0
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Some library entries don't get translated to a tsv file #91

Closed gsaxena888 closed 1 year ago

gsaxena888 commented 1 year ago

Attached is an input file and settings.yaml file that if run, will not generate a .tsv output file (though it will generate the .hdf5 file). Thoughts? (I used alphapeptdeep 1.0.1, i.e., the latest version)

settingsLibrary.yaml.gz first_search.mzid_forPred.tsv.gz

jalew188 commented 1 year ago

Check here https://github.com/MannLabs/alphapeptdeep/blob/main/peptdeep/constants/default_settings.yaml#L268

It is TRUE already..., can I check the log file?

gsaxena888 commented 1 year ago

peptdeep_library.log

I just tried with the setting to "true" for translate_mod_to_unimod_id. It did NOT make a difference. I've attached the log above.

jalew188 commented 1 year ago

That is wired, I can generate the tsv based on your input file... Maybe because I used the latest version (1.0.2)