alphabase
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MannLabs
Infrastructure of AlphaX ecosystem
this allows you to also utilize memory mapped temp arrays in multithreaded processes by explicitly passing the directory name without needing to rely on the global TEMP_DIR_NAME variable still being...
Allow to import DIA-NN .speclib files to alphaBase based on @jalew188 implementation [Link](https://github.com/jalew188/DiaNN-speclib).
Review this PR after #171 Changes: - Remove `alphabase.io.psm_reader` as all functionalities are already in `alphabase.psm_reader` module. - register_reader() for all reader modules - register_decoy() for protein_level_decoy
- Fix noqa: modify imports of `alphabase.constants.element` to `alphabase.constants.atom`; add FutureWarning. - Fix noqa: modify imports of `alphabase.peptide.precursor.is_precursor_sorted()` to `alphabase.peptide.precursor.is_precursor_refined()`; add FutureWarning. - Fix noqa: modify imports of `alphabase.peptide.precursor.calc_precursor_mz()` to...
https://github.com/MannLabs/alphabase/blob/development/alphabase/psm_reader/sage_reader.py#L81 The modification site in alphabase (`mod_sites`) is `1
Move the warning that was issues on importing the `tempmmap` module to the first call of the associated methods, to avoid effects like this:  @jalew188 we could think implementing...
In development branch, running IsotopeGenerator fails for unknown modifications and new nomenclature with "_" instead of " " (e.g. @Any_N-term instead of @Any N-term), but it works if you set...
When trying to read in the output of spectronaut_report file, the column called "FG.ApexIonMobility" is not being imported with the rest of the data (the column seems to be dropped)....
Possible solution is to start the server and GUI separately.