transfer library building with diverse frag types #423
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| @@ -1154,7 +1154,7 @@ def requantify_fragments( | |||
| config = plexscoring.CandidateConfig() | |||
| config.update( | |||
| { | |||
| "top_k_fragments": 1000, # Use all fragments ever expected, needs to be larger than charged_frag_types(8)*max_sequence_len(100?) | |||
| "top_k_fragments": 9999, # Use all fragments ever expected, needs to be larger than charged_frag_types(8)*max_sequence_len(100?) | |||
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why not add an order of magnitude here just to be on the safe side ;-)
| number_of_processes=number_of_processes, | ||
| processing_kwargs={ | ||
| "charged_frag_types": fragment.get_charged_frag_types( | ||
| self.config["transfer_library"]["fragment_types"].split(";"), |
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note that this is not compatible with #424
| charged_frag_types: list[str] | None = None, | ||
| ) -> SpecLibFlat: | ||
| """ | ||
| Parse an output folder and return a SpecLibFlat object containing the precursor and fragment data. |
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parse a folder? maybe be a bit more specific here
| foldername = os.path.basename(folder) | ||
| psm_df["raw_name"] = foldername |
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(nit) psm_df["raw_name"] = os.path.basename(folder)
| _ = pool.apply_async( | ||
| process_folder, | ||
| (folder,), | ||
| self._processing_kwargs, |
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this looks wrong (but isn't, I know ;-))
maybe
args=(folder,),
kwds=self._processing_kwargs,
| speclib._precursor_df = pd.DataFrame() | ||
| for col in psm_df.columns: | ||
| speclib._precursor_df[col] = psm_df[col] |
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is there a reason why we not just (deep)copy here?
| ) -> tuple[pd.DataFrame, pd.DataFrame]: | ||
| """ | ||
| Parse the output folder to get a precursor and fragment dataframe in the flat format. | ||
| def process_folder( |
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could we find a more specific name here? build_speclibflat_from_folder?
| # semicolon separated list of fragment types to include in the library. possible values are | ||
| # 'a', 'b', 'c', 'x', 'y', 'z' | ||
| # 'b_H2O', 'y_H2O', 'b_NH3', 'y_NH3', 'b_modloss', 'y_modloss', 'c_lossH', 'z_addH' | ||
| fragment_types: 'b;y' |
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note that this will cause a merge conflict with #424 .. maybe omit it here to make life easier (assuming it's the same information that is added)
Requires unrelease alphabase features (MannLabs/alphabase#265)
Adapts alphaDIA to allow transfer library building with arbitrary frag types.