add defaults to psm_reader.yaml #349
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…ardcoded charge column name in _pre_process() to instead use the configuration yaml
mschwoer
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Sep 26, 2025
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| available_charge_columns = load_yaml( | ||
| Path(CONST_FILE_FOLDER) / PSM_READER_YAML_FILE_NAME | ||
| )[self._reader_type]["column_mapping"]["charge"] | ||
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| self.precursor_charge_column = "PrecursorCharge" | ||
| for charge_col in available_charge_columns: | ||
| if charge_col in df.columns: | ||
| self.precursor_charge_column = charge_col | ||
| break |
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why is this extra logic required? isn't this covered by _translate_columns?
mschwoer
reviewed
Sep 26, 2025
| fixed_C57: False | ||
| column_mapping: | ||
| 'raw_name': 'ReferenceRun' | ||
| 'raw_name': ['ReferenceRun', 'R.Label'] |
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also here: please indicate the version (for those columns you know by heart right now ;-))
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What?
To accomodate for newer spectronaut version column names, fix hardcoded charge column name in _pre_process() to instead use the configuration yaml. In particular, adding to the spectronaut/column_mapping key in the psm_reader.yaml:
And to spectronaut/mod_seq_columns: