Add SpecLibFlat Interface for conversion #265
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mo-sameh
approved these changes
Jan 5, 2025
mschwoer
reviewed
Jan 9, 2025
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| additional_columns: list | None = None, | ||
| charged_frag_types: list | None = None, |
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unfortunately we still have __python_version__ = ">=3.8" .. should we go to >=3.9 @jalew188 ?
| - self._precursor_df["flat_frag_start_idx"], | ||
| ) | ||
| for col, df in df_collection.items(): | ||
| print(col) |
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| def to_SpecLibBase(self): | ||
| # raise a deprecation warning | ||
| warnings.warn( |
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| drop_columns = [ | ||
| col | ||
| for col in ["flat_frag_start_idx", "flat_frag_stop_idx"] | ||
| if col in speclib_base._precursor_df.columns | ||
| ] |
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could be removed by using drop(..., errors="ignore") cf. https://pandas.pydata.org/docs/reference/api/pandas.DataFrame.drop.html
mschwoer
reviewed
Jan 10, 2025
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| corresponding _fragment_<column>_df matrix. Including 'mz' in additional_columns will | ||
| use observed rather than calculated m/z values. |
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This behaviour (mz) is a bit implicit.
could this be an extra switch (use_observed_mz, defaulting to True) ?
Could users be interested also in the calculated mz values?
| import pandas as pd | ||
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| from alphabase.io.hdf import HDF_File | ||
| from alphabase.peptide.fragment import flatten_fragments, remove_unused_fragments | ||
| from alphabase.peptide.fragment import ( | ||
| _create_dense_matrices, |
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this should not be private
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Add new speclib flat conversion to SpecLibFlat object and remove old functions