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Add parquet support in Base PSMReader class default _load_file() method. #328

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Merged
boopthesnoot merged 2 commits into from
Aug 1, 2025
Merged

Add parquet support in Base PSMReader class default _load_file() method. #328

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b3845c9
Add parquet support in Base PSMReader class default _load_file() method.
vbrennsteiner Aug 1, 2025
645c1fe
nit: pathlib suffix resolution
boopthesnoot Aug 1, 2025
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18 changes: 14 additions & 4 deletions alphabase/psm_reader/psm_reader.py
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Original file line number Diff line number Diff line change
Expand Up @@ -256,11 +256,21 @@ def import_file(self, _file: str) -> pd.DataFrame:
def _load_file(self, filename: str) -> pd.DataFrame:
"""Load PSM file into a dataframe.

Different search engines may store PSMs in different ways: tsv, csv, HDF, XML, ...
This default implementation works for tsv and csv files and thus covers many readers.
Different search engines may store PSMs in different ways: tsv, csv, HDF, XML, parquet ...
This default implementation works for tsv, csv and parquet files and thus covers many readers.

Parameters
----------
filename : str
The file path to the PSM file.

"""
sep = _get_delimiter(filename)
return pd.read_csv(filename, sep=sep, keep_default_na=False)

if filename.endswith(".parquet"):

@mschwoer mschwoer Aug 1, 2025

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should we use pathlib.Path.extension here?

return pd.read_parquet(filename)
else:
sep = _get_delimiter(filename)
return pd.read_csv(filename, sep=sep, keep_default_na=False)

def _get_actual_column(
self,
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