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Various IO fixes #98

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merged 2 commits into from
Sep 10, 2024
Merged

Various IO fixes #98

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27d66f2
io.flashlfq: Fix writing PSMs without protein accession
RalfG Sep 10, 2024
37ba303
io: Fix sage filename pattern for automatic file type inference
RalfG Sep 10, 2024
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4 changes: 2 additions & 2 deletions psm_utils/io/__init__.py
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Original file line number Diff line number Diff line change
Expand Up @@ -105,13 +105,13 @@
"reader": sage.SageTSVReader,
"writer": None,
"extension": ".tsv",
"filename_pattern": r"^.*(?:_|\.).sage.tsv$",
"filename_pattern": r"^.*(?:_|\.)sage.tsv$",
},
"sage_parquet": {
"reader": sage.SageParquetReader,
"writer": None,
"extension": ".parquet",
"filename_pattern": r"^.*(?:_|\.).sage.parquet$",
"filename_pattern": r"^.*(?:_|\.)sage.parquet$",
},
"parquet": { # List after proteoscape and sage to avoid extension matching conflicts
"reader": parquet.ParquetReader,
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2 changes: 1 addition & 1 deletion psm_utils/io/flashlfq.py
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Expand Up @@ -224,5 +224,5 @@ def _psm_to_entry(psm: PSM) -> dict:
"Peptide Monoisotopic Mass": f"{psm.peptidoform.theoretical_mass:.6f}",
"Scan Retention Time": psm.retention_time,
"Precursor Charge": psm.peptidoform.precursor_charge,
"Protein Accession": ";".join(psm.protein_list),
"Protein Accession": ";".join(psm.protein_list) if psm.protein_list else None,
}
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