Merge pull request #98 from compomics/fix/various-io

Various IO fixes

Author: RalfG

psm_utils/io/__init__.py

@@ -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,

psm_utils/io/flashlfq.py

@@ -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,
         }