From 27d66f2b08993d14179a041ea1cb57e5e9564c62 Mon Sep 17 00:00:00 2001 From: RalfG Date: Tue, 10 Sep 2024 16:09:11 +0200 Subject: [PATCH 1/2] io.flashlfq: Fix writing PSMs without protein accession --- psm_utils/io/flashlfq.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/psm_utils/io/flashlfq.py b/psm_utils/io/flashlfq.py index 5bf3a21..e2dac9f 100644 --- a/psm_utils/io/flashlfq.py +++ b/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, } From 37ba303b00be50645def4a351065e5795075af74 Mon Sep 17 00:00:00 2001 From: RalfG Date: Tue, 10 Sep 2024 16:10:46 +0200 Subject: [PATCH 2/2] io: Fix sage filename pattern for automatic file type inference --- psm_utils/io/__init__.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/psm_utils/io/__init__.py b/psm_utils/io/__init__.py index 0b4bb66..28021c5 100644 --- a/psm_utils/io/__init__.py +++ b/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,