Merge pull request #99 from jonasscheid/robust-spectra-parsing-idxml

Parse idxmls with no spectra file info
compomics · Oct 1, 2024 · a9d0b2e · a9d0b2e
2 parents fcf34e9 + d8e4197
commit a9d0b2e
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diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -10,6 +10,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 ### Fixed
 
 - `io.flashlfq`: Fix column names `Peptide Monoisotopic Mass` and `Protein Accession`.
+- `io.idxml`: Fix parsing if spectra file name not present [#92](https://github.com/compomics/psm_utils/issues/92)
 
 ## [1.1.0] - 2024-09-05
 

diff --git a/psm_utils/io/idxml.py b/psm_utils/io/idxml.py
@@ -219,8 +219,10 @@ def _get_run(
  .getMetaValue("spectra_data")[peptide_id.getMetaValue("id_merge_index")]
  .decode()
  ).stem
- else:
+ elif protein_ids[0].metaValueExists("spectra_data"):
  run = Path(protein_ids[0].getMetaValue("spectra_data")[0].decode()).stem
+ else:
+ run = None
 
  # Convert back to None value (see writer)
  if run == "None":