Merge pull request #66 from compomics/psm_reading_error

remove error from parsing

psm_utils/io/tsv.py

@@ -49,6 +49,7 @@
 
 import ast
 import csv
+import logging
 from pathlib import Path
 from typing import Optional
 
@@ -59,6 +60,8 @@
 from psm_utils.psm import PSM
 from psm_utils.psm_list import PSMList
 
+logger = logging.getLogger(__name__)
+
 
 class TSVReader(ReaderBase):
     """Reader for psm_utils TSV format."""
@@ -71,7 +74,8 @@ def __iter__(self):
                 try:
                     yield PSM(**self._parse_entry(row))
                 except ValidationError as e:
-                    raise PSMUtilsIOException(f"Could not parse PSM from row: `{row}`") from e
+                    logger.warning("Could not parse PSM from row: `{row}`")
+                    continue
 
     @staticmethod
     def _parse_entry(entry: dict) -> dict: