removed mgf annotation verification

casanovo/denovo/model_runner.py

@@ -8,7 +8,7 @@
 import uuid
 import warnings
 from pathlib import Path
-from typing import Iterable, List, Optional, Union, TextIO
+from typing import Iterable, List, Optional, Union
 
 import depthcharge.masses
 import lightning.pytorch as pl
@@ -401,21 +401,6 @@ def _get_index(
 
         msg = msg.strip()
         filenames = _get_peak_filenames(peak_path, ext)
-        if annotated:
-            # Filter unannotated MGF files to avoid Depth Charge exception
-            filtered_fnames = list()
-            for fname in filenames:
-                if Path(
-                    fname
-                ).suffix.lower() == ".mgf" and not _mgf_is_annotated(fname):
-                    warnings.warn(
-                        f"Ignoring unannotated MGF peak file: {fname}",
-                        RuntimeWarning,
-                    )
-                else:
-                    filtered_fnames.append(fname)
-            filenames = filtered_fnames
-
         if not filenames:
             not_found_err = f"Cound not find {msg} peak files"
             logger.error(not_found_err + " from %s", peak_path)
@@ -459,32 +444,6 @@ def _get_strategy(self) -> Union[str, DDPStrategy]:
             return "auto"
 
 
-def _mgf_is_annotated(mgf_path: TextIO) -> bool:
-    """Check whether MGF file is annotated
-
-    Parameters
-    ----------
-    mgf_path : TextIO
-        MGF peak file to check
-
-    Returns
-    -------
-    bool
-        Whether MGF peak file is annotated
-    """
-    num_spectra = 0
-    num_annotations = 0
-
-    with open(mgf_path) as f:
-        for curr_line in f:
-            if curr_line.startswith("BEGIN IONS"):
-                num_spectra += 1
-            elif curr_line.startswith("SEQ="):
-                num_annotations += 1
-
-    return num_spectra == num_annotations
-
-
 def _get_peak_filenames(
     paths: Iterable[str], supported_ext: Iterable[str]
 ) -> List[str]: