fix: skip empty msms hit data

biorack · Mar 6, 2024 · 6a49640 · 6a49640
1 parent 677821f
commit 6a49640
Showing 1 changed file with 4 additions and 0 deletions.
diff --git a/metatlas/io/metatlas_get_data_helper_fun.py b/metatlas/io/metatlas_get_data_helper_fun.py
@@ -20,6 +20,7 @@
 from metatlas.datastructures import metatlas_objects as metob
 from metatlas.io import h5_query as h5q
 from metatlas.io import write_utils
+from metatlas.plots.dill2plots import convert_to_centroid
 
 logger = logging.getLogger(__name__)
 
@@ -54,6 +55,9 @@ def arrange_ms2_data(metatlas_dataset, keep_nonmatches, do_centroid):
             if 'data' not in file_compound_data['data']['msms']:
                 continue
 
+            if 'rt' not in file_compound_data['data']['msms']['data']:
+                continue
+
             cid = file_compound_data['identification']
             cid_name = cid.compound[0].name
             precursor_mz = cid.mz_references[0].mz