count for tmt mod when doing the alignment

wilhelm-lab · Nov 5, 2024 · a4074cd · a4074cd
1 parent e6bdead
commit a4074cd
Showing 1 changed file with 3 additions and 1 deletion.
diff --git a/oktoberfest/predict/alignment.py b/oktoberfest/predict/alignment.py
@@ -32,7 +32,9 @@ def _prepare_alignment_df(
     else:
         groups = ["RAW_FILE"]
 
-    hcd_targets = library.obs.query("(FRAGMENTATION == 'HCD') & ~REVERSE & ~(MODIFIED_SEQUENCE.str.contains('UNIMOD'))")
+    hcd_targets = library.obs.query("(FRAGMENTATION == 'HCD') & ~REVERSE)")
+    hcd_targets = hcd_targets[hcd_targets["MODIFIED_SEQUENCE"].str.match(r"^(?:[^U]*(?:\[UNIMOD:737\])?[^U]*)$")]
+
     hcd_targets = hcd_targets.sort_values(by="SCORE", ascending=False).groupby(groups)
     if len(hcd_targets)<2000:
         top_n= len(hcd_targets)*0.5