Merge pull request #255 from mwang87/bug-fixes

adding tests and filters for mass defect on MS2

Author: mwang87

massql/msql_engine_filters.py

@@ -248,11 +248,20 @@ def ms2prod_condition(condition, ms1_df, ms2_df, reference_conditions_register):
             mz_min = mz - mz_tol
             mz_max = mz + mz_tol
 
+            massdefect_min, massdefect_max = _get_massdefect_min(condition.get("qualifiers", None))
             intensity_mask = _get_intensity_mask(ms2_df, condition.get("qualifiers", None))
 
             ms2_filtered_df = ms2_df[(ms2_df["mz"] > mz_min) &
                                     (ms2_df["mz"] < mz_max) &
                                     intensity_mask]
+            
+            if massdefect_min > 0 or massdefect_max < 1:
+                ms2_filtered_df["mz_defect"] = ms2_filtered_df["mz"] - ms2_filtered_df["mz"].astype(int)
+
+                ms2_filtered_df = ms2_filtered_df[
+                    (ms2_filtered_df["mz_defect"] > massdefect_min) &
+                    (ms2_filtered_df["mz_defect"] < massdefect_max)
+                ]
 
         # Setting the intensity match register
         _set_intensity_register(ms2_filtered_df, reference_conditions_register, condition)
@@ -328,6 +337,7 @@ def ms2nl_condition(condition, ms1_df, ms2_df, reference_conditions_register):
             nl_min = mz - mz_tol
             nl_max = mz + mz_tol
 
+            massdefect_min, massdefect_max = _get_massdefect_min(condition.get("qualifiers", None))
             intensity_mask = _get_intensity_mask(ms2_df, condition.get("qualifiers", None))
 
             ms2_filtered_df = ms2_df[
@@ -336,6 +346,14 @@ def ms2nl_condition(condition, ms1_df, ms2_df, reference_conditions_register):
                 intensity_mask
             ]
 
+            if massdefect_min > 0 or massdefect_max < 1:
+                ms2_filtered_df["mz_defect"] = (ms2_filtered_df["precmz"] - ms2_filtered_df["mz"]) - (ms2_filtered_df["precmz"] - ms2_filtered_df["mz"]).astype(int)
+
+                ms2_filtered_df = ms2_filtered_df[
+                    (ms2_filtered_df["mz_defect"] > massdefect_min) &
+                    (ms2_filtered_df["mz_defect"] < massdefect_max)
+                ]
+
         # Setting the intensity match register
         _set_intensity_register(ms2_filtered_df, reference_conditions_register, condition)
 
@@ -402,6 +420,7 @@ def ms2prec_condition(condition, ms1_df, ms2_df, reference_conditions_register):
                 (ms2_filtered_df["precmz_defect"] < massdefect_max)
             ]
         else:
+            massdefect_min, massdefect_max = _get_massdefect_min(condition.get("qualifiers", None))
             mz_tol = _get_mz_tolerance(condition.get("qualifiers", None), mz)
             mz_min = mz - mz_tol
             mz_max = mz + mz_tol
@@ -411,6 +430,14 @@ def ms2prec_condition(condition, ms1_df, ms2_df, reference_conditions_register):
                 (ms2_df["precmz"] < mz_max)
             ]
 
+            if massdefect_min > 0 or massdefect_max < 1:
+                ms2_filtered_df["precmz_defect"] = ms2_filtered_df["precmz"] - ms2_filtered_df["precmz"].astype(int)
+
+                ms2_filtered_df = ms2_filtered_df[
+                    (ms2_filtered_df["precmz_defect"] > massdefect_min) &
+                    (ms2_filtered_df["precmz_defect"] < massdefect_max)
+                ]
+
         ms2_list.append(ms2_filtered_df)
 
     if len(ms2_list) == 1:
@@ -494,7 +521,7 @@ def ms1_condition(condition, ms1_df, ms2_df, reference_conditions_register, ms1_
                     (ms1_df["mz"] < mz_max) &
                     intensity_mask]
 
-                if massdefect_min > 0 or massdefect_max < 1:
+                if massdefect_min != 0 or massdefect_max != 1:
                     ms1_filtered_df["mz_defect"] = ms1_filtered_df["mz"] - ms1_filtered_df["mz"].astype(int)
 
                     ms1_filtered_df = ms1_filtered_df[
@@ -608,7 +635,7 @@ def ms1_filter(condition, ms1_df):
                 (ms1_df["mz"] < mz_max) &
                 intensity_mask]
 
-            if massdefect_min > 0 or massdefect_max < 1:
+            if massdefect_min != 0 or massdefect_max != 1:
                 ms1_filtered_df["mz_defect"] = ms1_filtered_df["mz"] - ms1_filtered_df["mz"].astype(int)
 
                 ms1_filtered_df = ms1_filtered_df[

tests/test_query.py

@@ -615,6 +615,26 @@ def test_massdefect_ANY_query():
     results_df = msql_engine.process_query(query, "tests/data/GNPS00002_A3_p.mzML")
     assert(len(results_df) == 77)
 
+def test_massdefect_bug_reproduction():
+    f = "tests/data/GNPS00002_A3_p.mzML"
+    
+    # MS2PROD MASSDEFECT
+    exclude_query = "QUERY MS2DATA WHERE MS2PROD=226.18:MASSDEFECT=massdefect(min=0.8,max=0.9)"
+    df_exclude = msql_engine.process_query(exclude_query, f)
+    assert len(df_exclude) == 0
+
+    # MS1MZ MASSDEFECT Full Range
+    full_range_query = "QUERY MS1DATA WHERE MS1MZ=226.18:MASSDEFECT=massdefect(min=0.0,max=1.0)"
+    df_full = msql_engine.process_query(full_range_query, f)
+    # Get baseline
+    df_all = msql_engine.process_query("QUERY MS1DATA WHERE MS1MZ=226.18", f)
+    assert len(df_full) == len(df_all)
+    
+    # MS1MZ MASSDEFECT Exclusion
+    exclude_ms1_query = "QUERY MS1DATA WHERE MS1MZ=226.18:MASSDEFECT=massdefect(min=0.8,max=0.9)"
+    df_ms1_exclude = msql_engine.process_query(exclude_ms1_query, f)
+    assert len(df_ms1_exclude) == 0
+
 def test_advanced_filters():
     query = """
         QUERY scansum(MS1DATA) FILTER MS1MZ=ANY:TOLERANCEMZ=35:MASSDEFECT=massdefect(min=0.1332, max=0.2112)