ref: clarity

new_mfql_parser/manually_run_mfql.py

 from mfql_Parser import parser
+from nearest import nearest
 from spectra_tools import get_triggerScan, specta_df_fromCSV, getMS1Negpeaks
 from var2df import var2df
 
@@ -27,7 +28,8 @@ if __name__ == '__main__':
 	FA1 IN MS2- AND
 	FA2 IN MS2-'''
     print('pr in ms1-')
-    MS1Neg_ser = getMS1Negpeaks(df)
+    MS1Neg_arr = getMS1Negpeaks(df)
+    nearest_idx = nearest(var_dfs['pr'].mz, MS1Neg_arr)
 
     print('do such that part')
     print('do report part')

new_mfql_parser/nearest.py

@@ -6,8 +6,8 @@ def nearest(ser1, ser2):
     # from https://stackoverflow.com/questions/2566412/find-nearest-value-in-numpy-array
     # TODO try https://stackoverflow.com/questions/9706041/finding-index-of-an-item-closest-to-the-value-in-a-list-thats-not-entirely-sort
     res = []
+    array = np.asarray(ser2)
     for value in ser1:
-        array = np.asarray(ser2)
         idx = (np.abs(array - value)).argmin()
         res.append(idx)
     return res

new_mfql_parser/spectra_tools.py

@@ -59,11 +59,11 @@ def getScansDF_fromPeaksDF(peaks_df):
     return unique_scan_df
 
 
-def getMS1Negpeaks(peaks_df):
+def getMS1Negpeaks(peaks_df, roundto=2):
     unique_scan_df = getScansDF_fromPeaksDF(peaks_df)
     MS1NegScans = unique_scan_df[(unique_scan_df['msLevel'] == 1) \
                                  & (unique_scan_df['mode'] == 'neg')]
 
     peaks_df_merge = peaks_df.merge(MS1NegScans, on='scanNum')
-    peaks_df_merge = peaks_df_merge.mz.round(2)
+    peaks_df_merge = peaks_df_merge.mz.round(roundto).unique()
     return peaks_df_merge