Corrected ranksorting for M1M, A2A etc. inside prescott.py!

prescott/prescott.py

@@ -659,10 +659,15 @@ def main():
         aaOrderList = list('ACDEFGHIKLMNPQRSTVWY')
         if(args.escottformat=='gemme'):
 
-            #Parse the file containing raw ESCOTT scores. 
-            scanningMatrix = parseGEMMEoutput(args.escottfile, verbose=False)
+            # Parse the file containing raw ESCOTT scores.
+            # The file is in GEMME format for backward compatibility! 
+            # scanningMatrix = parseGEMMEoutput(args.escottfile, verbose=False)
             
-
+            gemmeDF = pd.read_table(args.escottfile, sep="\s+")
+            #matrix = gemmeDF.to_numpy()
+            maxValue =np.nanmax(gemmeDF.to_numpy())
+            # print(maxValue)
+            scanningMatrix = gemmeDF.to_numpy(na_value=maxValue)
 
             writeSinglelineFormat(scanningMatrix, protein+'_singleline.txt', residueList = localResidueList,\
                             beg=0, end=None, aaOrder = aaOrderList, \
@@ -893,7 +898,7 @@ def main():
     # myBigMergedDF = myBigMergedDF['mutant'].apply(lambda x: x.upper())
     myBigMergedDF.to_csv(outfile+'-details.csv', index=None)
     
-    print(localResidueList)
+    # print(localResidueList)
 
     with open(outfile+'.csv', 'w') as my_file:
         my_file.write(",")