Small changes mainly in prescott.py

prescott/escott.py

 # -*- coding: utf-8 -*-
 
-# Copyright (c) 2018: Elodie Laine
 # Copyright (c) 2022-2023: Mustafa Tekpinar
 # This code is part of the prescott package and governed by its license.
 # Please see the LICENSE.txt file included as part of this package.

prescott/prescott.py

@@ -683,7 +683,14 @@ def main():
                                 selectedValuesList.append(temp2)
                                 selectedPositionsList.append(row['position'])
                                 selectedMutantsList.append(row['mutant'])                        
-
+                if(version==5):
+                    if(freq>freqCutoff):
+                        temp2 = temp1*0.0
+                        myBigMergedDF.at[index,'PRESCOTT'] = temp2
+                        if(label==0 or label==1):
+                            selectedValuesList.append(temp2)
+                            selectedPositionsList.append(row['position'])
+                            selectedMutantsList.append(row['mutant'])
     # myBigMergedDF.dropna(subset = ['labels'], inplace=True)
 
     clinvarLabeledDF = myBigMergedDF.loc[(myBigMergedDF['labels']==0) | (myBigMergedDF['labels']==1)]
@@ -737,6 +744,7 @@ def main():
 
     myBigMergedDF.to_csv(outfile+'-details.csv', index=None)
     myBigMergedDF.to_csv(outfile+'.txt', columns=['mutant', 'PRESCOTT'], index=False, header=None, sep=' ')
+    if(os.path.exists(protein+'_singleline.txt')):
         os.remove(protein+'_singleline.txt')
 
 if __name__ == "__main__":