Some changes in prescott module detailed csv file output.

.gitignore

@@ -2,8 +2,7 @@
 ._*
 .Rhistory
 example/.RData
-gemmeAnal.pyc
 __pycache__/*
-esgemme/__pycache__/
-esgemme.egg-info/*
+prescott/__pycache__/
+prescott.egg-info/*
 .RData
\ No newline at end of file

examples/example-prescott-script.sh

 #!/bin/bash
 
 #If you have gnomad data from GnomAD version 2.1.1 or version 3.1.2
-#prescott -e ../data/MLH1_normPred_evolCombi.txt -g ../data/gnomAD_v2.1.1_MLH1_HUMAN_ENSG00000076242.csv -s ../data/MLH1.fasta --gnomadversion 2
+prescott -e ../data/MLH1_normPred_evolCombi.txt -g ../data/gnomAD_v2.1.1_MLH1_HUMAN_ENSG00000076242.csv -s ../data/MLH1.fasta --gnomadversion 2
 
 #If you are using GnomAD v4.0.0 data.
-prescott -e ../data/MLH1_normPred_evolCombi.txt -g ../data/gnomAD_v4.0.0_MLH1_HUMAN_ENSG00000076242.csv -s ../data/MLH1.fasta --gnomadversion 4
+prescott -e ../data/MLH1_normPred_evolCombi.txt -g ../data/gnomAD_v4.0.0_MLH1_HUMAN_ENSG00000076242.csv -s ../data/MLH1.fasta

prescott/prescott.py

@@ -883,8 +883,13 @@ def main():
         plt.close()
         print("@> AUC= {:.3f} {:.3f}".format( AUC_ESCOTT, AUC_PRESCOTT))
 
+    # Renaming the column just to make clear that the frequency column in the csv 
+    # is actually log10 frequencies. Normally, one can deduce it from the values as well
+    # but it is always better to be clear. 
+    myBigMergedDF = myBigMergedDF.rename(columns={'frequency': 'log10frequency'})
+
     myBigMergedDF.to_csv(outfile+'-details.csv', index=None)
-    # myBigMergedDF.to_csv(outfile+'.txt', columns=['mutant', 'PRESCOTT'], index=False, header=None, sep=' ')
+    
     
     with open(outfile+'.csv', 'w') as my_file:
         my_file.write(",")