Improved prot_normPred_evolCombiTransposed.txt output.

esgemme.py

@@ -1058,11 +1058,18 @@ def doit(inAli,mutFile,retMet,bFile,fFile,n,N, jetfile, pdbfile, normWeightMode,
             #legibility.
             gemmeDF = pd.read_table(prot+"_normPred_evolCombi.txt", sep="\s+")
             gemmeDFtrans = gemmeDF.T
-            print(gemmeDF)
-#            gemmeDF.columns = gemmeDF.columns.str.upper()
+            # print(gemmeDF)
             gemmeDFtrans.columns = gemmeDFtrans.columns.str.upper()
-#            with open('./filename.txt', 'w') as fo:
-#                fo.write(gemmeDFtrans.__repr__())
+            aaAndPosition = []
+            oldNamesList = gemmeDF.columns.tolist()
+            for i in range(len(list(seq))):
+                aaAndPosition.append(list(seq)[i]+str(i+1))
+            # gemmeDFtrans = pd.DataFrame(gemmeDFtrans, index=aaAndPosition)
+            gemmeDFtrans.rename(index = dict(map(lambda i,j : (i,j) , oldNamesList,aaAndPosition)), inplace=True)
+            # gemmeDFtrans.set_axis(aaAndPosition)
+            # gemmeDFtrans.rename(index=aaAndPosition, inplace=True)
+            # gemmeDFtrans['pos'] = aaAndPosition
+            #print(df['pos'])
             gemmeDFtrans.to_csv(prot+"_normPred_evolCombiTransposed.txt", sep='\t', float_format='%.2f', na_rep='NaN')
             #sys.exit(-1)
             

examples/example-esgemme-script.sh

@@ -52,6 +52,6 @@ then
 else
     echo "Running EGEMME with a user-provided alignment file."
     echo "Since a pdb file is not provided, only evolutionary information will be used!"
-    python $ESGEMME_PATH/esgemme.py ../data/aliBLAT.fasta -r input -f ../data/aliBLAT.fasta
+    python3 $ESGEMME_PATH/esgemme.py ../data/aliBLAT.fasta -r input -f ../data/aliBLAT.fasta
     
 fi