Added a timer function to sgemme.py to show total compute time.

example/example-gemme-script.sh

@@ -9,27 +9,33 @@ then
     # rm -rf BLAT.fasta
     rm -rf BLAT*
     rm -f default.conf caracTest.dat
+    rm -rf bin*.fasta
     
 elif [ "$1" == "jetoff" ]
 then
     # If you have your own JET2 score file, you can turn off JET2 as follows:
     # In ../tests folder, you can find a sample JET2 file called BLAT_jet.res 
-    echo "Running GEMME with a user-provided alignment file."
+    echo "Running SGEMME with a user-provided alignment file."
     echo "Using a previously produced prot_jet.res file to check reproducibility!"
     cp ../tests/BLAT_jet.res .
-    python $GEMME_PATH/gemme.py aliBLAT.fasta -r input -f aliBLAT.fasta --jetfile BLAT_jet.res
+    python $SGEMME_PATH/sgemme.py aliBLAT.fasta -r input -f aliBLAT.fasta --jetfile BLAT_jet.res
 
 elif [ "$1" == "withpdb" ]
 then
 
     #Please note that CV isa structural feature and it can not be calculated if you don't specify a pdb file.
-    echo "Using blat-curated.pdb for the structural feature calculations!"
-    python $GEMME_PATH/gemme.py aliBLAT.fasta -r input -f aliBLAT.fasta --pdbfile blat-curated.pdb --normweightmode dfi
+    echo "Using blat-af2.pdb for the structural feature calculations!"
+    python $SGEMME_PATH/sgemme.py aliBLAT.fasta -r input -f aliBLAT.fasta --pdbfile blat-af2.pdb --normweightmode maxhalftracepchalftracecvhalfcvpc
 
-else
-    echo "Running GEMME with a user-provided alignment file."
-    python $GEMME_PATH/gemme.py aliBLAT.fasta -r input -f aliBLAT.fasta
+elif [ "$1" == "withpdb-withmutfile" ]
+then
 
-fi
+    #Please note that CV isa structural feature and it can not be calculated if you don't specify a pdb file.
+    echo "Using blat-af2.pdb for the structural feature calculations!"
+    python $SGEMME_PATH/sgemme.py aliBLAT.fasta -r input -f aliBLAT.fasta --pdbfile blat-af2.pdb --normweightmode maxhalftracepchalftracecvhalfcvpc -m Stiffler_2015_BLAT_ECOLX.mut
    
+else
+    echo "Running SGEMME with a user-provided alignment file."
+    python $SGEMME_PATH/sgemme.py aliBLAT.fasta -r input -f aliBLAT.fasta
     
+fi

sgemme.py

 # -*- coding: utf-8 -*-
 
 # Copyright (c) 2018: Elodie Laine
-# Copyright (c) 2022: Mustafa Tekpinar
+# Copyright (c) 2022-2023: Mustafa Tekpinar
 # This code is part of the gemme package and governed by its license.
 # Please see the LICENSE.txt file included as part of this package.
 
 import sys
 import os
+import time
 import argparse
 import re
 import subprocess
@@ -672,11 +673,17 @@ def doit(inAli,mutFile,retMet,bFile,fFile,n,N, jetfile, pdbfile, normWeightMode,
 
 
 def main():
+    tic = time.perf_counter()
+
     args = parse_command_line()
     doit(args.input,args.mutations,args.retrievingMethod,args.blastFile,\
          args.fastaFile,args.nIter,args.NSeqs, args.jetfile, args.pdbfile,\
          args.normweightmode, args.alphabet)
 
+    toc = time.perf_counter()
+    
+    print(f"S-GEMME computation finished in {toc - tic:0.4f} seconds!")
+
 if (__name__ == '__main__'):
     main()