Reorganized the code for pip installation.

.gitignore

@@ -3,4 +3,6 @@
 .Rhistory
 example/.RData
 gemmeAnal.pyc
-__pycache__/*
+__pycache__/*
\ No newline at end of file
+esgemme.egg-info/*
+.RData
\ No newline at end of file

esgemme/__init__.py

+"""
+Program Name: esgemme
+Author      : Mustafa TEKPINAR
+Copyright   : Mustafa TEKPINAR - Alessandra Carbone- 2022-2023
+Email       : tekpinar@buffalo.edu
+Purpose     : A Python program to predict mutational effects of proteins.
+"""
+
+__all__ = ['esgemme']
+
+__version__ = '1.3.0'

esgemme.py → esgemme/esgemme.py

@@ -13,7 +13,9 @@ import re
 import subprocess
 import math
 import numpy as np
-import matplotlib.pylab as plt
+import matplotlib.pyplot as plt
+import matplotlib
+matplotlib.use('Agg')
 import shutil
 import glob
 
@@ -944,7 +946,8 @@ def parse_command_line():
     return args
 
 
-def doit(inAli,mutFile,retMet,bFile,fFile,n,N, jetfile, pdbfile, normWeightMode, alphabet, verbosity):
+def doit(inAli,mutFile,retMet,bFile,fFile,n,N, jetfile, pdbfile, normWeightMode,\
+         alphabet, verbosity, offset, colormap):
     """
     Perfect explanation for a function: typing the function call exactly!
     doit is basically the main function in disguise!
@@ -1106,7 +1109,7 @@ def doit(inAli,mutFile,retMet,bFile,fFile,n,N, jetfile, pdbfile, normWeightMode,
     if(simple):
         print("generating the plots...")
         #Check if the normalized data files were created. 
-        if(os.path.exists(prot+"_normPred_evolEpi.txt") and args.verbose==True):
+        if(os.path.exists(prot+"_normPred_evolEpi.txt") and verbosity==True):
             gemmeData = parseGEMMEoutput(prot+"_normPred_evolEpi.txt", verbose=False)
             sequenceLength = len(gemmeData[0])
             beginning = 1
@@ -1118,19 +1121,21 @@ def doit(inAli,mutFile,retMet,bFile,fFile,n,N, jetfile, pdbfile, normWeightMode,
                     plotGEMMEmatrix(gemmeData, prot+"_normPred_evolEpi"+"_part_"+str(i+1), \
                         i*rowLength + beginning, \
                         (i+1)*rowLength + beginning -1,\
-                        colorMap='Blues_r', offSet=i*rowLength + args.offset, pixelType='square',\
+                        colorMap='Blues_r', offSet=i*rowLength + offset, pixelType='square',\
                         sequence=prot+".fasta", isColorBarOn=True)
                 if(sequenceLength%rowLength != 0):
                     plotGEMMEmatrix(gemmeData, prot+"_normPred_evolEpi"+"_part_"+str(i+2), \
                         (i+1)*rowLength + beginning, \
                         end,\
-                        colorMap='Blues_r', offSet=(i+1)*rowLength + args.offset, pixelType='square',\
+                        colorMap='Blues_r', offSet=(i+1)*rowLength + offset, pixelType='square',\
+                        sequence=prot+".fasta", isColorBarOn=True)
+            else:
+                plotGEMMEmatrix(gemmeData, prot+"_normPred_evolEpi", beginning, end,\
+                        colorMap='Blues_r', offSet=offset, pixelType='square',\
                         sequence=prot+".fasta", isColorBarOn=True)
-            # plotGEMMEmatrix(gemmeData, prot+"_normPred_evolEpi.png", 1, None,\
-            #                 colorMap='Blues_r', offSet=0, pixelType='square')
         
         #Check if the normalized data files were created. 
-        if(os.path.exists(prot+"_normPred_evolInd.txt") and args.verbose==True):
+        if(os.path.exists(prot+"_normPred_evolInd.txt") and verbosity==True):
             gemmeData = parseGEMMEoutput(prot+"_normPred_evolInd.txt", verbose=False)
             sequenceLength = len(gemmeData[0])
             beginning = 1
@@ -1142,16 +1147,18 @@ def doit(inAli,mutFile,retMet,bFile,fFile,n,N, jetfile, pdbfile, normWeightMode,
                     plotGEMMEmatrix(gemmeData, prot+"_normPred_evolInd"+"_part_"+str(i+1), \
                         i*rowLength + beginning, \
                         (i+1)*rowLength + beginning -1,\
-                        colorMap='Greens_r', offSet=i*rowLength + args.offset, pixelType='square',\
+                        colorMap='Greens_r', offSet=i*rowLength + offset, pixelType='square',\
                         sequence=prot+".fasta", isColorBarOn=True)
                 if(sequenceLength%rowLength != 0):
                     plotGEMMEmatrix(gemmeData, prot+"_normPred_evolInd"+"_part_"+str(i+2), \
                         (i+1)*rowLength + beginning, \
                         end,\
-                        colorMap='Greens_r', offSet=(i+1)*rowLength + args.offset, pixelType='square',\
+                        colorMap='Greens_r', offSet=(i+1)*rowLength + offset, pixelType='square',\
+                        sequence=prot+".fasta", isColorBarOn=True)
+            else:
+                plotGEMMEmatrix(gemmeData, prot+"_normPred_evolInd",beginning, end,\
+                        colorMap='Greens_r', offSet=offset, pixelType='square',\
                         sequence=prot+".fasta", isColorBarOn=True)
-            # plotGEMMEmatrix(gemmeData, prot+"_normPred_evolInd.png", 1, None,\
-            #                 colorMap='Greens_r', offSet=0, pixelType='square')
 
         #Check if the normalized data files were created. 
         if(os.path.exists(prot+"_normPred_evolCombi.txt")):        
@@ -1166,18 +1173,19 @@ def doit(inAli,mutFile,retMet,bFile,fFile,n,N, jetfile, pdbfile, normWeightMode,
                     plotGEMMEmatrix(gemmeData, prot+"_normPred_evolCombi"+"_part_"+str(i+1), \
                         i*rowLength + beginning, \
                         (i+1)*rowLength + beginning -1,\
-                        colorMap=args.colormap, offSet=i*rowLength + args.offset, pixelType='square',\
+                        colorMap=colormap, offSet=i*rowLength + offset, pixelType='square',\
                         sequence=prot+".fasta", isColorBarOn=True)
                 if(sequenceLength%rowLength != 0):
                     plotGEMMEmatrix(gemmeData, prot+"_normPred_evolCombi"+"_part_"+str(i+2), \
                         (i+1)*rowLength + beginning, \
                         end,\
-                        colorMap=args.colormap, offSet=(i+1)*rowLength + args.offset, pixelType='square',\
+                        colorMap=colormap, offSet=(i+1)*rowLength + offset, pixelType='square',\
                         sequence=prot+".fasta", isColorBarOn=True)
-
-
-            # plotGEMMEmatrix(gemmeData, prot+"_normPred_evolCombi.png", 1, None,\
-            #                 colorMap='Oranges_r', offSet=0, pixelType='square')
+                    
+            else:
+                plotGEMMEmatrix(gemmeData, prot+"_normPred_evolCombi",beginning, end,\
+                        colorMap=colormap, offSet=offset, pixelType='square',\
+                        sequence=prot+".fasta", interactive=False, isColorBarOn=True)
 
             #Convert standard combined output to a transposed format to increase
             #legibility.
@@ -1188,7 +1196,7 @@ def doit(inAli,mutFile,retMet,bFile,fFile,n,N, jetfile, pdbfile, normWeightMode,
             aaAndPosition = []
             oldNamesList = gemmeDF.columns.tolist()
             for i in range(len(list(seq))):
-                aaAndPosition.append(list(seq)[i]+str(i+1+args.offset))
+                aaAndPosition.append(list(seq)[i]+str(i+1+offset))
             # gemmeDFtrans = pd.DataFrame(gemmeDFtrans, index=aaAndPosition)
             gemmeDFtrans.rename(index = dict(map(lambda i,j : (i,j) , oldNamesList,aaAndPosition)), inplace=True)
             # gemmeDFtrans.set_axis(aaAndPosition)
@@ -1205,16 +1213,23 @@ def doit(inAli,mutFile,retMet,bFile,fFile,n,N, jetfile, pdbfile, normWeightMode,
 
     cleanTheMess(prot,bFile,fFile, chainID=chains[0], verbosity=verbosity)
 
-if (__name__ == '__main__'):
+def main():
+    """
+    Main function (and yes, I know. The name and the documentation are ingenious :). 
+    """
     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, args.verbose)
+         args.normweightmode, args.alphabet, args.verbose, args.offset, args.colormap)
 
     toc = time.perf_counter()
     
     print(f"ESGEMME computation finished in {toc - tic:0.4f} seconds!")
+
+if (__name__ == '__main__'):
+    main()
     
 

examples/example-esgemme-script.sh

@@ -18,7 +18,7 @@ then
     echo "Running ESGEMME with a user-provided alignment file."
     echo "Using a previously produced prot_jet.res file to check reproducibility!"
 
-    python $ESGEMME_PATH/esgemme.py ../data/aliBLAT.fasta -r input -f ../data/aliBLAT.fasta --jetfile ../data/BLAT_jet.res
+    esgemme ../data/aliBLAT.fasta -r input -f ../data/aliBLAT.fasta --jetfile ../data/BLAT_jet.res
 
 elif [ "$1" == "withpdb" ]
 then
@@ -26,7 +26,7 @@ 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-af2.pdb for the structural feature calculations!"
     echo "Entire mutational map of the protein will be calculated!"
-    python $ESGEMME_PATH/esgemme.py ../data/aliBLAT.fasta -r input -f ../data/aliBLAT.fasta \
+    esgemme ../data/aliBLAT.fasta -r input -f ../data/aliBLAT.fasta \
 	   --pdbfile ../data/blat-af2.pdb --normweightmode max
 
 elif [ "$1" == "withpdb-withmutfile" ]
@@ -35,7 +35,7 @@ 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-af2.pdb for the structural feature calculations!"
     echo "Only effects of mutations specified in the Stiffler_2015_BLAT_ECOLX.mut file will be calculated!"
-    python $ESGEMME_PATH/esgemme.py ../data/aliBLAT.fasta -r input -f ../data/aliBLAT.fasta  \
+    esgemme ../data/aliBLAT.fasta -r input -f ../data/aliBLAT.fasta  \
 	   --pdbfile ../data/blat-af2.pdb --normweightmode max \
 	   -m ../data/Stiffler_2015_BLAT_ECOLX.mut
 
@@ -45,7 +45,7 @@ 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-af2.pdb for the secondary structure based calculations!"
     echo "Only effects of mutations specified in the Stiffler_2015_BLAT_ECOLX.mut file will be calculated!"
-    python $ESGEMME_PATH/esgemme.py ../data/aliBLAT.fasta -r input -f ../data/aliBLAT.fasta \
+    esgemme ../data/aliBLAT.fasta -r input -f ../data/aliBLAT.fasta \
 	   --pdbfile ../data/blat-af2.pdb --normweightmode sstjetormax \
 	   -m ../data/Stiffler_2015_BLAT_ECOLX.mut
     #demust compare -i ../data/BLAT_ECOLX_Stiffler_2015_experimental.dat --itype singleline -j BLAT_normPred_evolCombi.txt --jtype singleline
@@ -55,7 +55,7 @@ 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-af2.pdb for the secondary structure based calculations!"
     echo "Only effects of mutations specified in the Stiffler_2015_BLAT_ECOLX.mut file will be calculated!"
-    python $ESGEMME_PATH/esgemme.py ../data/aliBLAT.fasta -r input -f ../data/aliBLAT.fasta \
+    esgemme ../data/aliBLAT.fasta -r input -f ../data/aliBLAT.fasta \
 	   --pdbfile ../data/blat-af2.pdb --normweightmode tjetormax \
 	   -m ../data/Stiffler_2015_BLAT_ECOLX.mut
     demust compare -i ../data/BLAT_ECOLX_Stiffler_2015_experimental.dat --itype singleline -j BLAT_normPred_evolCombi.txt --jtype singleline
@@ -63,6 +63,6 @@ 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!"
-    python3 $ESGEMME_PATH/esgemme.py ../data/aliBLAT.fasta -r input -f ../data/aliBLAT.fasta
+    esgemme ../data/aliBLAT.fasta -r input -f ../data/aliBLAT.fasta
     
 fi

requirements.txt

+numpy
+matplotlib
+scipy
+pandas
+biopython
+biotite
+prody
+

setup.py

+################################################################################
+# esgemme - A Python program to predict mutational effects of proteins.        #
+# Authors: Mustafa Tekpinar                                                    #
+# Copyright (c) Mustafa Tekpinar - Alessandra Carbone 2023                     #
+#                                                                              #
+# This file is part of esgemme.                                                #
+#                                                                              #
+# License: MIT License                                                         #
+#                                                                              #
+# Permission is hereby granted, free of charge, to any person obtaining a copy #
+# of this software and associated documentation files (the "Software"), to deal#
+# in the Software without restriction, including without limitation the rights #
+# to use, copy, modify, merge, publish, distribute, sublicense, and/or sell    #
+# copies of the Software, and to permit persons to whom the Software is        #
+# furnished to do so, subject to the following conditions:                     #
+#                                                                              #
+# The above copyright notice and this permission notice shall be included in   #
+# all copies or substantial portions of the Software.                          #
+#                                                                              #
+# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR   #
+# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,     #
+# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE  #
+# AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER       #
+# LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,#
+# OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE#
+# SOFTWARE.                                                                    #
+################################################################################
+
+from setuptools import setup, find_packages
+
+from esgemme import __version__ as cp_vers
+
+setup(name='esgemme',
+      version=cp_vers,
+      description="A Python program to predict mutational effects of proteins.",
+      long_description=open('README.md').read(),
+      long_description_content_type="text/markdown",
+      author="Mustafa Tekpinar",
+      author_email="tekpinar@buffalo.edu",
+      url="https://github.com/tekpinar/esgemme",
+      download_url="https://github.com/tekpinar/esgemme",
+      license="MIT",
+      classifiers=[
+          'Development Status :: 5 - Production/Stable',
+          'Environment :: Console',
+          'Operating System :: POSIX',
+          'Programming Language :: Python :: 3',
+          'Programming Language :: Python :: 3.6',
+          'Programming Language :: Python :: 3.7',
+          'Programming Language :: Python :: 3.8',
+          'Programming Language :: Python :: 3.9',
+          'License :: OSI Approved :: MIT License',
+          'Intended Audience :: Science/Research',
+          'Topic :: Scientific/Engineering :: Bio-Informatics',
+          'Topic :: Scientific/Engineering :: Chemistry'
+          ],
+      python_requires='>=3.6',
+      install_requires=[i for i in [l.strip() for l in open("requirements.txt").read().split('\n')] if i],
+      # zip_safe=False,
+      packages=[p for p in find_packages() if p != 'tests'],
+      # file where some variables must be fixed by install
+      entry_points={
+          'console_scripts': [
+              'esgemme=esgemme.esgemme:main'
+          ]
+      }
+      )