Changes to install prescott.py

Dockerfile

@@ -12,6 +12,7 @@ COPY ./JET2/ /usr/local/JET2
 COPY ./naccess2.1.1 /usr/local/naccess2.1.1
 
 COPY ./PRESCOTT/prescott/escott.py ./PRESCOTT/prescott/escott.py
+COPY ./PRESCOTT/prescott/prescott.py ./PRESCOTT/prescott/prescott.py
 COPY ./PRESCOTT/prescott/alphabets ./PRESCOTT/prescott/alphabets
 COPY ./PRESCOTT/prescott/__init__.py ./PRESCOTT/prescott/__init__.py
 COPY ./PRESCOTT/setup.py ./PRESCOTT/setup.py
@@ -96,21 +97,21 @@ RUN pip3 install https://github.com/debbiemarkslab/EVcouplings/archive/develop.z
 
 # If run command on M1 Mac with macOS Monterey, you can remove sudo
 # Build command
-# sudo docker build -t tekpinar/prescott-docker:v1.4.0 .
+# sudo docker build -t tekpinar/prescott-docker:v1.5.0 .
 # sudo docker login
-# sudo docker push tekpinar/prescott-docker:v1.4.0 
+# sudo docker push tekpinar/prescott-docker:v1.5.0 
 
 # Pull command on M1 Mac with macOS Monterey
-# sudo docker pull tekpinar/prescott-docker:v1.4.0
+# sudo docker pull tekpinar/prescott-docker:v1.5.0
 
 # Run commands
-# sudo docker run -i -t -v $(pwd) --platform linux/amd64 tekpinar/prescott-docker:v1.4.0 /bin/bash
+# sudo docker run -i -t -v $(pwd) --platform linux/amd64 tekpinar/prescott-docker:v1.5.0 /bin/bash
 
 # Bind your current folder to a particular folder in docker.
 # In this way, you fall into the bash terminal of the docker image. 
-# docker run -ti --rm --mount type=bind,source=$PWD,target=/home/tekpinar/research/lcqb tekpinar/prescott-docker:v1.4.0
+# docker run -ti --rm --mount type=bind,source=$PWD,target=/home/tekpinar/research/lcqb tekpinar/prescott-docker:v1.5.0
 
 #If you want to use the docker image like an executable file:
 # Please note that you must have aliBLAT.fasta and blat-af2.pdb inside your current folder and run this command!
-# sudo docker run --rm -v $PWD:/home/tekpinar/research/lcqb tekpinar/prescott-docker:v1.4.0 escott aliBLAT.fasta -f aliBLAT.fasta --pdbfile  blat-af2.pdb
+# sudo docker run --rm -v $PWD:/home/tekpinar/research/lcqb tekpinar/prescott-docker:v1.5.0 escott aliBLAT.fasta -f aliBLAT.fasta --pdbfile  blat-af2.pdb
 

examples/example-prescott-script.sh

+#!/bin/bash
+
+prescott -e ../data/MLH1_normPred_evolCombi_singleline_1-ranksort.txt -g ../data/gnomAD_v2.1.1_MLH1_HUMAN_ENSG00000076242.csv

prescott/__init__.py

@@ -8,4 +8,4 @@ Purpose     : A Python program to predict mutational effects of proteins.
 
 __all__ = ['prescott']
 
-__version__ = '1.4.0'
+__version__ = '1.5.0'

prescott/prescott.py

@@ -141,7 +141,7 @@ def getGnomADOverallFrequency(infile, usePopMax="true"):
     dfMissense['protein'] = proteinNameList
     return (dfMissense)
 
-if __name__ == "__main__":
+def main():
     # Adding the main parser
     main_parser = argparse.ArgumentParser(description=\
         "A Python toolkit to prepare, modify, visualize and analyze deep mutational scanning (DMS) data of proteins.")
@@ -208,7 +208,7 @@ if __name__ == "__main__":
     print("@> Name of the output file          : {}".format(args.outputfile))
     # End of argument parsing!
 
-    mainPath = "/mnt/data/tekpinar/ESGEMME_vs_EVE_all_data"
+    # mainPath = "/mnt/data/tekpinar/ESGEMME_vs_EVE_all_data"
     # dataFolder = "/esgemme-v-1-4-0-max-two-components-eve-msas-entire-single-point-mutations"
     # dataFolder = "/egemme-v-1-3-0-eve-msas-entire-single-point-mutations"
     # dataFolder = sys.argv[9]
@@ -270,7 +270,7 @@ if __name__ == "__main__":
     myBigMergedDF['labels'] = np.nan
     myBigMergedDF['position'] = ""
 
-    useFrequencies = "true"
+    useFrequencies = args.usefrequencies
     selectedPositionsList = []
     selectedValuesList = []
     selectedMutantsList = []
@@ -393,3 +393,6 @@ if __name__ == "__main__":
     myBigMergedDF.to_csv('myBigMergedDF-normalized-asm.csv', index=None)
     myBigMergedDF.to_csv(args.outputfile, columns=['mutant', 'PRESCOTT'], index=False, header=None, sep=' ')
     print("@> AUC= {:.3f} {:.3f}".format( AUC_ESCOTT, AUC_PRESCOTT))
+
+if __name__ == "__main__":
+    main()

setup.py

@@ -59,7 +59,8 @@ setup(name='prescott',
       # file where some variables must be fixed by install
       entry_points={
           'console_scripts': [
-              'escott=prescott.escott:main'
+              'escott=prescott.escott:main',
+              'prescott=prescott.prescott:main'
           ]
       },
       include_package_data=True,