uCRISPR - Unified energetics analysis to evaluate the Cas9 on-target activity and off-target effects.
Version 0.1
Author: Dong Zhang, Travis Hurst, Dongsheng Duan & Shi-Jie Chen
Email: chenshi@missouri.edu
Date: Feb 10, 2019

1. System Requirement

        Linux/Unix
        gcc compiler >4.8 version 

2. Compilation
  
    Step 1. Install RNAstructure package (http://rna.urmc.rochester.edu/RNAstructure.html)
            ***Specify the location of the thermodynamic parameters before the next step.
            ***RNAstructure uses a set of nearest neighbor thermodynamic parameters for predicting folding free energy changes of secondary structures. When an interface is
               invoked, these parameters are read from disk. The parameters come in the directory RNAstructure/data_tables/. To indicate the location of this directory, an
               environment variable, DATAPATH, needs to be set to this location.

            ***In general, this is accomplished with:
               command "vi ~/.bashrc"
               Add "export DATAPATH=[directory in which RNAstructure resides]/RNAstructure/data_tables/" to the end of "~/.bashrc" file
               command "source ~/.bashrc"

    Step 2. Set path for DATA (line #12) and RNAstructure (line #13) in "uCRISPR.cpp" file:
            string DATA="[Absolute path for directory in which uCRISPR resides]/uCRISPR/data/";
            string RNAstructure="[Absolute path for directory in which RNAstructure resides]/RNAstructure/exe/EnsembleEnergy"

    Step 3. Make: g++ -o uCRISPR uCRISPR.cpp -std=c++11

3. Usage: uCRISPR [options] 

     Options:
       -h         #Display help information
       -on file   #Evaluate on-target avtivities for on-target sites in file,
                   one site (23-mer or 30-mer sequence) per line.
                   See "./example/OntargetSite.dat" for an example.
       -off file  #Evaluate off-target efficiencies for off-target sites in file,
                   one site (20-mer/23-mer wild type sequence and 23-mer off target
                   sequence) per line in file. See "./example/OfftargetSite.dat" for an example.
    
4. Examples 

     a. uCRISPR -on  ./example/OntargetSite.dat   #Evaluate on-target sites given in file "./example/OntargetSite.dat",
                                                   predicted scores are shown on the screen(Also see ./example/OntargetSite.out).

     b. uCRISPR -off ./example/OfftargetSite.dat  #Evaluate off-target sites given in file "./example/OfftargetSite.dat"
                                                   predicted scores are shown on the screen(Also see ./example/OfftargetSite.out).