Metadata-Version: 1.0
Name: EpistaSim_Windows
Version: 1.1.0
Summary:  Simulator of Single nucleotide polymorphism (SNP) patetrn in a region from two loci through forward and coalescent process with mutation and recombination under selection model
Home-page: http://blog.useasp.net/
Author: Shaojun Zhang
Author-email: zhangsahojun@ems.hrbmu.edu.cn
License: MIT
Description: 
        ===============
        EpistaSim_wins
        ===============
        
        EpistaSim is a simulator that can estimate haplotype frequency and simulate DNA sequences in a region linking with target two loci under haplotype selective model through forward and backward process integrating with mutation and recombination. 
        The output of software was similar with Hudson's ms software (Hudson, 1990). EpistaSim is a flexible simulator so that it can incorporate different epistasis model. The software runs forward and coalescent simulations depending on the histories 
        (trajectories) of haplotype frequency which was output accompany with DNA sequences of the region in text files. EpistaSim included two parts forward and backward simulation.        
        
        
        -------------------------
        **Download and Install**
        -------------------------
        
        Download package "EpistaSim" and unzip
        
        Run cmd and enter the directory of EpistaSim
        
        Loading EpistaSim package, use following command:
                
                ::
                
                     python python setup.py install
        
        
        ------------------
        **Run EpistaSim**
        ------------------
        
        Open the window of python (Commond line) or Python Shell
        
        
        *Forward:*
        ^^^^^^^^^^^^^^^^^^^^^
        
        
        Simulate the DNA sequences and haplotype frequency through forward process, using fowllowing command:
                
                ::
                
                     import Forward
                     Forward.main()
                     
           
        *Examples:*        
                ::
                         
                     import Forward
                     Forward.main()
        
                     A prompt of input arguments as follow:
                               Enter haplotype frequency split by space: 0.25 0.25 0.25 0.25
                               
                               Enter Epistasis selective model (If you want to use default value press space key): M1
                               
                               Enter selective haplotype or allele from two-locus(You must seperate by comma between alleles from two-locus corresponding to M3 or M4; If you want to use default value press space key): 11
                               
                               Enter selective coefficient (If you specified M3 or M4, input two selective coefficients from two locus seperated by comma; If you want to use default value press space key): 0.01
                               
                               Enter the number of simulated samples ( If you want to use default value press space key): 10
                               
                               Enter the number of replication ( If you want to use default value press space key): 5
                               
                               Enter the length of simulated region ( If you want to use default value press space key): 1000
                               
                               Enter the number of generation ( If you want to use default value press space key): 200
                               
                               Enter position of two selective loci  split by space ( If you want to use random position press space key): 10 100
                               
                               Enter recombination rate per generation per bp ( If you want to use default value press space key): 
                               
                               Enter mutation rate per generation per bp ( If you want to use default value press space key): 0.0000001
                               
                               Enter the number of segsites in the region ( If you want to use random value press space key): 
                               
                               Enter the outputfile name of simulated sequence: forward.out
                               
                               Enter the outputfile name of haplotype frequency trajectories: hapfre.out
                               
                     The running information of Forward was illustrated as follow:
                     
                     Generate the initial population
                     
                     Print the track file of haplotype frequency
                     
                     Simulation the offspring
                     
                     simulation the 0th replication
                     
                     A region of 1000bp include 12 segsites were simulated for 200 generations with sample size 10 for 1 replication.
                     
                     ..........
                     
        
        *Backward:*
        ^^^^^^^^^^^^^^^^^^^^^
        
        Simulate the DNA sequences and haplotype frequency through coalescent process, using fowllowing command:
                
                ::
                
                     import Backward
                     Backward.main()
                     
           
        *Examples*
                
                ::
                         
                     import Backward
                     Backward.main()
        
                     A prompt of input arguments as follow:
                               Enter haplotype frequency split by space: 0.3 0.1 0.1 0.5
                               
                               Enter selective haplotype from two-locus(If you want to use default value press space key): 11
                                                      
                               Enter selective coefficient ( If you want to use default value press space key): 0.01
                               
                               Enter the number of simulated samples ( If you want to use default value press space key): 10
                               
                               Enter the number of replication ( If you want to use default value press space key): 5
                               
                               Enter the length of simulated region ( If you want to use default value press space key): 1000
                               
                               Enter position of two selective loci  split by space ( If you want to use random position press space key): 10 100
                               
                               Enter recombination rate per generation per bp ( If you want to use default value press space key): 0.0000001
                               
                               Enter mutation rate per generation per bp ( If you want to use default value press space key): 0.0000001
                               
                               Enter the number of segsites in the region ( If you want to use random value press space key): 
                               
                               Enter the outputfile name of simulated sequence: backward.out
                               
                               Enter the outputfile name of haplotype frequency trajectories: hapfre.out
                               
                     The running information of Forward was illustrated as follow:
                     
                     
                     Print the track file of haplotype frequency
                     
                     Simulation the offspring
                     
                     simulation the 0th replication
                     
                     A region of 1000bp include 9 segsites were simulated  with sample size 10 for 1 replication.
                     
                     ..........
                                  
        ------------------------
        **Output of EpistaSim**
        ------------------------
        The outputs of Forward and Backward are the sames and similar with Hudson's ms software (Hudson, 1990).
        
        According to the up arguments, the results as fowllow:
        
            
        *Output of DNA sequence*
        ^^^^^^^^^^^^^^^^^^^^^^^^^
                
                ::
                        
                     //
                     Segsites: 12
                     Selected two_locus: 10 100 
                     Positions: 10 100 125 158 258 309 472 631 756 818 858 886 
                     111011011111
                     111011011110
                     111010010110
                     111111000111
                     111001011011
                     101100011111
                     001110011111
                     001000011111
                     001011011111
                     011100000001
                     //
                     ........
                     
        *Output of haplotype frequency*
        ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
                
                ::
                        
                     //
                     T	00	01	10	11
                     0	0.25	0.25	0.25	0.25	
                     1	0.248079102592	0.253290720757	0.254300434135	0.244329742516	
                     2	0.250079789017	0.260533576401	0.254926425626	0.234460208956	
                     3	0.247683161282	0.257852724706	0.259331708331	0.235132405681	
                     ......
                     199	0.174483716477	0.147128461696	0.166087155013	0.512300666814	
                     200	0.175953877557	0.145569161198	0.163958437969	0.514518523277
        
        
Keywords: epistasis simulation
Platform: UNKNOWN
Classifier: Development Status :: 3 - Alpha
Classifier: Intended Audience :: Science/Research
Classifier: Topic :: Software Development :: Build Tools
Classifier: License :: OSI Approved :: Python Software Foundation License
Classifier: Environment :: Win32 (MS Windows)
Classifier: Operating System :: Microsoft :: Windows
Classifier: Operating System :: Microsoft :: Windows :: Windows 7
Classifier: Operating System :: Microsoft :: Windows :: Windows NT/2000
Classifier: Operating System :: Microsoft :: Windows :: Windows XP
Classifier: Natural Language :: English
Classifier: Programming Language :: Python :: 2.6
Classifier: Programming Language :: Python :: 2.7
