windows下snp模式的上位机模拟
EpistaSim_Windows的Python项目详细描述
上位酶是在单倍型选择模型下，通过前向和后向的结合突变和重组过程，估计单倍型频率并模拟与目标两个位点相连区域的dna序列的模拟器。 软件的输出与hudson的ms软件相似（hudson，1990）。EpistaSim是一种灵活的仿真器，可以引入不同的上位模型。软件根据历史向前运行并合并模拟 （轨迹）单倍型频率，与文本文件中该区域的DNA序列一起输出。epistasim包括前后两部分的仿真。
下载并安装
下载“epistasim”软件包并解压缩
运行cmd并输入epistasim的目录
正在加载EpistaSim包，请使用以下命令：
python setup.py install
运行EpistaSim
打开python（Commond line）或python Shell窗口
转发：
使用fowlowing命令，通过正向过程模拟dna序列和单倍型频率：
import Forward Forward.main()
- 示例：
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. ..........
向后：
使用fowlowing命令，通过结合过程模拟dna序列和单倍型频率：
import Backward Backward.main()
示例
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.
..........
epistasim的输出
正向和反向的输出是sames，与Hudson的ms软件（Hudson，1990）类似
根据up参数，结果为fowllow:
输出DNA序列
// 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 // ........
单倍型频率输出
// 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
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