bootamova1.02.c

生物学种群遗传结构随机生成

#include<fstream.h>
#include <strstrea.h>
#include <stdio.h>
#include <stdlib.h>
#include <conio.h>
#include <math.h>
#include <string.h>
#include <iostream.h>
#include <ctype.h>
#include <iomanip.h>


#include <time.h>


#define num 2000

struct HapMatrix
{
	char Nam[10];
	int fi;
	char ATGC[num],Freq[2];

}HapM[20];

int main(int argc, char* argv[])

{ 

srand( (unsigned)time( NULL ) ); 

char strtemp[num];
int NbSamples;
char NamPop[20][10];
int  SampSiz, NumHap;
char seq[100][num];
char ch,*ptr=NULL;
int length;

int boot;
cout<<"Input the number of bootstrap for AMOVA:"<<endl;
cin>>boot;

for(int ib=0;ib<boot;ib++)

{
/*open input.txt and read data*/

ifstream fin("input.txt", ios::in | ios::nocreate);
	        if (!fin) {  

                          cerr<<"input.txt file not open!"<<endl;

                          exit(1);
	                  }	

/**/
/*open out.txt and write */
ofstream fout("out.dat", ios::app);
             if (!fout) {  
             cerr<<"out.dat file not open!"<<endl;
             exit(1);}

fout<<ib+1<<"   ===================================="<<endl;
fout<<endl;
fout<<endl;

fout<<"[Profile]"<<endl;
fout<<"Title=\"random data set fo r AMOVA\""<<endl;
fout<<endl;


/*read NbSamples write initial information for AMOVA*/
fin.getline(strtemp,num,ch='\n');
			 NbSamples=atoi(strtemp);

			 cout<<NbSamples<<"#"<<endl;

fout<<"               NbSamples="<<NbSamples<<endl;
fout<<"               GenotypicData=0"<<endl;
fout<<"               DataType=DNA"<<endl;
fout<<"               LocusSeparator=NONE"<<endl;
fout<<"               MissingData='?'"<<endl;
fout<<"[Data]"<<endl;
fout<<endl;
fout<<"     [[Samples]]"<<endl;



/*read name of population into NamPop[][]*/
for (int i=0;i<NbSamples;i++)
{
fin.getline(strtemp,num,ch='\n');
strcpy(NamPop[i],strtemp);

}

/*read data from all population and output random datasets*/

for(int ABZ=0;ABZ<NbSamples;ABZ++)
{
/*read name of population and output*/
fin.getline(strtemp,num,ch='\n');
fout<<"               SampleName="<<"\""<<strtemp<<"\""<<endl;


/*read sample size and number of haplotye*/
fin.getline(strtemp,num,ch='\n');

SampSiz=atoi(strtemp);
fin.getline(strtemp,num,ch='\n');
NumHap=atoi(strtemp);

fout<<"               SampleSize="<<SampSiz<<endl;
cout<<"read sample size and number of haplotye"<<endl;
fout<<"               SampleData= {"<<endl;
cout<<"SampleData= {"<<endl;

/*read sequence data into seq[][]*/

for(i=0;i<NumHap;i++)
{
fin.getline(strtemp,num,ch='\n');

length=strlen(strtemp);
strtemp[length]='\0';


strcpy(seq[i],strtemp);
strncpy(HapM[i].Nam,strtemp,10);


strncpy(HapM[i].Freq,strtemp+10,2);

HapM[i].fi=atoi(HapM[i].Freq);
ptr=strstr(strtemp," ");
strcpy(strtemp,ptr);
ptr=strstr(strtemp,"  ");
strcpy(HapM[i].ATGC,ptr+2);


}
int k1=0;

for(int j=0;j<NumHap;j++)

{
	for(int k=0;k<HapM[j].fi;k++)

	{
	strcpy(seq[k1],HapM[j].ATGC);
	
	k1++;
   cout<<"k1="<<k1<<endl;
	/*seq[j+k1][strlen(HapM[j].ATGC)]='\0';*/

	
	}
	
	

}



/*cout<<seq[0]<<endl<<"&&"<<endl;
cout<<seq[7]<<endl<<"&&"<<endl;*/

for(i=0;i<NumHap;i++)
{
HapM[i].fi=0;
}


for(i=0;i<SampSiz;i++)
{
int RandNum;
if(SampSiz>1)
RandNum=1+rand() % (SampSiz-1);
else RandNum=0;
/*strcpy(strtemp,seq[RandNum]);
strtemp[length]='\0';*/

for (j=0;j<NumHap;j++)

{

	
	int ptr1;
strncpy(strtemp,seq[RandNum],strlen(HapM[j].ATGC));
strtemp[strlen(HapM[j].ATGC)]='\0';	
ptr1 = strcmpi(HapM[j].ATGC,strtemp);

/*cout<<HapM[j].ATGC<<endl;
cout<<strtemp<<"!"<<endl;*/
if(ptr1==0)
HapM[j].fi++;
}

/*cout<<"RandNum="<<RandNum<<endl;*/


/*fout<<strtemp<<endl;*/

}

for(j=0;j<NumHap;j++)
{
	if(!HapM[j].fi==0)
fout<<HapM[j].Nam<<" "<<HapM[j].fi<<" "<<HapM[j].ATGC<<endl;

}

fout<<"               }"<<endl;
cout<<"HapM[j].fi="<<HapM[0].fi<<endl;
cout<<"HapM[j].fi="<<HapM[1].fi<<endl;
cout<<"HapM[j].fi="<<HapM[2].fi<<endl;


/*for(i=0;i<SampSiz;i++)
{
cout<<seq[i]<<endl;
}*/
/*}*/		 
}


fout<<endl;
fout<<"#Definition of the group structure:"<<endl;
fout<<"        [[Structure]]"<<endl;
fout<<"               StructureName=\"Geographical division\""<<endl;
fout<<"               NbGroups=1"<<endl;
fout<<"               IndividualLevel=0"<<endl;
fout<<"               Group={"<<endl;

for(i=0;i<NbSamples;i++)

{fout<<"               "<<NamPop[i]<<endl;

}
 fout<<"               }"<<endl;
 fout<<endl;
 fout<<endl;
 fout<<endl;
fin.close();
fout.close();

}

return 0; 

}