/*
@author: joao lopes
@workplace: Reading University
@date: 8th May 2009
*/
#include "interface.h"
/*
It creates an ABC .len file given an GenePop input file.
@arg length format filename
@arg output filename
*/
int createFreqTab3(char *input,char *output){
int cloc, cpop, cdna, csamp, i, j, cplo, //iterators
nsamp, //total nr. of samples
loctype, //0 = locus divided by ','; 1 = locus divided by lines
searchInd, //check if ',' is found in the sample file
reachEND, //check if EOF have been reached
searchPop, //check if the word 'pop' is found in the sample file
npop, //number of populations
nloc, //number of loci
equalDna, //auxiliar to build the .len file
outsize, //size of output file name
*ldna, //number of different dna data by loci
*lplo, //nr of markers per loci
*lsamp = NULL, //total number of samples per loci
***freq, //freq of dna data by no_pop by no. of diff dna data
**valM, //list of all the diff microsatellite sizes
**IDsort, //list of the order of the diff microsatellite sizes
***genotM2, //list of all the individual's haplotype per pop per loci
****genotM; //list of all the individual's haplotype per pop per loci
char c1, //gets the value of a char temporarly
info[LOCMAXCHAR+1], //information of a locus
info1[LOCMAXCHAR+1], //information of a locus
info2[LOCMAXCHAR+1], //information of a locus
aux[MAXCHAR], //auxiliar
*outname, //name of the output file
**locname; //name of the loci
FILE *inp, //pntr to the input file
*outp; //pntr to the output file
time_t startClock; //time when the program starts
const struct tm *startTime; //struct time when the program starts
inp = fopen(input,"r");
if(inp == NULL)
return 1; //cannot open sample file
outsize = strlen(output) + 5;
outname = (char *)malloc(outsize*sizeof(char));
strcpy(outname,output);
outp = fopen(strcat(outname,".len"),"w");
if(outp == NULL)
return 2; //cannot create .len file
time( &startClock ); // Get time in seconds
startTime = localtime( &startClock ); // Convert time to struct tm form
//get nloc
fgets(aux,MAXCHAR,inp);
nloc=1;
loctype=1;
fgets(aux,MAXCHAR,inp);
for(i=0;i<strlen(aux);i++){
if(aux[i]==','){
loctype=0;
nloc+=1;
}
}
if(loctype){
searchPop=1;
i=0;
while(searchPop){
fgets(aux,MAXCHAR,inp);
if(feof(inp))
return 3; //file ended before the display of data
j=0;
while(isspace(aux[j])||aux[j]=='\t')
j++;
if(aux[j]=='P'||aux[j]=='p'){
if(aux[j+1]=='O'||aux[j+1]=='o')
if(aux[j+2]=='P'||aux[j+2]=='p')
searchPop=0;
}
else
i++;
}
nloc+=i;
}
else
fgets(aux,MAXCHAR,inp);
//get npop, lsamp
reachEND=0;
cpop=0;
while(!reachEND){
lsamp = (int *)myAlloc(lsamp,(cpop+1)*sizeof(int));
csamp=0;
searchPop=1;
while(searchPop && !reachEND){
fgets(aux,MAXCHAR,inp);
if(feof(inp))
reachEND=1;
j=0;
while(isspace(aux[j])||aux[j]=='\t')
j++;
if(aux[j]=='P'||aux[j]=='p')
if(aux[j+1]=='O'||aux[j+1]=='o')
if(aux[j+2]=='P'||aux[j+2]=='p')
searchPop=0;
searchInd=1;
for( ; j<strlen(aux) && searchInd; j++){
if(aux[j]==','){
csamp++;
searchInd=0;
}
}
}
lsamp[cpop]=csamp;
cpop++;
}
npop=cpop;
rewind(inp);
//print first line to output file
fprintf(outp,"# GenePop file converted to .len file with genepop2table1.0\n");
fprintf(outp,"# input file: %s\n",input);
fprintf(outp,"# output file: %s.len\n",output);
fprintf(outp,"# date: %s#\n#",asctime(startTime));
fgets(aux,MAXCHAR,inp);
for(i=0;!isendline(aux[i]);i++)
fprintf(outp,"%c",aux[i]);
fprintf(outp,"\n");
//get locus names
locname=(char**)malloc(nloc*sizeof(char*));
if(loctype){
for(cloc=0;cloc<nloc;cloc++){
locname[cloc] = malloc(MAXCHAR*sizeof(char));
fgets(aux,MAXCHAR,inp);
for(i=0;!isendline(aux[i]);i++)
locname[cloc][i]=aux[i];
locname[cloc][i]='\0';
}
}
else{
fgets(aux,MAXCHAR,inp);
for(j=0,cloc=0; cloc<nloc; cloc++){
i=0;
locname[cloc] = malloc(MAXCHAR*sizeof(char));
while(aux[j]!=','&& !isendline(aux[j])){
locname[cloc][i++]=aux[j++];
}
j++;
locname[cloc][i]='\0';
}
}
//allocate memory to lsamp, lplo and genotM
lplo = (int *)malloc(nloc*sizeof(int));
genotM = (int****)malloc(nloc*sizeof(int***));
for(cloc=0;cloc<nloc;cloc++){
genotM[cloc] = (int***)malloc(npop*sizeof(int**));
for(cpop=0; cpop<npop; cpop++){
genotM[cloc][cpop] = (int**)malloc(lsamp[cpop]*sizeof(int*));
for(csamp=0; csamp<lsamp[cpop]; csamp++)
genotM[cloc][cpop][csamp]=(int*)malloc(NPLOIDY*sizeof(int));
}
}
//fill genotM[cloc][cpop][csamp][cplo]
for(cpop=0 ; cpop<npop ; cpop++){
fgets(aux,MAXCHAR,inp);
for(csamp=0; csamp<lsamp[cpop] ; csamp++){
fgets(aux,MAXCHAR,inp);
j=0;
while(aux[j]!=',')
j++;
for(cloc=0; cloc<nloc; cloc++){
for( ; !isdigit(aux[j]); j++){
if(isendline(aux[j])){
fgets(aux,MAXCHAR,inp);
j=0;
}
}
for(i=0;isdigit(aux[j]);i++,j++){
info[i]=aux[j];
}
info[i]='\0';
if(strlen(info)==2){
genotM[cloc][cpop][csamp][0]=atoi(info);
lplo[cloc]=1;
}
else if(strlen(info)==3){
genotM[cloc][cpop][csamp][0]=atoi(info);
lplo[cloc]=1;
}
else if(strlen(info)==4){
for(i=0;i<2;i++){
info1[i]=info[i];
info2[i]=info[i+2];
}
info1[i]='\0';
info2[i]='\0';
genotM[cloc][cpop][csamp][0]=atoi(info1);
genotM[cloc][cpop][csamp][1]=atoi(info2);
lplo[cloc]=2;
}
else if(strlen(info)==6){
for(i=0;i<3;i++){
info1[i]=info[i];
info2[i]=info[i+3];
}
info1[i]='\0';
info2[i]='\0';
genotM[cloc][cpop][csamp][0]=atoi(info1);
genotM[cloc][cpop][csamp][1]=atoi(info2);
lplo[cloc]=2;
}
else
return 4; //incorrect number of digits in locus
}
}
}
genotM2=(int***)malloc(nloc*sizeof(int**));
for(cloc=0; cloc<nloc; cloc++){
genotM2[cloc] = (int**)malloc(npop*sizeof(int*));
for(cpop=0; cpop<npop; cpop++){
genotM2[cloc][cpop] = (int*)malloc((lsamp[cpop]*NPLOIDY)*sizeof(int));
for(i=0, csamp=0; csamp<lsamp[cpop]; csamp++){
for(cplo=0; cplo<lplo[cloc]; cplo++){
genotM2[cloc][cpop][i]=genotM[cloc][cpop][csamp][cplo];
i++;
}
}
}
}
nsamp=0;
for(cpop=0; cpop<npop; cpop++){
nsamp+=lsamp[cpop];
}
//allocate memory to freq, valM, IDsort, valS and ldna
valM = (int **)malloc(nloc*sizeof(int *));
IDsort = (int **)malloc(nloc*sizeof(int *));
ldna = (int *)malloc((nloc+1)*sizeof(int));
for(cloc=0; cloc<nloc; cloc++){
ldna[cloc]=0;
valM[cloc] = malloc(nsamp*sizeof(int));
IDsort[cloc] = malloc(nsamp*sizeof(int));
}
freq = (int ***)malloc(npop*sizeof(int **));
for(cpop=0; cpop<npop; cpop++){
freq[cpop] = (int **)malloc(nloc*sizeof(int *));
for(cloc=0; cloc<nloc ; cloc++){
freq[cpop][cloc] = (int *)malloc(nsamp*sizeof(int));
}
}
//fill freq[cpop][cloc][cdna], valM[cloc][cdna] and IDsort[cloc][cdna]
for(cloc=0;cloc<nloc;++cloc){
for(cpop=0;cpop<npop;cpop++){
for(i=0,csamp=0;csamp<lsamp[cpop];++csamp){
for(cplo=0; cplo<lplo[cloc]; cplo++){
//check if there is information in the current individual
if(genotM2[cloc][cpop][i] == 0){
i++;
continue;
}
//check if the current haplotype is already listed
for(cdna=0;cdna<ldna[cloc];++cdna){
equalDna = 1;
if(genotM2[cloc][cpop][i] != valM[cloc][cdna])
equalDna = 0;
if(equalDna){
++freq[cpop][cloc][cdna]; //increase freq of current haplotype
break;
}
}
//current haplotype is not listed yet
if(cdna>=ldna[cloc]){
for(j=0;j<npop;++j){
freq[j][cloc][ldna[cloc]] = 0; //initiate as 0 the freq of current haplotype in other populations
}
freq[cpop][cloc][ldna[cloc]] = 1; //initiate as 1 the freq of current haplotype in its population
valM[cloc][cdna] = genotM2[cloc][cpop][i]; //adds current haplotype to valM[][]
++ldna[cloc]; //increase by one the number of different haplotypes of a particular locus
}
i++;
}
}
}
}
//writes the output file
for(cpop=0; cpop<npop; cpop++)
fprintf(outp,"#Population %d - pop%d\n",cpop+1,cpop+1);
for(cloc=0;cloc<nloc;++cloc){
fprintf(outp,"#Locus %d - %s\n",cloc+1,locname[cloc]);
}
fprintf(outp,"\n%d\n",npop); //outp: npop
fprintf(outp,"%d\n",nloc); //outp: nloc
for(cloc=0 ; cloc<nloc ; cloc++){
fprintf(outp,"m "); //outp: ltype
}
fprintf(outp,"\n\n");
for(cloc=0; cloc<nloc ; cloc++){
fprintf(outp,"%d\n",ldna[cloc]); //outp: ndna
isorti('a',ldna[cloc],valM[cloc],IDsort[cloc]);
for(cpop=0;cpop<npop;++cpop){
for(cdna=0;cdna<ldna[cloc];++cdna){
fprintf(outp,"%4d ",freq[cpop][cloc][IDsort[cloc][cdna]]); //outp: freq[][]
}
fprintf(outp,"\n");
}
fprintf(outp,"\n");
for(cdna=0;cdna<ldna[cloc];++cdna){
fprintf(outp,"%4d ",valM[cloc][IDsort[cloc][cdna]]); //outp: valM[]
}
fprintf(outp,"\n\n");
}
//free stuff
for(cloc=0 ; cloc<nloc ; cloc++){
for(cpop=0 ; cpop<npop ; cpop++){
for(csamp=0 ; csamp<lsamp[cpop] ; csamp++){
free(genotM[cloc][cpop][csamp]);
}
free(genotM[cloc][cpop]);
}
free(genotM[cloc]);
}
free(genotM);
for(cloc=0; cloc<nloc ; cloc++){
for(cpop=0 ; cpop<npop ; cpop++){
free(genotM2[cloc][cpop]);
}
free(genotM2[cloc]);
}
free(genotM2);
for(cpop=0; cpop<npop ; cpop++){
for(cloc=0; cloc<nloc ; cloc++){
free(freq[cpop][cloc]);
}
free(freq[cpop]);
}
free(freq);
for(cloc=0; cloc<nloc ; cloc++){
free(valM[cloc]);
free(IDsort[cloc]);
}
free(valM);
free(IDsort);
for(cloc=0 ; cloc<nloc ; cloc++){
free(locname[cloc]);
}
free(locname);
free(lplo);
free(ldna);
free(lsamp);
free(outname);
//close files
fclose(inp);
fclose(outp);
return 0;
} //end of main
