Revision e6a0334445b5755bb52a0d2209120ee4e251e7b4 authored by Joao Sollari Lopes on 13 November 2017, 18:32:56 UTC, committed by Joao Sollari Lopes on 13 November 2017, 18:32:56 UTC
0 parent
interface.c
/*
@author: joao lopes
@workplace: Reading University
@date: 12th May 2009
*/
#include "interface.h"
/*
Presents the main menu to user
*/
void mainMenu();
/*
Simulates data sets
@return errors
*/
int simulate();
/*
Run the ABC algorithm
@return errors
*/
int runAbc();
/*
Presents the customize ABC menu to user
*/
void customMenu();
/*
Run the simulation step of ABC algorithm
@return errors
*/
int runabc1();
/*
Run the rejection step of ABC algorithm
@return errors
*/
int runabc2();
/*
Check for suitability of performing the regression step of ABC Algorithm
@return errors
*/
int runabc3();
/*
Presents the tools menu to user
*/
void toolsMenu();
/*
Build a prior file (.prs)
@return errors
*/
int buildprior();
/*
Check if a population still exists
@arg avlpop list of all available populations
@pop population which existence should be checked
@size number of existing populations
@return int (0 - if pop doesn't exist; 1 - if pop exists)
*/
int exists(int *avlpop,int pop, int size);
/*
Take out a pop from the list of available pop
@arg avlpop list of all available populations
@pop population to be taken out
@size number of existing populations
@return updated list of the available pop
*/
int *takeout(int *avlpop,int pop,int size);
/*
Build a summary statistics set file (.sst)
@return errors
*/
int buildsstats();
/*
Create a target (.trg) and a sample size (.ssz) files from a table file (.len)
@return errors
*/
int buildtarget();
/*
Convert a sample file (.pop) into a table file (.len)
@return errors
*/
int createtab();
/*
Convert a IMa sample file into a table file (.len)
@return errors
*/
int createtab2();
/*
Convert a GenePop file into a table file (.len)
@return errors
*/
int createtab3();
/*
Convert a Nexus file (.nex) into a table file (.len)
@return errors
*/
int createtab4();
/*
Convert a table file (.len) into a sample file (.pop)
@return errors
*/
int createpop();
/*
Join files together
@return errors
*/
int joinfiles();
/*
Find segregating sites (.sgs)
@return errors
*/
int segsites();
/*
It creates an ASCII interface to run ABC approachs to Populacional Biology problems
*/
int main(int argc, char *argv[]){
int i, //iterator
cut; //auxiliar to work around strings
/*get the path from where the progam is being run*/
Exepathsize = strlen(argv[0])+ 5;
Exepath = (char *)malloc(Exepathsize*sizeof(char));
strcpy(Exepath,argv[0]);
for(cut=-1,i=Exepathsize-1 ; Exepath[i]!='/' && Exepath[i]!='\\' && i >= 0 ; cut++,i--){
Exepath[i]='\0';
}
Exepath = realloc(Exepath,(Exepathsize-cut)*sizeof(char));
printf("\n\n ----------------------------------\n");
printf(" popABC - Mark Beaumont & Joao Lopes\n\n");
printf(" version: 1.0 12/05/09\n");
printf("\n ----------------------------------\n");
mainMenu();
//free stuff
free(Exepath);
} //end of main
void mainMenu(){
char str[MAXCHAR];
int option,
r;
do {
printf("\n\n *Main Menu*\n\n");
printf(" 1. Create a simulated \"real\" data\n\n");
printf(" 2. Run the ABC algorithm on \"real\" data\n\n");
printf(" 3. Customize the ABC algorithm\n\n");
printf(" 4. Tools\n\n");
printf(" 5. Exit\n\n");
printf(" choose an option: ");
scanf("%s",&str);
option = atoi(str);
switch (option){
case 1:
printf("\n\n\n *Simulate Data with ABC*\n\n");
r = simulate();
if(r==0)
printf("\n\n>simulation completed (report created).");
else if(r==1)
printf("\n\n>error::cannot open the .prs file!");
else if(r==2)
printf("\n\n>error::cannot open the .ssz file!");
else if(r==3)
printf("\n\n>error::cannot open the .sst file!");
else if(r==4)
printf("\n\n>error::cannot create .dat file!");
else if(r==5)
printf("\n\n>error::cannot create info file!");
else if(r==6)
printf("\n\n>error::while reading .ssz file!");
else if(r==7)
printf("\n\n>error::while reading .sst file!");
else if(r==8)
printf("\n\n>error::following sstats can only be chosen with 2 or more pops: Nm_H; Nm_S; privS; S(1)!");
else if(r==9)
printf("\n\n>error::wrong topology prior type!");
else if(r==10)
printf("\n\n>error::with 1 or 2 pops only topology prior type 0 or 3 can be used!");
else if(r==11)
printf("\n\n>error::wrong Ne prior type!");
else if(r==12)
printf("\n\n>error::type-2 tev is followed by another type-2 tev!");
else if(r==13)
printf("\n\n>error::if using tev type 3 prior, define prior only once!");
else if(r==14)
printf("\n\n>error::if using tev type 4 prior, define prior only once!");
else if(r==15)
printf("\n\n>error::wrong Tev prior type!");
else if(r==16)
printf("\n\n>error::wrong Mig prior type!");
else if(r==17)
printf("\n\n>error::wrong Mut prior type (Microsatellites)!");
else if(r==18)
printf("\n\n>error::wrong Mut prior type (Sequence Data)!");
else if(r==19)
printf("\n\n>error::wrong Rec prior type (Microsatellites)!");
else if(r==20)
printf("\n\n>error::wrong Rec prior type (Sequence Data)!");
else if(r==21)
printf("\n\n>error::to use migration weights matrix, topology must be defined (option 1,2,4 or 5)!");
else if(r==22)
printf("\n\n>error::wrong migration weights matrix option!");
else if(r==23)
printf("\n\n>error::.dat file would be too big to be analyzed!");
else if(r==24)
printf("\n\n>error::when using rec with STR all STR loci must have the same scalar!");
else if(r==25)
printf("\n\n>error::when using rec with STR all STR loci must have the same samples per population!");
else if(r==26)
printf("\n\n>error::cannot create .mut file!");
else if(r==27)
printf("\n\n>error::cannot create .rec file!");
else if(r==28)
printf("\n\n>error::times are not monotonic increasing!");
else if(r==29)
printf("\n\n>error::choosing branching sequence!");
else if(r==30)
printf("\n\n>error::with more than 5 populations the topology as to be fixed using option 2 or 5!");
else if(r==31)
printf("\n\n>error::the locus have less than samples, it should be cleared!");
else if(r==32)
printf("\n\n>error::migration weights for the considered population have to be 0!");
else if(r==33)
printf("\n\n>error::the sum of the prob for a given migration as to be 1.0!");
else if(r==34)
printf("\n\n>error::cannot create .len file!");
break;
case 2:
printf("\n\n\n *Run ABC algorithm*\n\n");
r = runAbc();
if(r==0)
printf("\n\n>ABC run completed\n");
else if(r==1)
printf("\n\n>error::cannot open .len file!");
else if(r==2)
printf("\n\n>error::cannot open .sst file!");
else if(r==3)
printf("\n\n>error::cannot create .trg file!");
else if(r==4)
printf("\n\n>error::cannot create .ssz file!");
else if(r==5)
printf("\n\n>error::cannot create info file!");
else if(r==6)
printf("\n\n>error::reading .sst file!");
else if(r==7)
printf("\n\n>error::following sstats can only be chosen with 2 or more pops: Nm_H; Nm_S; privS; S(1)!");
else if(r==8)
printf("\n\n>error::sequence data locus without information, discard it!");
else if(r==101)
printf("\n\n>error::cannot open the .prs file!");
else if(r==102)
printf("\n\n>error::cannot open the .ssz file!");
else if(r==103)
printf("\n\n>error::cannot open the .sst file!");
else if(r==104)
printf("\n\n>error::cannot create .dat file!");
else if(r==105)
printf("\n\n>error::cannot create info file!");
else if(r==106)
printf("\n\n>error::while reading .ssz file!");
else if(r==107)
printf("\n\n>error::while reading .sst file!");
else if(r==108)
printf("\n\n>error::following sstats can only be chosen with 2 or more pops: Nm_H; Nm_S; privS; S(1)!");
else if(r==109)
printf("\n\n>error::wrong topology prior type!");
else if(r==110)
printf("\n\n>error::with 1 or 2 pops only topology prior type 0 or 3 can be used!");
else if(r==111)
printf("\n\n>error::wrong Ne prior type!");
else if(r==112)
printf("\n\n>error::type-2 tev is followed by another type-2 tev!");
else if(r==113)
printf("\n\n>error::if using tev type 3 prior, define prior only once!");
else if(r==114)
printf("\n\n>error::if using tev type 4 prior, define prior only once!");
else if(r==115)
printf("\n\n>error::wrong Tev prior type!");
else if(r==116)
printf("\n\n>error::wrong Mig prior type!");
else if(r==117)
printf("\n\n>error::wrong Mut prior type (Microsatellites)!");
else if(r==118)
printf("\n\n>error::wrong Mut prior type (Sequence Data)!");
else if(r==119)
printf("\n\n>error::wrong Rec prior type (Microsatellites)!");
else if(r==120)
printf("\n\n>error::wrong Rec prior type (Sequence Data)!");
else if(r==121)
printf("\n\n>error::to use migration weights matrix, topology must be defined (option 1,2,4 or 5)!");
else if(r==122)
printf("\n\n>error::wrong migration weights matrix option!");
else if(r==123)
printf("\n\n>error::.dat file would be too big to be analyzed!");
else if(r==124)
printf("\n\n>error::when using rec with STR all STR loci must have the same scalar!");
else if(r==125)
printf("\n\n>error::when using rec with STR all STR loci must have the same samples per population!");
else if(r==126)
printf("\n\n>error::cannot create .mut file!");
else if(r==127)
printf("\n\n>error::cannot create .rec file!");
else if(r==128)
printf("\n\n>error::times are not monotonic increasing!");
else if(r==129)
printf("\n\n>error::choosing branching sequence!");
else if(r==130)
printf("\n\n>error::with more than 5 populations the topology as to be fixed using option 2 or 5!");
else if(r==131)
printf("\n\n>error::the locus have less than samples, it should be cleared!");
else if(r==132)
printf("\n\n>error::migration weights for the considered population have to be 0!");
else if(r==133)
printf("\n\n>error::the sum of the prob for a given migration as to be 1.0!");
else if(r==134)
printf("\n\n>error::cannot create .len file!");
else if(r==201)
printf("\n\n>error::could't open .dat file!");
else if(r==202)
printf("\n\n>error::cannot open .trg file!");
else if(r==203)
printf("\n\n>error::cannot create .rej file!");
else if(r==204)
printf("\n\n>error::cannot create .pri file!");
else if(r==205)
printf("\n\n>error::cannot create .txt file!");
else if(r==206)
printf("\n\n>error::file .dat ended prematurely!");
else if(r==207)
printf("\n\n>error::.dat file is too big to be analysed!");
break;
case 3:
customMenu();
break;
case 4:
toolsMenu();
break;
case 5:
printf("\n\n...exiting popABC\n\n");
break;
default:
printf("\n\n>error::option not available\n");
break;
}
}
while (option != 5);
} // end of mainMenu
int simulate(){
char str[MAXCHAR], //auxiliar to get the input from the user
input_prs[MAXCHAR], //input file name
input_ssz[MAXCHAR], //input file name
input_sst[MAXCHAR], //input file name
output[MAXCHAR]; //input file name
//input filename
printf("\n choose prior file (.prs) (max %d character)",MAXCHAR-1);
printf("\n SHOULD HAVE ONLY ONE ITERATION: ");
scanf("%s",input_prs);
//input filename
printf("\n choose sample size file (.ssz) (max %d character): ",MAXCHAR-1);
scanf("%s",input_ssz);
//input filename
printf("\n choose summary statistics set file (.sst) (max %d character): ",MAXCHAR-1);
scanf("%s",input_sst);
//output filename
printf("\n insert name for output file (no extension) (max %d character): ",MAXCHAR-1);
scanf("%s",output);
return abc(input_prs,input_ssz,input_sst,output,1,1,1);
} //ends of simulate
int runAbc(){
int lsstats[MAXSSTATS], //list of the summary statistics used
printMut, //choose if the mutation rates should be print
printRec, //choose if the recombination rates should be print
nparam, //number of parameters
nstats, //number of summary statistics
error; //gets any error
double tol; //tolerance for the rejection method
char str[MAXCHAR], //auxiliar to get the input from the user
input_len[MAXCHAR], //.len file name
input_trg[MAXCHAR], //.trg file name
input_prs[MAXCHAR], //.prs file name
input_ssz[MAXCHAR], //.ssz file name
input_sst[MAXCHAR], //input file name
input_dat[MAXCHAR], //.dat file name
input_rej[MAXCHAR]; //.rej file name
//input filename
printf("\n choose table file (.len) (max %d character): ",MAXCHAR-1);
scanf("%s",input_len);
//input filename
printf("\n choose summary statistics set file (.sst) (max %d character): ",MAXCHAR-1);
scanf("%s",input_sst);
//input filename
printf("\n insert name for target file (no extension) (max %d character): ",MAXCHAR-1);
scanf("%s",input_trg);
error = maketarget(input_len,input_sst,input_trg);
if(error)
return error;
else
printf("\n\n>'real' data summarization completed (report created).\n\n");
//.prs filename
printf("\n choose prior file (.prs) (max %d character): ",MAXCHAR-1);
scanf("%s",input_prs);
//.dat filename
printf("\n insert name for data file (no extension) (max %d character): ",MAXCHAR-1);
scanf("%s",input_dat);
//choose if file with mutation rate will be created
printf("\n");
do{
printf(" choose if file with mutation rate will be created (0 - file not created;");
printf("\n 1 - file created): ");
scanf("%s",&str);
printMut = atoi(str);
}
while(printMut !=0 && printMut !=1);
//choose if file with recombination rate will be created
printf("\n");
do{
printf(" choose if file with recombination rate will be created (0 - file not created;");
printf("\n 1 - file created): ");
scanf("%s",&str);
printRec = atoi(str);
}
while(printRec !=0 && printRec !=1);
strcpy(input_ssz,input_trg);
strcat(input_ssz,".ssz");
error = abc(input_prs,input_ssz,input_sst,input_dat,0,printMut,printRec);
if(error)
return error+100;
else printf("\n\n>simulations completed (report created).\n\n");
//.rej filename
printf("\n insert name for rejection file (no extension) (max %d character): ",MAXCHAR-1);
scanf("%s",input_rej);
//choose number of parameters
printf("\n");
do{
printf(" specify the number of parameters used (>0): ");
scanf("%s",&str);
nparam = atof(str);
}
while(nparam <=0);
//choose number of summary statistics
printf("\n");
do{
printf(" specify the number of summary statistics used (>0): ");
scanf("%s",&str);
nstats = atof(str);
}
while(nstats <=0);
//choose tolerance
printf("\n");
do{
printf(" choose tolerance for rejection step (0 < tol < 1): ");
scanf("%s",&str);
tol = atof(str);
}
while(tol <=0 || tol >=1);
strcat(input_dat,".dat");
strcat(input_trg,".trg");
error = firstpass(input_dat,input_trg,input_rej,nparam,nstats,tol);
if(error)
return error+200;
else
printf("\n\n>rejection step completed (report created).\n\n");
return 0;
} //end of runABC
void customMenu(){
char str[MAXCHAR];
int option,
r;
do {
printf("\n\n\n *Customize ABC Menu*\n\n");
printf(" 1. Summarize 'real' data with summstats set\n\n");
printf(" 2. Run simulations\n\n");
printf(" 3. Perform rejection step\n\n");
printf(" 4. Exit to Main Menu\n\n");
printf(" choose an option: ");
scanf("%s",&str);
option = atoi(str);
switch (option){
case 1:
printf("\n\n\n *Run ABC - 'real' data summarization step*\n\n");
r = buildtarget();
if(r==0)
printf("\n\n>'real' data summarization completed (report created).");
else if(r==1)
printf("\n\n>error::cannot open the .len file!");
else if(r==2)
printf("\n\n>error::cannot open the .sst file!");
else if(r==3)
printf("\n\n>error::cannot create .trg file!");
else if(r==4)
printf("\n\n>error::cannot create .ssz file!");
else if(r==5)
printf("\n\n>error::cannot create info file!");
else if(r==6)
printf("\n\n>error::reading .sst file!");
else if(r==7)
printf("\n\n>error::following sstats can only be chosen with 2 or more pops: Nm_H; Nm_S; privS; S(1)!");
else if(r==8)
printf("\n\n>error::sequence data locus without information, discard it!");
break;
case 2:
printf("\n\n\n *Run ABC - simulation step*\n\n");
r = runabc1();
if(r==0)
printf("\n\n>simulation step completed (report created).");
else if(r==1)
printf("\n\n>error::cannot open the .prs file!");
else if(r==2)
printf("\n\n>error::cannot open the .ssz file!");
else if(r==3)
printf("\n\n>error::cannot open the .sst file!");
else if(r==4)
printf("\n\n>error::cannot create .dat file!");
else if(r==5)
printf("\n\n>error::cannot create info file!");
else if(r==6)
printf("\n\n>error::while reading .ssz file!");
else if(r==7)
printf("\n\n>error::while reading .sst file!");
else if(r==8)
printf("\n\n>error::following sstats can only be chosen with 2 or more pops: Nm_H; Nm_S; privS; S(1)!");
else if(r==9)
printf("\n\n>error::wrong topology prior type!");
else if(r==10)
printf("\n\n>error::with 1 or 2 pops only topology prior type 0 or 3 can be used!");
else if(r==11)
printf("\n\n>error::wrong Ne prior type!");
else if(r==12)
printf("\n\n>error::type-2 tev is followed by another type-2 tev!");
else if(r==13)
printf("\n\n>error::if using tev type 3 prior, define prior only once!");
else if(r==14)
printf("\n\n>error::if using tev type 4 prior, define prior only once!");
else if(r==15)
printf("\n\n>error::wrong Tev prior type!");
else if(r==16)
printf("\n\n>error::wrong Mig prior type!");
else if(r==17)
printf("\n\n>error::wrong Mut prior type (Microsatellites)!");
else if(r==18)
printf("\n\n>error::wrong Mut prior type (Sequence Data)!");
else if(r==19)
printf("\n\n>error::wrong Rec prior type (Microsatellites)!");
else if(r==20)
printf("\n\n>error::wrong Rec prior type (Sequence Data)!");
else if(r==21)
printf("\n\n>error::to use migration weights matrix, topology must be defined (option 1,2,4 or 5)!");
else if(r==22)
printf("\n\n>error::wrong migration weights matrix option!");
else if(r==23)
printf("\n\n>error::.dat file would be too big to be analyzed!");
else if(r==24)
printf("\n\n>error::when using rec with STR all STR loci must have the same scalar!");
else if(r==25)
printf("\n\n>error::when using rec with STR all STR loci must have the same samples per population!");
else if(r==26)
printf("\n\n>error::cannot create .mut file!");
else if(r==27)
printf("\n\n>error::cannot create .rec file!");
else if(r==28)
printf("\n\n>error::times are not monotonic increasing!");
else if(r==29)
printf("\n\n>error::choosing branching sequence!");
else if(r==30)
printf("\n\n>error::with more than 5 populations the topology as to be fixed using option 2 or 5!");
else if(r==31)
printf("\n\n>error::the locus have less than samples, it should be cleared!");
else if(r==32)
printf("\n\n>error::migration weights for the considered population have to be 0!");
else if(r==33)
printf("\n\n>error::the sum of the prob for a given migration as to be 1.0!");
else if(r==34)
printf("\n\n>error::cannot create .len file!");
break;
case 3:
printf("\n\n\n *Run ABC - rejection step*\n\n");
r = runabc2();
if(r==0)
printf("\n\n>rejection step completed (report created).");
else if(r==1)
printf("\n\n>error::cannot open .dat file!");
else if(r==2)
printf("\n\n>error::cannot open .trg file!");
else if(r==3)
printf("\n\n>error::cannot create .rej file!");
else if(r==4)
printf("\n\n>error::cannot create .pri file!");
else if(r==5)
printf("\n\n>error::cannot create .txt file!");
else if(r==6)
printf("\n\n>error::file .dat ended prematurely!");
else if(r==7)
printf("\n\n>error::.dat file is too big to be analysed!");
break;
case 4:
break;
default:
printf("\n\n>error::option not available\n");
break;
}
}
while (option != 4);
} //end of customMenu
int buildtarget(){
int cstat,i, //iterators
lsstats[MAXSSTATS], //list of the summary statistics used
nmarks, //param number of markers used (0-no marks; 2-two marks; 3-three marks; 4- four marks)
cmark, //auxiliar to choose the sample populations
mark1, //marker of first sample population (only if npop >= 3 AND nsample == 2)
mark2, //marker of second sample population (only if npop >= 3 AND nsample == 2 OR 3 OR 4)
mark3; //marker of third sample population (only if npop >= 3 AND nsample == 3 OR 4)
char str[MAXCHAR], //auxiliar to get the input from the user
input_len[MAXCHAR],//input file name
input_sst[MAXCHAR],//input file name
output[MAXCHAR], //input file name
type; //analysis type (M - microsatellites; S - sequence data; B - both)
//input filename
printf("\n choose a table file (.len) (max %d characters): ",MAXCHAR-1);
scanf("%s",input_len);
//input filename
printf("\n choose a summary statistics set file (.sst) (max %d characters): ",MAXCHAR-1);
scanf("%s",input_sst);
//output filename
printf("\n choose a name for the target file (no extension) (max %d",MAXCHAR-1);
printf("\n characters): ");
scanf("%s",output);
return maketarget(input_len,input_sst,output);
} //end of buildtarget
int runabc1(){
int printIt, //choose if the table files of the simulations should be printed
printMut, //choose if the mutation rates should be printed
printRec; //choose if the recombination rates should be printed
char str[MAXCHAR], //auxiliar to get the input from the user
input_prs[MAXCHAR], //input file name
input_ssz[MAXCHAR], //input file name
input_sst[MAXCHAR], //input file name
output[MAXCHAR]; //input file name
//input filename
printf("\n choose prior file (.prs) (max %d character): ",MAXCHAR-1);
scanf("%s",input_prs);
//input filename
printf("\n choose sample size file (.ssz) (max %d character): ",MAXCHAR-1);
scanf("%s",input_ssz);
//input filename
printf("\n choose summary statistics set file (.sst) (max %d character): ",MAXCHAR-1);
scanf("%s",input_sst);
//output filename
printf("\n insert name for output file (no extension) (max %d character): ",MAXCHAR-1);
scanf("%s",output);
//choose if table files of the simulations should be printed
printf("\n");
do{
printf(" choose if table files (.len) for each simulation will be created (0 - file");
printf("\n not created;1 - file created)");
printf("\n THIS OPTION MEANS ONE .LEN FILE PER SIMULATION: ");
scanf("%s",&str);
printIt = atoi(str);
}
while(printIt !=0 && printIt !=1);
//choose if file with mutation rate will be created
printf("\n");
do{
printf(" choose if file with mutation rate will be created (0 - file not created;");
printf("\n 1 - file created): ");
scanf("%s",&str);
printMut = atoi(str);
}
while(printMut !=0 && printMut !=1);
//choose if file with recombination rate will be created
printf("\n");
do{
printf(" choose if file with recombination rate will be created (0 - file not created;");
printf("\n 1 - file created): ");
scanf("%s",&str);
printRec = atoi(str);
}
while(printRec !=0 && printRec !=1);
return abc(input_prs,input_ssz,input_sst,output,printIt,printMut,printRec);
} //end of runabc1
int runabc2(){
int nparam, //number of parameters
nstats; //number of summary statistics
double tol; //tolerance for the rejection method
char str[MAXCHAR], //auxiliar to get the input from the user
input_dat[MAXCHAR], //.dat file name
input_trg[MAXCHAR], //.trg file name
input_rej[MAXCHAR]; //.rej file name
//.dat filename
printf("\n choose data file (.dat) (max %d character): ",MAXCHAR-1);
scanf("%s",input_dat);
//.trg filename
printf("\n choose target file (.trg) (max %d character): ",MAXCHAR-1);
scanf("%s",input_trg);
//.rej filename
printf("\n insert name for rejection file (no extension) (max %d character): ",MAXCHAR-1);
scanf("%s",input_rej);
//choose number of parameters
printf("\n");
do{
printf(" specify the number of parameters used (>0): ");
scanf("%s",&str);
nparam = atof(str);
}
while(nparam <=0);
//choose number of summary statistics
printf("\n");
do{
printf(" specify the number of summary statistics used (>0): ");
scanf("%s",&str);
nstats = atof(str);
}
while(nstats <=0);
//choose tolerance
printf("\n");
do{
printf(" choose tolerance for rejection step (0 < tol < 1): ");
scanf("%s",&str);
tol = atof(str);
}
while(tol <=0 || tol >=1);
return firstpass(input_dat,input_trg,input_rej,nparam,nstats,tol);
} //end of runabc2
void toolsMenu(){
char str[MAXCHAR];
int option,
r;
do {
printf("\n\n\n *Tools Menu*\n\n");
printf(" 1. Build prior file (.prs)\n\n");
printf(" 2. Build summary statistics set file (.sst)\n\n");
printf(" 3. Convert sample file (.pop) to table file (.len)\n\n");
printf(" 4. Convert IMa input file to table file (.len)\n\n");
printf(" 5. Convert GenePop input file to table file (.len)\n\n");
printf(" 6. Convert Nexus file (.nex) to table file (.len)\n\n");
printf(" 7. Create sample file (.pop) from table file (.len)\n\n");
printf(" 8. Join data files together (.dat)\n\n");
printf(" 9. Exit to Main Menu\n\n");
printf(" choose an option: ");
scanf("%s",&str);
option = atoi(str);
switch (option)
{
case 1:
printf("\n\n\n *Build prior file (.prs)*\n\n");
r = buildprior();
if(r==0)
printf("\n\n>prior file (.prs) created.");
else if(r==1)
printf("\n\n>error::cannot create .prs file!");
break;
case 2:
printf("\n\n\n *Build summary statistics set file (.prs)*\n\n");
r = buildsstats();
if(r==0)
printf("\n\n>summary statistics set file (.sst) created.");
else if(r==1)
printf("\n\n>error::cannot create .sst file!");
break;
case 3:
printf("\n\n\n *Convert sample file (.pop) to table file (.len)*\n\n");
r = createtab();
if(r==0)
printf("\n\n>table file (.len) build.");
else if(r==1)
printf("\n\n>error::cannot open .pop file!");
else if(r==2)
printf("\n\n>error::cannot create .len file!");
else if(r==3)
printf("\n\n>error::individual has no information!");
else if(r==4)
printf("\n\n>error::different number of ploidy or number of sites in alleles of a loci!");
break;
case 4:
printf("\n\n\n *Convert IMa file to table file (.len)*\n\n");
r = createtab2();
if(r==0)
printf("\n\n>table file (.len) build.");
else if(r==1)
printf("\n\n>error::cannot open sample file!");
else if(r==2)
printf("\n\n>error::cannot create .len file!");
else if(r==3)
printf("\n\n>error::cannot deal with specified data type!");
break;
case 5:
printf("\n\n\n *Convert GenePop file to table file (.len)*\n\n");
r = createtab3();
if(r==0)
printf("\n\n>table file (.len) build.");
else if(r==1)
printf("\n\n>error::cannot open sample file!");
else if(r==2)
printf("\n\n>error::cannot create .len file!");
else if(r==3)
printf("\n\n>error::file ended before the display of data!");
else if(r==4)
printf("\n\n>error::incorrect number of digits in locus!");
break;
case 6:
printf("\n\n\n *Convert Nexus file (.nex) to table file (.len)*\n\n");
r = createtab4();
if(r==0)
printf("\n\n>table file (.len) build.");
else if(r==1)
printf("\n\n>error::cannot open .nex file!");
else if(r==2)
printf("\n\n>error::cannot create .len file!");
else if(r==3)
printf("\n\n>error::cannot deal with specified data type!");
else if(r==4)
printf("\n\n>error::problems reading MATRIX!");
else if(r==5)
printf("\n\n>error::problems reading TAXSET!");
else if(r==6)
printf("\n\n>error::problem defining TAXSET: n1>=n2!");
else if(r==7)
printf("\n\n>error::unrecognized specifier after BEGIN SETS (use TAXSET)!");
else if(r==8)
printf("\n\n>error::unrecognized specifier after BEGIN (use DATA or SETS)!");
else if(r==9)
printf("\n\n>error::unrecognized command (only BEGIN accepted)!");
break;
case 7:
printf("\n\n\n *Create sample file (.pop) from table file (.len)*\n\n");
r = createpop();
if(r==0)
printf("\n\n>sample file (.pop) converted.");
else if(r==1)
printf("\n\n>error::cannot open .pop files!");
else if(r==2)
printf("\n\n>error::cannot create .len file!");
break;
case 8:
printf("\n\n\n *Join data files (.dat) together*\n\n");
r = joinfiles();
if(r==0)
printf("\n\n>files joined.");
else if(r==1)
printf("\n\n>error::cannot create output file!");
else if(r==2)
printf("\n\n>error::cannot open an input files!");
break;
case 9:
break;
default:
printf("\n\n>error::option not available\n");
break;
}
}
while (option != 9);
} //end of toolsMenu
int buildprior(){
int cloc,cpop,ctev,i,j,cpop2, //iterator
allTev, //check if only on prior for all tevs is used
error, //saves the error type
d1, //auxiliar to get info from the user
from,to, //auxiliars to construct the fixed topology when the option 2 is chosen
niter, //number of iterations
genet, //generation time
npop, //number of populations
ntev, //number of time events
psize, //number of populations (used in topology prior type 2)
nloc, //number of loci
*avlpop; //populations available to chose from when fixing the topology with option 2
double *lplo; //list of the ploidy per loci
char str[MAXCHAR], //auxiliar to get the input from the user
output[MAXCHAR], //output filename
*ltype; //list of the DNA types analysed per loci
struct prior pr_top, //topology prior parameters
pr_mutSTR, //STR mutation prior parameters
pr_mutSNP, //SNP mutation prior parameters
pr_recSTR, //STR recombination prior parameters
pr_recSNP, //SNP recombination prior parameters
*pr_mig, //list of the mig prior parameters
*pr_Ne, //list of the Ne prior parameters
*pr_tev; //list of the tev prior paramters
struct migweights migw; //matrix with the migration weigths
/*number of iterations*/
do{
printf(" choose the number of iterations (>0): ");
scanf("%s",&str);
niter = atoi(str);
}
while(niter <=0);
/*generation time*/
printf("\n");
do{
printf(" choose the generation time (>0): ");
scanf("%s",&str);
genet = atoi(str);
}
while(genet <=0);
/*number of pop*/
printf("\n");
do{
printf(" choose the number of populations (>0): ");
scanf("%s",&str);
npop = atoi(str);
}
while(npop <=0);
/*number of loci*/
printf("\n");
do{
printf(" choose the number of loci (>0): ");
scanf("%s",&str);
nloc = atoi(str);
}
while(nloc <=0);
/*inherety scalar*/
lplo = (double*)malloc(nloc*sizeof(double));
if(nloc==1){
printf("\n");
do{
printf(" choose the hereditary scalar of the locus [autossome = 1.00; X-linked = 0.75;\n");
printf(" haploid = 0.5; mitochodrial DNA or Y-linked = 0.25]: ");
scanf("%s",&str);
lplo[0] = atof(str);
}
while(lplo[0]!=1.0 && lplo[0]!=0.75 && lplo[0]!=0.5 && lplo[0]!=0.25);
}
else{
printf("\n choose %d scalars, one for each loci [autossome = 1.00; X-linked = 0.75;\n",nloc);
printf(" haploid = 0.5; mitochodrial DNA or Y-linked = 0.25]:\n");
for(cloc=0; cloc<nloc; cloc++){
do{
printf(" locus %d: ",cloc+1);
scanf("%s",&str);
lplo[cloc] = atof(str);
}
while(lplo[0]!=1.0 && lplo[0]!=0.75 && lplo[0]!=0.5 && lplo[0]!=0.25);
}
}
/*DNA types*/
ltype = (char*)malloc(nloc*sizeof(char));
if(nloc==1){
printf("\n");
do{
printf(" choose the DNA type of the locus [s - DNA sequence or m - microsatellites]: ");
scanf("%s",&str);
ltype[0] = str[0];
}
while(ltype[0]!='m' && ltype[0]!='s' && ltype[0]!='M' && ltype[0]!='S');
}
else{
printf("\n choose the DNA type of each locus [s - DNA sequence or m - microsatellites]:\n");
for(cloc=0; cloc<nloc; cloc++){
do{
printf(" locus %d: ",cloc+1);
scanf("%s",&str);
ltype[cloc] = str[0];
}
while(ltype[cloc]!='m' && ltype[cloc]!='s' && ltype[cloc]!='M' && ltype[cloc]!='S');
}
}
/*topology priors*/
if(npop<=2){
printf("\n");
do{
printf(" choose to add a marker to the simulations [0 - no marker; 3 - marker]: ");
scanf("%s",&str);
pr_top.type = atoi(str);
}
while(pr_top.type!=0 && pr_top.type!=3);
}
else if(npop<=5){
printf("\n");
do{
printf(" choose the topology prior and to add or not a marker to the simulations \n");
printf(" [No marker: 0 - random; 1 - predefined topology; 2 - write topology] \n");
printf(" [With marker: 3 - random; 4 - predefined topology; 5 - write topology]: ");
scanf("%s",&str);
pr_top.type = atoi(str);
}
while(pr_top.type!=0 && pr_top.type!=1 && pr_top.type!=2 && pr_top.type!=3 && pr_top.type!=4 && pr_top.type!=5);
}
else{
printf("\n");
do{
printf(" choose to add a marker to the simulations [2 - no marker; 5 - marker]: ");
scanf("%s",&str);
pr_top.type = atoi(str);
}
while(pr_top.type!=2 && pr_top.type!=5);
}
if(pr_top.type==1){
pr_top.p = (double *)malloc(sizeof(double));
if(npop == 3){
printf("\n");
do{
printf(" choose the predifined topology [1 to 3 (See user-guide)]: ");
scanf("%s",&str);
pr_top.p[0] = atof(str);
}
while(pr_top.p[0]<1 || pr_top.p[0]>3);
}
else if(npop == 4){
printf("\n");
do{
printf(" choose the predifined topology [1 to 18 (See user-guide)]: ");
scanf("%s",&str);
pr_top.p[0] = atoi(str);
}
while(pr_top.p[0]<1 || pr_top.p[0]>18);
}
else if(npop == 5){
printf("\n");
do{
printf(" choose the predifined topology [1 to 180 (See user-guide)]: ");
scanf("%s",&str);
pr_top.p[0] = atoi(str);
}
while(pr_top.p[0]<1 || pr_top.p[0]>180);
}
}
else if(pr_top.type==2){
pr_top.p = (double *)malloc(2*(npop+1)*sizeof(double));
avlpop = (int*)malloc(npop*sizeof(int));
for(i=0; i<npop; i++)
avlpop[i] = i;
psize = npop;
printf("\n choose the topology to be used (%d numbers)",2*(npop-1));
for(i=0; i<2*(npop-1) ;i=i+2){
printf("\n available populations:(");
for(j=0; j<psize-1; j++)
printf("%d ",avlpop[j]);
printf("%d)\n",avlpop[j]);
do{
printf(" from - ");
scanf("%s",&str);
from = atoi(str);
printf(" to - ");
scanf("%s",&str);
to = atoi(str);
}
while(!exists(avlpop,from,npop) || !exists(avlpop,to,npop) || from == to);
pr_top.p[i] = from;
pr_top.p[i+1] = to;
avlpop = takeout(avlpop,from,psize);
psize --;
}
}
else if(pr_top.type==3){
pr_top.p = (double *)malloc(sizeof(double));
if(npop <= 4){
printf("\n");
do{
printf(" choose the marker to be used (>=0): ");
scanf("%s",&str);
pr_top.p[0] = atof(str);
}
while(pr_top.p[0]<0);
}
}
else if(pr_top.type==4){
pr_top.p = (double *)malloc(2*sizeof(double));
if(npop == 3){
printf("\n");
do{
printf(" choose the predifined topology [1 to 3 (See user-guide)]: ");
scanf("%s",&str);
pr_top.p[0] = atof(str);
}
while(pr_top.p[0]<1 || pr_top.p[0]>3);
printf("\n");
do{
printf(" choose the marker to be used (>=0): ");
scanf("%s",&str);
pr_top.p[1] = atof(str);
}
while(pr_top.p[1]<0);
}
else if(npop==4){
printf("\n");
do{
printf(" choose the predifined topology [1 to 18 (See user-guide)]: ");
scanf("%s",&str);
pr_top.p[0] = atoi(str);
}
while(pr_top.p[0]<1 || pr_top.p[0]>18);
printf("\n");
do{
printf(" choose the marker to be used (>=0): ");
scanf("%s",&str);
pr_top.p[1] = atof(str);
}
while(pr_top.p[1]<0);
}
else if(npop==5){
printf("\n");
do{
printf(" choose the predifined topology [1 to 180 (See user-guide)]: ");
scanf("%s",&str);
pr_top.p[0] = atoi(str);
}
while(pr_top.p[0]<1 || pr_top.p[0]>180);
printf("\n");
do{
printf(" choose the marker to be used (>=0): ");
scanf("%s",&str);
pr_top.p[1] = atof(str);
}
while(pr_top.p[1]<0);
}
}
else if(pr_top.type==5){
pr_top.p = (double *)malloc((1+2*(npop+1))*sizeof(double));
avlpop = (int*)malloc(npop*sizeof(int));
for(i=0; i<npop; i++)
avlpop[i] = i;
psize = npop;
printf("\n choose the topology to be used (%d numbers)",2*(npop-1));
for(i=0; i<2*(npop-1) ;i=i+2){
printf("\n available populations:(");
for(j=0; j<psize-1; j++)
printf("%d ",avlpop[j]);
printf("%d)\n",avlpop[j]);
do{
printf(" from - ");
scanf("%s",&str);
from = atoi(str);
printf(" to - ");
scanf("%s",&str);
to = atoi(str);
}
while(!exists(avlpop,from,npop) || !exists(avlpop,to,npop) || from == to);
pr_top.p[i] = from;
pr_top.p[i+1] = to;
avlpop = takeout(avlpop,from,psize);
psize --;
}
printf("\n");
do{
printf(" choose the marker to be used (>=0): ");
scanf("%s",&str);
pr_top.p[i] = atof(str);
}
while(pr_top.p[i]<0);
}
/*Ne priors*/
pr_Ne = (struct prior *)malloc((npop*2-1)*sizeof(struct prior));
for(cpop=0; cpop<npop*2-1; cpop++){
if(cpop<npop){
printf("\n");
do{
printf(" choose the Ne%d prior [1 - uniform distribution; 2 - generalized gamma\n",cpop+1);
printf(" distribution]: ");
scanf("%s",&str);
pr_Ne[cpop].type = atoi(str);
}
while(pr_Ne[cpop].type!=1 && pr_Ne[cpop].type!=2 && pr_Ne[cpop].type!=3);
}
else{
printf("\n");
do{
printf(" choose the NeAnc%d prior [1 - uniform distribution; 2 - generalized gamma\n",cpop+1-npop);
printf(" distribution]: ");
scanf("%s",&str);
pr_Ne[cpop].type = atoi(str);
}
while(pr_Ne[cpop].type!=1 && pr_Ne[cpop].type!=2 && pr_Ne[cpop].type!=3);
}
if(pr_Ne[cpop].type==1){
pr_Ne[cpop].p = (double *)malloc(2*sizeof(double));
do{
printf(" choose lower boundary of the prior(>=0): ");
scanf("%s",&str);
pr_Ne[cpop].p[0] = atof(str);
printf(" choose upper boundary of the prior(>0): ");
scanf("%s",&str);
pr_Ne[cpop].p[1] = atof(str);
}
while(pr_Ne[cpop].p[0]>pr_Ne[cpop].p[1] || pr_Ne[cpop].p[0]<0 || pr_Ne[cpop].p[1]<=0);
}
else{
pr_Ne[cpop].p = (double *)malloc(4*sizeof(double));
do{
printf(" choose location parameter (=>0): ");
scanf("%s",&str);
pr_Ne[cpop].p[0] = atof(str);
}
while(pr_Ne[cpop].p[0]<0);
do{
printf(" choose scale parameter (>0): ");
scanf("%s",&str);
pr_Ne[cpop].p[1] = atof(str);
}
while(pr_Ne[cpop].p[1]<=0);
do{
printf(" choose shape parameter (>0): ");
scanf("%s",&str);
pr_Ne[cpop].p[2] = atof(str);
}
while(pr_Ne[cpop].p[2]<=0);
do{
printf(" choose 2nd shape parameter (>0): ");
scanf("%s",&str);
pr_Ne[cpop].p[3] = atof(str);
}
while(pr_Ne[cpop].p[3]<=0);
}
}
if(npop>1){
/*tev priors*/
ntev = npop-1;
pr_tev = (struct prior *)malloc((ntev)*sizeof(struct prior));
allTev = 0;
for(ctev=0; ctev<ntev; ctev++){
if(!allTev){
printf("\n");
if(ctev==0 && npop>2){
do{
printf(" choose the Tev%d prior [1 - uniform distribution; 2 - generalized gamma\n",ctev+1);
printf(" distribution; 3 - uniform distribution (for all tev) 4 - generalized\n");
printf(" gamma distribution (for all tev)]: ");
scanf("%s",&str);
pr_tev[ctev].type = atoi(str);
}
while(pr_tev[ctev].type!=1 && pr_tev[ctev].type!=2 && pr_tev[ctev].type!=3 && pr_tev[ctev].type!=4);
}
else{
do{
printf(" choose the Tev%d prior [1 - uniform distribution; 2 - generalized gamma\n",ctev+1);
printf(" distribution]: ");
scanf("%s",&str);
d1 = atoi(str);
pr_tev[ctev].type= d1;
}
while(pr_tev[ctev].type!=1 && pr_tev[ctev].type!=2);
}
if(pr_tev[ctev].type==3||pr_tev[ctev].type==4){
allTev=1;
}
if(pr_tev[ctev].type==1||pr_tev[ctev].type==3){
pr_tev[ctev].p = (double *)malloc(2*sizeof(double));
do{
printf(" choose lower boundary of the prior (>=0): ");
scanf("%s",&str);
pr_tev[ctev].p[0] = atof(str);
printf(" choose upper boundary of the prior (>0): ");
scanf("%s",&str);
pr_tev[ctev].p[1] = atof(str);
}
while(pr_tev[ctev].p[0]>pr_tev[ctev].p[1] || pr_tev[ctev].p[0]<0 || pr_tev[ctev].p[1]<=0);
}
else if(pr_tev[ctev].type==2||pr_tev[ctev].type==4){
pr_tev[ctev].p = (double *)malloc(4*sizeof(double));
do{
printf(" choose location parameter (>=0): ");
scanf("%s",&str);
pr_tev[ctev].p[0] = atof(str);
}
while(pr_tev[ctev].p[0]<0);
do{
printf(" choose scale parameter (>0): ");
scanf("%s",&str);
pr_tev[ctev].p[1] = atof(str);
}
while(pr_tev[ctev].p[1]<=0);
do{
printf(" choose shape parameter (>0): ");
scanf("%s",&str);
pr_tev[ctev].p[2] = atof(str);
}
while(pr_tev[ctev].p[2]<=0);
do{
printf(" choose 2nd shape parameter (>0): ");
scanf("%s",&str);
pr_tev[ctev].p[3] = atof(str);
}
while(pr_tev[ctev].p[3]<=0);
}
}
}
/*migration priors*/
pr_mig = (struct prior *)malloc((npop*2-2)*sizeof(struct prior));
for(cpop=0; cpop<npop*2-2; cpop++){
if(cpop<npop){
printf("\n");
do{
printf(" choose the mig%d rate prior [0 - zero migration; 1 - uniform\n",cpop+1);
printf(" distribution; 2 - generalized gamma distribution; 3 - uniform\n");
printf(" distribution (on number of migrations); 4 - generalized gamma\n");
printf(" distribution(on number of migrations)]: ");
scanf("%s",&str);
pr_mig[cpop].type = atoi(str);
}
while(pr_mig[cpop].type!=0 && pr_mig[cpop].type!=1 && pr_mig[cpop].type!=2 && pr_mig[cpop].type!=3 && pr_mig[cpop].type!=4 && pr_mig[cpop].type!=5);
}
else{
printf("\n");
do{
printf(" choose the migA%d rate prior [0 - zero migration; 1 - uniform\n",cpop+1-npop);
printf(" distribution; 2 - generalized gamma distribution; 3 - uniform\n");
printf(" distribution (on number of migrations); 4 - generalized gamma\n");
printf(" distribution(on number of migrations)]: ");
scanf("%s",&str);
pr_mig[cpop].type = atoi(str);
}
while(pr_mig[cpop].type!=0 && pr_mig[cpop].type!=1 && pr_mig[cpop].type!=2 && pr_mig[cpop].type!=3 && pr_mig[cpop].type!=4 && pr_mig[cpop].type!=5);
}
if(pr_mig[cpop].type==1||pr_mig[cpop].type==3){
pr_mig[cpop].p = (double *)malloc(2*sizeof(double));
do{
printf(" choose lower boundary of the prior (>=0): ");
scanf("%s",&str);
pr_mig[cpop].p[0] = atof(str);
printf(" choose upper boundary of the prior (>0): ");
scanf("%s",&str);
pr_mig[cpop].p[1] = atof(str);
}
while(pr_mig[cpop].p[0]>pr_mig[cpop].p[1] || pr_mig[cpop].p[0]<0 || pr_mig[cpop].p[1]<=0);
}
else if(pr_mig[cpop].type==2||pr_mig[cpop].type==4){
pr_mig[cpop].p = (double *)malloc(4*sizeof(double));
do{
printf(" choose location parameter (=>0): ");
scanf("%s",&str);
pr_mig[cpop].p[0] = atof(str);
}
while(pr_mig[cpop].p[0]<0);
do{
printf(" choose scale parameter (>0): ");
scanf("%s",&str);
pr_mig[cpop].p[1] = atof(str);
}
while(pr_mig[cpop].p[1]<=0);
do{
printf(" choose shape parameter (>0): ");
scanf("%s",&str);
pr_mig[cpop].p[2] = atof(str);
}
while(pr_mig[cpop].p[2]<=0);
do{
printf(" choose 2nd shape parameter (>0): ");
scanf("%s",&str);
pr_mig[cpop].p[3] = atof(str);
}
while(pr_mig[cpop].p[3]<=0);
}
}
}
/*mutation priors*/
printf("\n");
if(nloc==1){
do{
printf(" choose STR mutation rate prior [0 - no mutation; 1 - lognormal distribution];\n");
printf(" 2 - normal distribution]: ");
scanf("%s",&str);
pr_mutSTR.type = atoi(str);
}
while(pr_mutSTR.type!=0 && pr_mutSTR.type!=1 && pr_mutSTR.type!=2);
}
else{
do{
printf(" choose STR mutation rate hiperprior [0 - no mutation; 1 - lognormal\n");
printf(" distribution; 2 - normal distribution]: ");
scanf("%s",&str);
pr_mutSTR.type = atoi(str);
}
while(pr_mutSTR.type!=0 && pr_mutSTR.type!=1 && pr_mutSTR.type!=2);
}
if(pr_mutSTR.type==1){
pr_mutSTR.p = (double *)malloc(4*sizeof(double));
if(nloc==1){
do{
printf(" choose the mean of the prior [lognormal scale (<0)]: ");
scanf("%s",&str);
pr_mutSTR.p[0] = atof(str);
}
while(pr_mutSTR.p[0]>=0);
pr_mutSTR.p[1] = 0;
do{
printf(" choose the stdev of the prior [lognormal scale(>=0)]: ");
scanf("%s",&str);
pr_mutSTR.p[2] = atof(str);
}
while(pr_mutSTR.p[2]<0);
pr_mutSTR.p[3] = 0;
}
else{
do{
printf(" choose the mean of all means [lognormal scale (<0)]: ");
scanf("%s",&str);
pr_mutSTR.p[0] = atof(str);
}
while(pr_mutSTR.p[0]>=0);
do{
printf(" choose the stdev of all means (>=0): ");
scanf("%s",&str);
pr_mutSTR.p[1] = atof(str);
}
while(pr_mutSTR.p[1]<0);
do{
printf(" choose the mean of all stdevs [lognormal scale(>=0)]: ");
scanf("%s",&str);
pr_mutSTR.p[2] = atof(str);
}
while(pr_mutSTR.p[2]<0);
do{
printf(" choose the stdev of all stdevs (>=0): ");
scanf("%s",&str);
pr_mutSTR.p[3] = atof(str);
}
while(pr_mutSTR.p[3]<0);
}
}
if(pr_mutSTR.type==2){
pr_mutSTR.p = (double *)malloc(4*sizeof(double));
if(nloc==1){
do{
printf(" choose the mean of the prior (>0)]: ");
scanf("%s",&str);
pr_mutSTR.p[0] = atof(str);
}
while(pr_mutSTR.p[0]<=0);
pr_mutSTR.p[1] = 0;
do{
printf(" choose the stdev of the prior (>=0)]: ");
scanf("%s",&str);
pr_mutSTR.p[2] = atof(str);
}
while(pr_mutSTR.p[2]<0);
pr_mutSTR.p[3] = 0;
}
else{
do{
printf(" choose the mean of all means (>0)]: ");
scanf("%s",&str);
pr_mutSTR.p[0] = atof(str);
}
while(pr_mutSTR.p[0]<=0);
do{
printf(" choose the stdev of all means (>=0): ");
scanf("%s",&str);
pr_mutSTR.p[1] = atof(str);
}
while(pr_mutSTR.p[1]<0);
do{
printf(" choose the mean of all stdevs (>=0)]: ");
scanf("%s",&str);
pr_mutSTR.p[2] = atof(str);
}
while(pr_mutSTR.p[2]<0);
do{
printf(" choose the stdev of all stdevs (>=0): ");
scanf("%s",&str);
pr_mutSTR.p[3] = atof(str);
}
while(pr_mutSTR.p[3]<0);
}
}
printf("\n");
if(nloc==1){
do{
printf(" choose SNP mutation rate prior [0 - no mutation; 1 - lognormal distribution];\n");
printf(" 2 - normal distribution]: ");
scanf("%s",&str);
pr_mutSNP.type = atoi(str);
}
while(pr_mutSNP.type!=0 && pr_mutSNP.type!=1 && pr_mutSNP.type!=2);
}
else{
do{
printf(" choose SNP mutation rate hiperprior [0 - no mutation; 1 - lognormal\n");
printf(" distribution; 2 - normal distribution]: ");
scanf("%s",&str);
pr_mutSNP.type = atoi(str);
}
while(pr_mutSNP.type!=0 && pr_mutSNP.type!=1 && pr_mutSNP.type!=2);
}
if(pr_mutSNP.type==1){
pr_mutSNP.p = (double *)malloc(4*sizeof(double));
if(nloc==1){
do{
printf(" choose the mean of the prior [lognormal scale (<0)]: ");
scanf("%s",&str);
pr_mutSNP.p[0] = atof(str);
}
while(pr_mutSNP.p[0]>=0);
pr_mutSNP.p[1] = 0;
do{
printf(" choose the stdev of the prior [lognormal scale(>=0)]: ");
scanf("%s",&str);
pr_mutSNP.p[2] = atof(str);
}
while(pr_mutSNP.p[2]<0);
pr_mutSNP.p[3] = 0;
}
else{
do{
printf(" choose the mean of all means [lognormal scale (<0)]: ");
scanf("%s",&str);
pr_mutSNP.p[0] = atof(str);
}
while(pr_mutSNP.p[0]>=0);
do{
printf(" choose the stdev of all means (>=0): ");
scanf("%s",&str);
pr_mutSNP.p[1] = atof(str);
}
while(pr_mutSNP.p[1]<0);
do{
printf(" choose the mean of all stdevs [lognormal scale(>=0)]: ");
scanf("%s",&str);
pr_mutSNP.p[2] = atof(str);
}
while(pr_mutSNP.p[2]<0);
do{
printf(" choose the stdev of all stdevs (>=0): ");
scanf("%s",&str);
pr_mutSNP.p[3] = atof(str);
}
while(pr_mutSNP.p[3]<0);
}
}
if(pr_mutSNP.type==2){
pr_mutSNP.p = (double *)malloc(4*sizeof(double));
if(nloc==1){
do{
printf(" choose the mean of the prior (>0)]: ");
scanf("%s",&str);
pr_mutSNP.p[0] = atof(str);
}
while(pr_mutSNP.p[0]<=0);
pr_mutSNP.p[1] = 0;
do{
printf(" choose the stdev of the prior (>=0)]: ");
scanf("%s",&str);
pr_mutSNP.p[2] = atof(str);
}
while(pr_mutSNP.p[2]<0);
pr_mutSNP.p[3] = 0;
}
else{
do{
printf(" choose the mean of all means (>0)]: ");
scanf("%s",&str);
pr_mutSNP.p[0] = atof(str);
}
while(pr_mutSNP.p[0]<=0);
do{
printf(" choose the stdev of all means (>=0): ");
scanf("%s",&str);
pr_mutSNP.p[1] = atof(str);
}
while(pr_mutSNP.p[1]<0);
do{
printf(" choose the mean of all stdevs (>=0)]: ");
scanf("%s",&str);
pr_mutSNP.p[2] = atof(str);
}
while(pr_mutSNP.p[2]<0);
do{
printf(" choose the stdev of all stdevs (>=0): ");
scanf("%s",&str);
pr_mutSNP.p[3] = atof(str);
}
while(pr_mutSNP.p[3]<0);
}
}
/*recombination priors*/
printf("\n");
if(nloc==1){
do{
printf(" choose STR recombination prior [0 - no recombination; 1 - lognormal\n");
printf(" distribution]; 2 - normal distribution]: ");
scanf("%s",&str);
pr_recSTR.type = atoi(str);
}
while(pr_recSTR.type!=0 && pr_recSTR.type!=1 && pr_recSTR.type!=2);
}
else{
do{
printf(" choose STR recombination rate hiperprior [0 - no recombination; 1 - lognormal\n");
printf(" distribution; 2 - normal distribution]: ");
scanf("%s",&str);
pr_recSTR.type = atoi(str);
}
while(pr_recSTR.type!=0 && pr_recSTR.type!=1 && pr_recSTR.type!=2);
}
if(pr_recSTR.type==1){
pr_recSTR.p = (double *)malloc(4*sizeof(double));
if(nloc==1){
do{
printf(" choose the mean of the prior [lognormal scale (<0)]: ");
scanf("%s",&str);
pr_recSTR.p[0] = atof(str);
}
while(pr_recSTR.p[0]>=0);
pr_recSTR.p[1] = 0;
do{
printf(" choose the stdev of the prior [lognormal scale(>=0)]: ");
scanf("%s",&str);
pr_recSTR.p[2] = atof(str);
}
while(pr_recSTR.p[2]<0);
pr_recSTR.p[3] = 0;
}
else{
do{
printf(" choose the mean of all means [lognormal scale (<0)]: ");
scanf("%s",&str);
pr_recSTR.p[0] = atof(str);
}
while(pr_recSTR.p[0]>=0);
do{
printf(" choose the stdev of all means (>=0): ");
scanf("%s",&str);
pr_recSTR.p[1] = atof(str);
}
while(pr_recSTR.p[1]<0);
do{
printf(" choose the mean of all stdevs [lognormal scale(>=0)]: ");
scanf("%s",&str);
pr_recSTR.p[2] = atof(str);
}
while(pr_recSTR.p[2]<0);
do{
printf(" choose the stdev of all stdevs (>=0): ");
scanf("%s",&str);
pr_recSTR.p[3] = atof(str);
}
while(pr_recSTR.p[3]<0);
}
}
if(pr_recSTR.type==2){
pr_recSTR.p = (double *)malloc(4*sizeof(double));
if(nloc==1){
do{
printf(" choose the mean of the prior (>0)]: ");
scanf("%s",&str);
pr_recSTR.p[0] = atof(str);
}
while(pr_recSTR.p[0]<=0);
pr_recSTR.p[1] = 0;
do{
printf(" choose the stdev of the prior (>=0)]: ");
scanf("%s",&str);
pr_recSTR.p[2] = atof(str);
}
while(pr_recSTR.p[2]<0);
pr_recSTR.p[3] = 0;
}
else{
do{
printf(" choose the mean of all means (>0)]: ");
scanf("%s",&str);
pr_recSTR.p[0] = atof(str);
}
while(pr_recSTR.p[0]<=0);
do{
printf(" choose the stdev of all means (>=0): ");
scanf("%s",&str);
pr_recSTR.p[1] = atof(str);
}
while(pr_recSTR.p[1]<0);
do{
printf(" choose the mean of all stdevs (>=0)]: ");
scanf("%s",&str);
pr_recSTR.p[2] = atof(str);
}
while(pr_recSTR.p[2]<0);
do{
printf(" choose the stdev of all stdevs (>=0): ");
scanf("%s",&str);
pr_recSTR.p[3] = atof(str);
}
while(pr_recSTR.p[3]<0);
}
}
printf("\n");
if(nloc==1){
do{
printf(" choose SNP recombination rate prior [0 - no recombination; 1 - lognormal\n");
printf(" distribution]; 2 - normal distribution]: ");
scanf("%s",&str);
pr_recSNP.type = atoi(str);
}
while(pr_recSNP.type!=0 && pr_recSNP.type!=1 && pr_recSNP.type!=2);
}
else{
do{
printf(" choose SNP recombination rate hiperprior [0 - no recombination; 1 - lognormal\n");
printf(" distribution; 2 - normal distribution]: ");
scanf("%s",&str);
pr_recSNP.type = atoi(str);
}
while(pr_recSNP.type!=0 && pr_recSNP.type!=1 && pr_recSNP.type!=2);
}
if(pr_recSNP.type==1){
pr_recSNP.p = (double *)malloc(4*sizeof(double));
if(nloc==1){
do{
printf(" choose the mean of the prior [lognormal scale (<0)]: ");
scanf("%s",&str);
pr_recSNP.p[0] = atof(str);
}
while(pr_recSNP.p[0]>=0);
pr_recSNP.p[1] = 0;
do{
printf(" choose the stdev of the prior [lognormal scale(>=0)]: ");
scanf("%s",&str);
pr_recSNP.p[2] = atof(str);
}
while(pr_recSNP.p[2]<0);
pr_recSNP.p[3] = 0;
}
else{
do{
printf(" choose the mean of all means [lognormal scale (<0)]: ");
scanf("%s",&str);
pr_recSNP.p[0] = atof(str);
}
while(pr_recSNP.p[0]>=0);
do{
printf(" choose the stdev of all means (>=0): ");
scanf("%s",&str);
pr_recSNP.p[1] = atof(str);
}
while(pr_recSNP.p[1]<0);
do{
printf(" choose the mean of all stdevs [lognormal scale(>=0)]: ");
scanf("%s",&str);
pr_recSNP.p[2] = atof(str);
}
while(pr_recSNP.p[2]<0);
do{
printf(" choose the stdev of all stdevs (>=0): ");
scanf("%s",&str);
pr_recSNP.p[3] = atof(str);
}
while(pr_recSNP.p[3]<0);
}
}
if(pr_recSNP.type==2){
pr_recSNP.p = (double *)malloc(4*sizeof(double));
if(nloc==1){
do{
printf(" choose the mean of the prior (>0)]: ");
scanf("%s",&str);
pr_recSNP.p[0] = atof(str);
}
while(pr_recSNP.p[0]<=0);
pr_recSNP.p[1] = 0;
do{
printf(" choose the stdev of the prior (>=0)]: ");
scanf("%s",&str);
pr_recSNP.p[2] = atof(str);
}
while(pr_recSNP.p[2]<0);
pr_recSNP.p[3] = 0;
}
else{
do{
printf(" choose the mean of all means (>0)]: ");
scanf("%s",&str);
pr_recSNP.p[0] = atof(str);
}
while(pr_recSNP.p[0]<=0);
do{
printf(" choose the stdev of all means (>=0): ");
scanf("%s",&str);
pr_recSNP.p[1] = atof(str);
}
while(pr_recSNP.p[1]<0);
do{
printf(" choose the mean of all stdevs (>=0)]: ");
scanf("%s",&str);
pr_recSNP.p[2] = atof(str);
}
while(pr_recSNP.p[2]<0);
do{
printf(" choose the stdev of all stdevs (>=0): ");
scanf("%s",&str);
pr_recSNP.p[3] = atof(str);
}
while(pr_recSNP.p[3]<0);
}
}
/*migration matrix*/
if(npop>=3 && (pr_top.type==1 || pr_top.type==2 || pr_top.type==4 || pr_top.type==5)){
printf("\n");
do{
printf(" choose to set or not migration weights [0 - do not use; 1 - use]: ");
scanf("%s",&str);
migw.type = atoi(str);
}
while(migw.type!=0 && migw.type!=1);
if(migw.type==1){
migw.m = (double ***)malloc(npop*sizeof(double**));
for(cpop=0;cpop<npop;cpop++){
migw.m[cpop] = (double **)malloc(ntev*sizeof(double*));
for(ctev=0;ctev<ntev;ctev++)
migw.m[cpop][ctev] = (double *)malloc(npop*sizeof(double));
}
printf("\n choose the percentage of migrants:\n");
for(cpop=0;cpop<npop;cpop++){
for(ctev=0;ctev<ntev;ctev++){
for(cpop2=0;cpop2<npop;cpop2++){
if(cpop==cpop2)
migw.m[cpop][ctev][cpop2] = 0;
else{
do{
printf(" in pop %d from pop %d at time %d (0 <= per <= 1): ",cpop,cpop2,ctev);
scanf("%s",&str);
migw.m[cpop][ctev][cpop2] = atof(str);
}
while(migw.m[cpop][ctev][cpop2]<0 || migw.m[cpop][ctev][cpop2]>1);
}
}
}
}
}
}
else
migw.type=0;
/*output filename*/
printf("\n insert name for prior file (no extension) (max %d character): ",MAXCHAR-1);
scanf("%s",output);
/*run makeprior()*/
error = makeprior(output,niter,genet,npop,nloc,lplo,ltype,pr_top,pr_Ne,pr_tev,pr_mig,
pr_mutSTR,pr_mutSNP,pr_recSTR,pr_recSNP,migw);
/*free stuff*/
if(pr_top.type==2||pr_top.type==5){
free(avlpop);
}
return error;
} //ends of buildprior
int exists(int *avlpop,int pop,int size){
int i,
foundit;
foundit = 0;
for(i=0; i<size && !foundit; i++){
if(avlpop[i] == pop)
foundit = 1;
}
return foundit;
} //end of exists
int *takeout(int *avlpop,int pop, int size){
int i, //iterator
foundit, //check if the pop was found
*aftlist; //updated list
aftlist = (int *)malloc((size-1)*sizeof(int));
foundit = 0;
for(i=0; i<size; i++){
if(foundit)
aftlist[i-1] = avlpop[i];
else{
if(avlpop[i]==pop)
foundit = 1;
else
aftlist[i] = avlpop[i];
}
}
//free stuff
free(avlpop);
return aftlist;
} //end of takeout
int buildsstats(){
int cstat, //iterator
lsstats[MAXSSTATS]; //list of the summary statistics used
char str[MAXCHAR], //auxiliar to get the input from the user
output[MAXCHAR]; //output filename
//summary statistics
for(cstat=0; cstat<MAXSSTATS; cstat++)
lsstats[cstat]=0;
printf(" choose the summary statistics to be used (0 - absent; 1 - present):\n");
for(cstat=0; cstat<MAXSSTATS; cstat++){
do{
switch(cstat){
case 0:
printf("\n microsatellites data\n");
printf(" heterozygosity: ");
break;
case 1:
printf(" variance of alleles length: ");
break;
case 2:
printf(" number of alleles: ");
break;
case 3:
printf(" curtosis of alleles length: ");
break;
case 4:
printf(" Shanon's index: ");
break;
case 5:
printf(" Nm estimator based on H: ");
break;
case 6:
printf("\n sequence data\n");
printf(" mean of pairwise differences: ");
break;
case 7:
printf(" number of segregating sites: ");
break;
case 8:
printf(" number of haplotypes: ");
break;
case 9:
printf(" Shanon's index: ");
break;
case 10:
printf(" mean of MFS: ");
break;
case 11:
printf(" stdev of MFS: ");
break;
case 12:
printf(" Nm estimator based on S: ");
break;
case 13:
printf(" private segregating sites: ");
break;
case 14:
printf(" S(1): ");
break;
}
scanf("%s",&str);
lsstats[cstat] = atoi(str);
}
while(lsstats[cstat]!=1 && lsstats[cstat]!=0);
}
/*output filename*/
printf("\n insert name for summary statistics set file (no extension)");
printf("\n (max %d character): ",MAXCHAR-1);
scanf("%s",output);
/*run makestats()*/
return makestats(output,lsstats);
} //ends of buildsstats
int createtab(){
char str[MAXCHAR], //auxiliar to get the input from the user
input[MAXCHAR], //input file name
output[MAXCHAR]; //input file name
//input filename
printf("\n choose sample file (.pop) (max %d character): ",MAXCHAR-1);
scanf("%s",input);
//output filename
printf("\n insert name for table file (no extension) (max %d character): ",MAXCHAR-1);
scanf("%s",output);
return createFreqTab(input,output);
} //end of createtab1
int createtab2(){
char str[MAXCHAR], //auxiliar to get the input from the user
input[MAXCHAR], //input file name
output[MAXCHAR]; //input file name
//input filename
printf("\n choose IMa sample file (max %d character): ",MAXCHAR-1);
scanf("%s",input);
//output filename
printf("\n insert name for table file (no extension) (max %d character): ",MAXCHAR-1);
scanf("%s",output);
return createFreqTab2(input,output);
} //end of createtab2
int createtab3(){
char str[MAXCHAR], //auxiliar to get the input from the user
input[MAXCHAR], //input file name
output[MAXCHAR]; //input file name
//input filename
printf("\n choose GenePop sample file (max %d character): ",MAXCHAR-1);
scanf("%s",input);
//output filename
printf("\n insert name for table file (no extension) (max %d character): ",MAXCHAR-1);
scanf("%s",output);
return createFreqTab3(input,output);
} //end of createtab3
int createtab4(){
char str[MAXCHAR], //auxiliar to get the input from the user
input[MAXCHAR], //input file name
output[MAXCHAR]; //input file name
//input filename
printf("\n choose Nexus file (.nex) (max %d character): ",MAXCHAR-1);
scanf("%s",input);
//output filename
printf("\n insert name for table file (no extension) (max %d character): ",MAXCHAR-1);
scanf("%s",output);
return createFreqTab4(input,output);
} //end of createtab4
int createpop(){
char str[MAXCHAR], //auxiliar to get the input from the user
input[MAXCHAR], //input file name
output[MAXCHAR]; //input file name
//input filename
printf("\n choose table file (.len) (max %d character): ",MAXCHAR-1);
scanf("%s",input);
//output filename
printf("\n insert name for sample file (no extension) (max %d character): ",MAXCHAR-1);
scanf("%s",output);
return makepop(input,output);
} //end of convertTab
int joinfiles(){
int i, //iterator
error, //saves the error type
ninp; //number of files to join
char outp[MAXCHAR], //output file name
str[MAXCHAR], //auxiliar to get the input from the user
**linp; //list of the files to join together
//number of files to join
do{
printf(" choose the number of files to join (>1): ");
scanf("%s",&str);
ninp = atoi(str);
}
while(ninp <=1);
//path of the files to join
linp = (char**)malloc(ninp*sizeof(char*));
printf("\n choose %d files to be joint (.dat)\n",ninp);
for(i=0; i<ninp; i++){
linp[i] = (char*)malloc(MAXCHAR*sizeof(char));
printf(" file %d (max %d character): ",i+1,MAXCHAR-1);
scanf("%s",linp[i]);
}
//output filename
printf("\n insert name for created file (.dat) (max %d character): ",MAXCHAR-1);
scanf("%s",outp);
//run joindata()
error = joindata(ninp,linp,outp);
//free stuff
for(i=0; i<ninp; i++){
free(linp[i]);
}
free(linp);
return error;
} //end of joinfiles
Computing file changes ...
