void analyse_param_cds( int argc, char *argv[], long long* s,
double *e, char *input, char *output_file)
{
int i;
int g_data = -1;
int g_e = 0;
int g_s = 0;
for (i = 1; i < argc; i++) {
if (argv[i][0] == '-') {
switch (argv[i][1]) {
// seed
case 's':
i++;
if (argc == i || argv[i][0] == '-')
print_error_cds("cmd","s (seed number)");
*s = atoi(argv[i]);
g_s = 1;
break;
// percentage of masked genotype
case 'r':
i++;
if (argc == i || argv[i][0] == '-')
print_error_cds("cmd","r (percentage of masked data)");
*e = (double) atof(argv[i]);
if (*e < 0)
*e = 0;
if (*e > 1)
*e = 1;
g_e = 1;
break;
// help
case 'h':
print_help_cds();
exit(1);
break;
// licence
case 'l':
print_licence_snmf();
exit(1);
break;
// input file
case 'x':
i++;
if (argc == i || argv[i][0] == '-')
print_error_cds("cmd","x (genotype file)");
g_data = 0;
strcpy(input,argv[i]);
break;
// output file
case 'o':
i++;
if (argc == i || argv[i][0] == '-')
print_error_cds("cmd","o (genotype file with masked genotypes)");
strcpy(output_file,argv[i]);
break;
default: print_error_cds("basic",NULL);
}
} else {
print_error_cds("basic",NULL);
}
}
// no data file
if (g_data == -1)
print_error_cds("option","-x genotype_file");
// no seed
if (g_s && *s <= 0)
*s = -1;
// percentage not in [0,1]
if (g_e && (*e <= 0 || *e >= 1))
print_error_cds("missing","");
// write output file name
change_ext(input, output_file, "_I.geno");
}
void analyse_param_ce( int argc, char *argv[], int* m,
int* K, char *input, char* input_file_Q,
char* input_file_F, char *input_file_I)
{
int i;
int g_data = -1;
char *tmp_file;
char tmp[512];
int g_m = 0;
for (i = 1; i < argc; i++) {
if (argv[i][0] == '-') {
switch (argv[i][1]) {
// the number of ancestral populations
case 'K':
i++;
if (argc == i || argv[i][0] == '-')
print_error_ce("cmd","K (number of ancestral populations)");
*K = atoi(argv[i]);
strcpy(tmp,argv[i]);
break;
// the ploidy
case 'm':
i++;
if (argc == i || argv[i][0] == '-')
print_error_ce("cmd","m (number of alleles)");
*m = atoi(argv[i]);
g_m = 1;
break;
// help
case 'h':
print_help_ce();
exit(1);
break;
// licence
case 'l':
print_licence_snmf();
exit(1);
break;
// genotypic file
case 'x':
i++;
if (argc == i || argv[i][0] == '-')
print_error_ce("cmd","x (genotype file)");
g_data = 0;
strcpy(input,argv[i]);
break;
// individual admixture file
case 'q':
i++;
if (argc == i || argv[i][0] == '-')
print_error_ce("cmd","q (individual admixture coefficients file)");
strcpy(input_file_Q,argv[i]);
break;
// ancestral genotype frequency file
case 'g':
i++;
if (argc == i || argv[i][0] == '-')
print_error_ce("cmd","g (ancestral genotype frequencies file)");
strcpy(input_file_F,argv[i]);
break;
// genotypic file with masked data
case 'i':
i++;
if (argc == i || argv[i][0] == '-')
print_error_ce("cmd","i (genotype file with masked genotypes)");
strcpy(input_file_I,argv[i]);
break;
default: print_error_ce("basic",NULL);
}
} else {
print_error_ce("basic",NULL);
}
}
// no genotypic file
if (g_data == -1)
print_error_ce("option","-x genotype_file");
// ploidy and negative
if (g_m && *m <= 0)
print_error_ce("missing", NULL);
// negative K
if (*K <= 0)
print_error_ce("missing",NULL);
// write output file names
tmp_file = remove_ext(input,'.','/');
if (!strcmp(input_file_F,"")) {
strcpy(input_file_F,tmp_file);
strcat(input_file_F,"_I.");
strcat(input_file_F,tmp);
strcat(input_file_F,".G");
}
if (!strcmp(input_file_Q,"")) {
strcpy(input_file_Q,tmp_file);
strcat(input_file_Q,"_I.");
strcat(input_file_Q,tmp);
strcat(input_file_Q,".Q");
}
if (!strcmp(input_file_I,"")) {
strcpy(input_file_I,tmp_file);
strcat(input_file_I,"_I.geno");
}
free(tmp_file);
}
void analyse_param_snmf(int argc, char *argv[], sNMF_param param)
{
int i;
int g_data = -1;
char *tmp_file;
char tmp[512];
int g_c = 0;
int g_m = 0;
for (i = 1; i < argc; i++) {
if (argv[i][0] == '-') {
switch (argv[i][1]) {
case 'K':
i++;
if (argc == i || argv[i][0] == '-')
print_error_nmf("cmd","K (number of clusters)",0);
param->K = atoi(argv[i]);
strcpy(tmp,argv[i]);
break;
case 's':
i++;
if (argc == i || argv[i][0] == '-')
print_error_nmf("cmd","s (seed number)",0);
param->seed= atoll(argv[i]);
break;
case 'm':
i++;
if (argc == i || argv[i][0] == '-')
print_error_nmf("cmd","m (number of alleles)",0);
param->m = atoi(argv[i]);
g_m = 1;
break;
case 'a':
i++;
if (argc == i || argv[i][0] == '-')
print_error_nmf("cmd","alpha (regularization parameter)",0);
param->alpha = (double) atof(argv[i]);
if (param->alpha < 0) {
param->alpha = 0;
}
break;
case 'h': // global
print_help_snmf();
exit(1);
break;
case 'l': // global
print_licence_snmf();
exit(1);
break;
case 'e':
i++;
if (argc == i || argv[i][0] == '-')
print_error_nmf("cmd","e (tolerance error in the algorithm)",0);
param->tolerance = (double) atof(argv[i]);
if (param->tolerance < 0) {
param->tolerance = 0;
}
break;
case 'c':
i++;
if (argc == i || argv[i][0] == '-') {
param->pourcentage = 0.05;
i--;
} else {
param->pourcentage = (double) atof(argv[i]);
}
g_c = 1;
break;
case 'i':
i++;
if (argc == i || argv[i][0] == '-')
print_error_nmf("cmd","i (number of iterations)",0);
param->maxiter = atoi(argv[i]);
break;
case 'I':
i++;
if (argc == i || argv[i][0] == '-') {
param->I = -1;
i--;
} else
param->I = (int) atoi(argv[i]);
break;
case 'x':
i++;
if (argc == i || argv[i][0] == '-')
print_error_nmf("cmd","x (genotype file)",0);
g_data = 0;
strcpy(param->input_file,argv[i]);
break;
case 'q':
i++;
if (argc == i || argv[i][0] == '-')
print_error_nmf("cmd","q (individual admixture coefficients file)",0);
strcpy(param->output_file_Q,argv[i]);
break;
case 'Q':
i++;
if (argc == i || argv[i][0] == '-')
print_error_nmf("cmd","Q (admixture coefficients initialization file)",0);
strcpy(param->input_file_Q,argv[i]);
break;
case 'g':
i++;
if (argc == i || argv[i][0] == '-')
print_error_nmf("cmd","g (ancestral genotype frequencies file)",0);
strcpy(param->output_file_F,argv[i]);
break;
case 'p':
i++;
if (argc == i || argv[i][0] == '-')
print_error_nmf("cmd","p (number of processes)",0);
param->num_thrd = atoi(argv[i]);
break;
default: print_error_nmf("basic",NULL,0);
}
} else {
print_error_nmf("basic",NULL,0);
}
}
if (g_data == -1)
print_error_nmf("option","-x genotype_file",0);
if (param->K <= 0)
print_error_nmf("missing",NULL,0);
if (param->num_thrd <= 0)
print_error_nmf("missing",NULL,0);
if (g_m && param->m <= 0)
print_error_nmf("missing",NULL,0);
if (param->maxiter <= 0)
print_error_nmf("missing",NULL,0);
if (g_c && (param->pourcentage <= 0 || param->pourcentage >= 1))
print_error_nmf("missing",NULL,0);
// write output file name
tmp_file = remove_ext(param->input_file,'.','/');
if (!strcmp(param->output_file_Q,"")) {
strcpy(param->output_file_Q,tmp_file);
strcat(param->output_file_Q,".");
strcat(param->output_file_Q,tmp);
strcat(param->output_file_Q,".Q");
}
if (!strcmp(param->output_file_F,"")) {
strcpy(param->output_file_F,tmp_file);
strcat(param->output_file_F,".");
strcat(param->output_file_F,tmp);
strcat(param->output_file_F,".G");
}
free(tmp_file);
}
