//input first the fasta file, then the sample_1000.out file run on the fasta, then options
int main(int argc, char *argv[]) {
int i, h, minh,p;
HASHTBL *deleteHash;
FILE *fp;
Set *set;
Options *opt;
if (argc < 3) {
fprintf(stderr,"Not enough arguments\n");
exit(EXIT_FAILURE);
}
set = make_Set(argv[2]);
opt = set->opt;
for (i = 3; i < argc; i++) {
//printf("argv[%d] is %s\n",i,argv[i]);
if (!strcmp(argv[i],"-h")) {
if ((i + 1 <= argc - 1) && sscanf(argv[i+1],"%f",&(opt->HC_FREQ))) {
opt->HC_FREQ = atof(argv[i+1]);
if (opt->HC_FREQ < 0 || opt->HC_FREQ > 100) {
fprintf(stderr,"Error: invalid input %f for frequency threshold\n",opt->HC_FREQ);
opt->HC_FREQ = 0;
}
i++;
}
}
else if (!strcmp(argv[i],"-p")) {
if ((i + 1 <= argc - 1) && sscanf(argv[i+1],"%f",&(opt->PROF_FREQ))) {
opt->PROF_FREQ = atof(argv[i+1]);
if (opt->PROF_FREQ < 0 || opt->PROF_FREQ > 100) {
fprintf(stderr,"Error: invalid input %f for frequency threshold\n",opt->PROF_FREQ);
opt->PROF_FREQ = 0;
}
i++;
}
}
else if (!strcmp(argv[i],"-c")) {
if ((i + 1 <= argc - 1) && sscanf(argv[i+1],"%f",&(opt->COVERAGE))) {
opt->COVERAGE = atof(argv[i+1]);
i++;
}
}
else if (!strcmp(argv[i],"-f")) {
if ((i + 1 <= argc - 1) && sscanf(argv[i+1],"%d",&(opt->NUM_FHC))) {
opt->NUM_FHC = atoi(argv[i+1]);
i++;
}
}
else if (!strcmp(argv[i],"-s")) {
if ((i + 1 <= argc - 1) && sscanf(argv[i+1],"%d",&(opt->NUM_SPROF))) {
opt->NUM_SPROF = atoi(argv[i+1]);
i++;
}
}
else if (!strcmp(argv[i],"-l")) {
if ((i + 1 <= argc - 1) && sscanf(argv[i+1],"%d",&(opt->MIN_HEL_LEN))) {
opt->MIN_HEL_LEN = atoi(argv[i+1]);
i++;
}
}
else if (!strcmp(argv[i],"-u")) {
if ((i + 1 <= argc - 1) && sscanf(argv[i+1],"%d",&(opt->NUMSTRUCTS))) {
opt->NUMSTRUCTS = atoi(argv[i+1]);
i++;
}
}
else if (!strcmp(argv[i],"-m")) {
if (i + 1 <= argc - 1) {
opt->PNOISE = atoi(argv[i+1]);
i++;
}
}
else if (!strcmp(argv[i],"-o")) {
if (i + 1 <= argc - 1) {
opt->OUTPUT = argv[i+1];
i++;
}
}
else if (!strcmp(argv[i],"-i")) {
if (i + 1 <= argc - 1) {
opt->INPUT = argv[i+1];
i++;
}
}
else if (!strcmp(argv[i],"-n")) {
if (i + 1 <= argc - 1) {
opt->NATIVE = argv[i+1];
i++;
}
}
else if (!strcmp(argv[i],"-k")) {
if (i + 1 <= argc - 1) {
opt->CYCLES = argv[i+1];
i++;
}
}
else if (!strcmp(argv[i],"-v"))
opt->VERBOSE = 1;
else if (!strcmp(argv[i],"-g"))
opt->GRAPH = 0;
else if (!strcmp(argv[i],"-r"))
opt->REP_STRUCT = 1;
else if (!strcmp(argv[i],"-t"))
opt->TOPDOWN = 1;
else if (!strcmp(argv[i],"-a"))
opt->ALTTHRESH = 0;
}
input_seq(set,argv[1]);
process_structs(set);
reorder_helices(set);
minh = print_all_helices(set);
printf("Total number of helix classes: %d\n",set->hc_num);
if (set->opt->TOPDOWN) {
printf("Total number of extended profiles: %d\n",set->prof_num);
h = top_down_h(set,minh);
//if (set->opt->VERBOSE)
printf("Number of featured helix classes: %d\n",h+1);
find_freq(set);
p = top_down_p(set,h);
//if (set->opt->VERBOSE)
printf("Number of selected profiles: %d\n",p+1);
print_topdown_prof(set,h,p);
} else {
if (set->opt->NUM_FHC)
set->opt->HC_FREQ = set_num_fhc(set);
else if (set->opt->HC_FREQ==0)
set->opt->HC_FREQ = set_threshold(set,H_START);
if (set->opt->VERBOSE) {
printf("Threshold to find frequent helices: %.1f\%\n",set->opt->HC_FREQ);
printf("Number of structures processed: %d\n",set->opt->NUMSTRUCTS);
}
find_freq(set);
printf("Total number of featured helix classes: %d\n",set->num_fhc);
make_profiles(set);
printf("Total number of profiles: %d\n",set->prof_num);
print_profiles(set);
if (set->opt->NUM_SPROF)
set->opt->PROF_FREQ = set_num_sprof(set);
else if (set->opt->PROF_FREQ == 0) {
set->opt->PROF_FREQ = set_p_threshold(set,P_START);
}
if (set->opt->VERBOSE)
printf("setting p to %.1f\n",set->opt->PROF_FREQ);
select_profiles(set);
printf("Total number of selected profiles: %d\n",set->num_sprof);
}
//input first the fasta file, then the sample_1000.out file run on the fasta, then options
int main(int argc, char *argv[]) {
int i,COVERAGE = 50;
HASHTBL *deleteHash;
FILE *fp;
Set *set;
Options *opt;
if (argc < 3) {
fprintf(stderr,"Not enough arguments\n");
exit(EXIT_FAILURE);
}
set = make_Set(argv[2]);
opt = set->opt;
for (i = 3; i < argc; i++) {
//printf("argv[%d] is %s\n",i,argv[i]);
if (!strcmp(argv[i],"-h")) {
if ((i + 1 <= argc - 1) && sscanf(argv[i+1],"%f",&(opt->HC_FREQ))) {
opt->HC_FREQ = atof(argv[i+1]);
if (opt->HC_FREQ < 0 || opt->HC_FREQ > 100) {
fprintf(stderr,"Error: invalid input %f for frequency threshold\n",opt->HC_FREQ);
opt->HC_FREQ = 0;
}
i++;
}
}
else if (!strcmp(argv[i],"-p")) {
if ((i + 1 <= argc - 1) && sscanf(argv[i+1],"%f",&(opt->PROF_FREQ))) {
opt->PROF_FREQ = atof(argv[i+1]);
if (opt->PROF_FREQ < 0 || opt->PROF_FREQ > 100) {
fprintf(stderr,"Error: invalid input %f for frequency threshold\n",opt->PROF_FREQ);
opt->PROF_FREQ = 0;
}
i++;
}
}
else if (!strcmp(argv[i],"-l")) {
if ((i + 1 <= argc - 1) && sscanf(argv[i+1],"%d",&(opt->MIN_HEL_LEN))) {
opt->MIN_HEL_LEN = atoi(argv[i+1]);
i++;
}
}
else if (!strcmp(argv[i],"-s")) {
if ((i + 1 <= argc - 1) && sscanf(argv[i+1],"%d",&(opt->NUMSTRUCTS))) {
opt->NUMSTRUCTS = atoi(argv[i+1]);
i++;
}
}
else if (!strcmp(argv[i],"-o")) {
if (i + 1 <= argc - 1) {
opt->OUTPUT = argv[i+1];
i++;
}
}
else if (!strcmp(argv[i],"-i")) {
if (i + 1 <= argc - 1) {
opt->INPUT = argv[i+1];
i++;
}
}
else if (!strcmp(argv[i],"-n")) {
if (i + 1 <= argc - 1) {
opt->NATIVE = argv[i+1];
i++;
}
}
else if (!strcmp(argv[i],"-v"))
opt->VERBOSE = 1;
else if (!strcmp(argv[i],"-g"))
opt->GRAPH = 0;
else if (!strcmp(argv[i],"-r"))
opt->REP_STRUCT = 1;
}
input_seq(set,argv[1]);
process_structs(set);
reorder_helices(set);
if (set->opt->HC_FREQ==0)
set->opt->HC_FREQ = set_threshold(set,H_START);
if (set->opt->VERBOSE) {
printf("Threshold to find frequent helices: %.1f\%\n",set->opt->HC_FREQ);
printf("Number of structures processed: %d\n",set->opt->NUMSTRUCTS);
}