int main (int argc, char* argv[]) {
char filename1[200];
char filename2[200];
char pairs_file[200];
char fileout[200];
FILE* query_fp = 0;
FILE* reference_fp = 0;
FILE* fp_pairs = 0;
FILE* fpout = stdout;
int total_pairs = 0;
pair_struct* pairs = 0;
extern FILE *scaninfo_file;
setup_match_types();
/* Set Default Parameter Values*/
length_5p_for_weighting = 8; /* The 5' sequence length to be weighted except for the last residue */
scale = 4.0; /* The 5' miRNA scaling parameter */
strict = 0; /* Strict seed model on/off*/
debug = 0; /* Debugging mode on/off*/
key_value_pairs = 0;
gap_open = -9.0; /* Gap-open Penalty*/
gap_extend = -4.0; /* Gap-extend Penalty*/
score_threshold = 140.0; /* SW Score Threshold for reporting hits*/
score_ceiling = 0; /* Default upper limit to score. If zero, this is not used. */
energy_threshold = 1.0; /* Energy Threshold (DG) for reporting hits*/
verbosity = 1; /* Verbose mode on/off*/
brief_output = 0; /* Brief output off by default */
rusage_output = 0; /* rusage output off by default */
outfile = 0; /* Dump to file on/off*/
truncated = 0; /* Truncate sequences on/off*/
no_energy = 1; /* Turn off Energy Calcs - FASTER*/
restricted = 0; /* Perform restricted search space*/
parse_command_line(argc, argv, filename1, filename2, fileout, pairs_file);
if (gap_open > 0.0 || gap_extend > 0.0) {
fprintf(stderr, "Error: gap penalties may not be greater than 0\n");
return 1;
}
if (truncated < 0) {
fprintf(stderr, "Error: negative value give for UTR truncation\n");
return 1;
}
if ((query_fp = fopen(filename1, "r")) == NULL) {
fprintf(stderr, "Error: Cannot open file %s\n", filename1);
return 1;
}
if ((reference_fp = fopen(filename2, "r")) == NULL) {
fprintf(stderr, "Error: Cannot open file %s\n", filename2);
return 1;
}
fclose(reference_fp);
if ((outfile) && ((fpout = fopen(fileout, "w")) == NULL)) {
fprintf(stderr, "Error: Cannot create output file %s\n", fileout);
return 1;
}
if (restricted) {
if ((fp_pairs = fopen(pairs_file, "r")) == NULL) {
fprintf(stderr, "Error: Cannot open restrict pairs file %s\n", pairs_file);
return 1;
}
/* Initialize the pairs list for restriced searches*/
total_pairs = load_pairs(fp_pairs, &pairs);
fclose(fp_pairs);
}
fflush(fpout);
initialize_globals();
if(!brief_output)
print_parameters(filename1, filename2, fpout);
if (restricted && verbosity) {
printf("Performing Restricted Scan on:%d pairs\n", total_pairs);
}
find_targets(query_fp, fpout, pairs, total_pairs, filename2);
#ifdef USE_RUSAGE
if(rusage_output)
{
struct rusage ru;
if(getrusage(RUSAGE_SELF,&ru) != 0)
{
fprintf(stderr,"Could not get rusage data\n");
if(errno)
fprintf(stderr,"Reason: %s",strerror(errno));
}
else
{
printf("User CPU time: %ld.%06ld\n",ru.ru_utime.tv_sec,ru.ru_utime.tv_usec);
printf("Max RSS: %ld KB\n",ru.ru_maxrss);
}
}
#endif // RUSAGE
destroy_globals();
if (outfile) fclose(fpout);
if (scaninfo_file != stdout && scaninfo_file != stderr && scaninfo_file != NULL)
fclose(scaninfo_file);
json_close();
fclose(query_fp);
return 0;
}
int main (int argc, char* argv[]) {
char filename1[200];
char filename2[200];
char pairs_file[200];
char fileout[200];
FILE* query_fp = 0;
FILE* reference_fp = 0;
FILE* fp_pairs = 0;
FILE* fpout = stdout;
int total_pairs = 0;
pair_struct* pairs = 0;
/* Set Default Parameter Values*/
length_5p_for_weighting = 8; /* The 5' sequence length to be weighed except for the last residue*/
scale = 4.0; /* The 5' miRNA scaling parameter*/
strict = 0; /* Strict seed model on/off*/
debug = 0; /* Debugging mode on/off*/
key_value_pairs = 0;
gap_open = -9.0; /* Gap-open Penalty*/
gap_extend = -4.0; /* Gap-extend Penalty*/
score_threshold = 140.0; /* SW Score Threshold for reporting hits*/
energy_threshold = 1.0; /* Energy Threshold (DG) for reporting hits*/
verbosity = 1; /* Verbose mode on/off*/
outfile = 0; /* Dump to file on/off*/
truncated = 0; /* Truncate sequences on/off*/
no_energy = 0; /* Turn off Vienna Energy Calcs - FASTER*/
restricted = 0; /* Perform restricted search space*/
parse_command_line(argc, argv, filename1, filename2, fileout, pairs_file);
if (gap_open > 0.0 || gap_extend > 0.0) {
fprintf(stderr, "Error: gap penalties may not be greater than 0\n");
return 1;
}
if (truncated < 0) {
fprintf(stderr, "Error: negative value give for UTR truncation\n");
return 1;
}
if ((query_fp = fopen(filename1, "r")) == NULL) {
fprintf(stderr, "Error: Cannot open file %s\n", filename1);
return 1;
}
if ((reference_fp = fopen(filename2, "r")) == NULL) {
fprintf(stderr, "Error: Cannot open file %s\n", filename2);
return 1;
}
fclose(reference_fp);
if ((outfile) && ((fpout = fopen(fileout, "w")) == NULL)) {
fprintf(stderr, "Error: Cannot create output file %s\n", fileout);
return 1;
}
if (restricted) {
if ((fp_pairs = fopen(pairs_file, "r")) == NULL) {
fprintf(stderr, "Error: Cannot open restrict pairs file %s\n", pairs_file);
return 1;
}
/* Initialize the pairs list for restriced searches*/
total_pairs = load_pairs(fp_pairs, &pairs);
fclose(fp_pairs);
}
initialize_globals();
print_parameters(filename1, filename2, fpout);
if (restricted && verbosity) {
printf("Performing Restricted Scan on:%d pairs\n", total_pairs);
}
find_targets(query_fp, fpout, pairs, total_pairs, filename2);
destroy_globals();
if (outfile) fclose(fpout);
fclose(query_fp);
return 0;
}
