int main() {
EESA eesa;
PSSM pssm;
Hits hits;
unsigned int i;
/*
* NOTE: It can only load one matrix at the monment!
* Should be changed to return a PSSMSet
*/
pssm = load_log_matrices("small-wm", 4);
print_pssm(pssm);
eesa = load_fasta_DNA("sequences", 0);
calcAndSetThresholds(pssm, -0.5);
/*
* This is stupid when you are doing many searches. Use SESA
* instead.
*/
hits = single_search(eesa, pssm);
for (i = 0; i < hits->nScores; i++) {
printf("HIT: %3i is in seq %3i at pos %5i with score %lf\n", i, hits->pScores[i].seq, hits->pScores[i].pos, hits->pScores[i].score);
}
exit(0);
}
// ---------------------------------------------------
// ----------- Main procedure for the bwsearch tool
// ---------------------------------------------------
int main(int argc, char *argv[])
{
int getopt(int argc, char * const *argv, const char *options);
void unbwi(char *);
void multi_search(char *);
void single_search(char *, int);
extern char *optarg;
extern int optind, opterr, optopt;
char *infile_name, *pattern;
int c, num_opt, pattern_from_file, multiple_search,decompress;
if(argc<3) {
fprintf(stderr, "Usage:\n\t%s ",argv[0]);
fprintf(stderr,"-d [-x 1|2|3] [-c perc] bwifile \n");
fprintf(stderr,"to decompress a file, or\n\t%s ",argv[0]);
fprintf(stderr,"[-lmoprv][-x 1|2|3][-s len][-c perc] pattern bwifile\n");
fprintf(stderr,"to search a pattern. ");
fprintf(stderr,"Valid options are:\n");
fprintf(stderr,"\t-d decompress file\n");
fprintf(stderr,"\t-l locate occurrences\n");
fprintf(stderr,"\t-m multiple search (kills option -osr)\n");
fprintf(stderr,"\t-o one line report (kills options -rls)\n");
fprintf(stderr,"\t-p *pattern* gives the pattern file name\n");
fprintf(stderr,"\t-r report the position of the occurrences\n");
fprintf(stderr,"\t-s display len chars sourronding each occ ");
fprintf(stderr,"(kills options -rl)\n");
fprintf(stderr,"\t-v produces a verbose output\n");
fprintf(stderr,"\t-c percentage of cached buckets (default 0)\n");
fprintf(stderr,"\t-x data access: 1=Ext, 2=Mmap, 3=In (default 1)\n\n");
exit(1);
}
/* ----------------- read options --------------------- */
Verbose=0;
infile_name=NULL;
num_opt = opterr=0;
pattern_from_file = 0;
multiple_search = 0;
Type_mem_ops = EXT_MEM;
Cache_percentage = 0;
Report_occ = 0;
Locate_occ = 0;
Display_occ = 0;
Oneline_report = 0;
decompress = 0;
while ((c=getopt(argc, argv, "dlomrpvs:c:x:")) != -1) {
switch (c)
{
case 'd':
decompress=1;
case 'v':
Verbose++; break;
case 'l':
Locate_occ=1; break;
case 'r':
Report_occ=1; break;
case 'x':
Type_mem_ops = atoi(optarg); break;
case 's':
Display_occ = atoi(optarg); break;
case 'c':
Cache_percentage = atof(optarg); break;
case 'p':
pattern_from_file = 1; break;
case 'm':
multiple_search = 1; break;
case 'o':
Oneline_report = 1; break;
case '?':
fprintf(stderr,"Unknown option: %c -main-\n", optopt);
exit(1);
}
num_opt++;
}
if(decompress) {
/* ------- read filename only ----- */
infile_name = (char *) argv[optind];
pattern = NULL;
}
else {
/* ------- read pattern and filename --------- */
if(optind!=argc-2) {
fprintf(stderr,"You must supply a pattern and a filename! -main-\n");
exit(1);
}
else {
pattern = (char *) argv[optind++];
infile_name = (char *) argv[optind];
}
if(strlen(pattern)<=0) {
fprintf(stderr,"Invalid pattern -main-\n");
exit(1);
}
}
if((Cache_percentage < 0) || (Cache_percentage > 1)) {
fprintf(stderr,"Cache percentage must be in [0,1] -main-\n");
exit(1);
}
if(strlen(infile_name)<=0) {
fprintf(stderr,"Invalid file name -main-\n");
exit(1);
}
if (check_bwi_suffix(infile_name) == 0){
fprintf(stderr,"The file name must end with .bwi -main-\n");
exit(1);
}
if(Report_occ)
Locate_occ = 1; // report implies locate
if(Display_occ)
Report_occ=Locate_occ = 0; //display text kills report and locate
if(Oneline_report) {
Display_occ=Report_occ=Locate_occ = 0;
}
if(Verbose>1) {
fprintf(stderr,"\n*****************************************************");
fprintf(stderr,"\n bwsearch Ver 1.0\n");
fprintf(stderr,"Created on %s at %s from %s\n",__DATE__,__TIME__,__FILE__);
fprintf(stderr,"*****************************************************\n");
}
if(Verbose) {
fprintf(stderr,"Command line: ");
for(c=0;c<argc;c++)
fprintf(stderr,"%s ",argv[c]);
fprintf(stderr,"\n");
}
/* ----- Hilights the type of memory management ------ */
if(Verbose)
switch(Type_mem_ops)
{
case EXT_MEM:
fprintf(stderr,"Memory management: via fopen, fread, getc, ...\n");
break;
case EXT_MMAP:
fprintf(stderr,"Memory management: via mmap() system call ...\n");
break;
case IN_MEM:
fprintf(stderr,"Memory management: internal memory ...\n");
break;
default:
fprintf(stderr,"Error: -- type mem ops --\n"); exit(1); break;
}
/* --------- open input file ------------- */
my_open_file(infile_name);
/* --------- Initialize the Cache System ------------- */
init_bwi_cache();
if(decompress)
unbwi(infile_name);
else if(multiple_search)
multi_search(pattern);
else
single_search(pattern,pattern_from_file);
/* --------- Report Cache Usage Information ------------- */
if (Verbose)
report_bwi_cache_usage();
my_fclose(Infile);
return 0;
}
