/*
* change the device name to a raw devname
*/
char *
getfullrawname(char *cp)
{
struct stat64 buf;
char *dp;
char *new_path;
dev_t blk_dev;
if (cp == NULL)
return (strdup(""));
/*
* Create a fully qualified name.
*/
if ((cp = getfullname(cp)) == NULL)
return (NULL);
if (*cp == '\0')
return (cp);
if (stat64(cp, &buf) != 0) {
free(cp);
return (strdup(""));
}
if (S_ISCHR(buf.st_mode))
return (cp);
if (!S_ISBLK(buf.st_mode)) {
free(cp);
return (strdup(""));
}
blk_dev = buf.st_rdev;
if ((dp = getvfsspecial(cp, GET_RAW)) != NULL) {
free(cp);
return (strdup(dp));
}
/*
* We have a block device name, go find the raw name.
*/
if ((dp = strstr(cp, "/dsk/")) == NULL &&
(dp = strstr(cp, "/" LOFI_BLOCK_NAME "/")) == NULL &&
(dp = strstr(cp, "/" RD_BLOCK_NAME "/")) == NULL &&
(dp = strstr(cp, "/" SNAP_BLOCK_NAME "/")) == NULL &&
(dp = strrchr(cp, '/')) == NULL) {
/* this is not really possible */
free(cp);
return (strdup(""));
}
dp++;
if ((new_path = malloc(strlen(cp)+2)) == NULL) {
free(cp);
return (NULL);
}
(void) strncpy(new_path, cp, dp - cp);
/* fill in the rest of the raw name */
new_path[dp - cp] = 'r';
(void) strcpy(new_path + (dp - cp) + 1, dp);
if (test_if_raw(new_path, blk_dev)) {
free(cp);
return (new_path);
}
free(new_path);
dp = getrawcomplete(cp, &buf);
free(cp);
return (dp);
}
int main(int argc, char** argv) {
dictionary<ATOMIC>* dict[MAXSPECIES];
dictionary<ATOMIC>* filter;
conservation_table* cons[MAXSPECIES];
int i,j;
FILE *configfile, *metacalc;
wordexp_t exp_result;
char buff[MAXBUFFLENGTH];
char tag[MAXBUFFLENGTH];
char aux[MAXBUFFLENGTH];
char path[MAXBUFFLENGTH]="";
char suffix[MAXBUFFLENGTH]="";
char configfilename[MAXBUFFLENGTH];
char restrictionfilename[MAXBUFFLENGTH];
char metacalcfilename[MAXBUFFLENGTH]="";
char maffilename[MAXBUFFLENGTH]="";
int n_species=0;
char* file_name[MAXSPECIES];
double weight[MAXSPECIES];
double threshold=0;
double tot_weight=0;
int halfsize=4;
int gap=2;
int min_gc=1;
int repeat_length=2;
int length_limit=0;
subset *restriction=NULL;
index_t p,q,r,s;
word_t a;
char *pc;
char *p_file_name;
int reverse_complement=0;
/***************************************************************************************************************************************/
if(argc==1) {
fprintf(stderr, "TRIM - this program takes sequences, creates corresponding hash tables, and intersects them by trimmming\n");
fprintf(stderr, "Usage: %s -i config_file [-maf maf_file_name] -r restriction_file -o output_metafile\n",argv[0]);
fprintf(stderr, "Other parameters are:\n -verbose [suppress verbose output]\n -rc [reverse complement sequences before adding]\n");
exit(1);
}
timestamp_set();
maffilename[0]=0;
for(i=1;i<argc;i++) {
pc = argv[i];
if(*pc == '-') {
if(strcmp(pc+1,"i") == 0) {
configfile = fopen(argv[++i],"r");
if(configfile==NULL) {
fprintf(logfile,"Input file (%s) cannot be opened, exiting", argv[i]);
exit(1);
}
n_species = 0;
tot_weight= 0;
while(fgets(buff,MAXBUFFLENGTH,configfile)) {
tag[0]=0;
sscanf(buff,"%s %*s",tag);
if(strcmp(tag,"path")==0) sscanf(buff,"%*s %s", &path[0]);
if(strcmp(tag,"extention")==0) sscanf(buff,"%*s %s", &suffix[0]);
if(strcmp(tag,"halfsize")==0) sscanf(buff,"%*s %i", &halfsize);
if(strcmp(tag,"gap")==0) sscanf(buff,"%*s %i", &gap);
if(strcmp(tag,"repeatmask")==0) sscanf(buff,"%*s %i", &repeat_length);
if(strcmp(tag,"gccontent")==0) sscanf(buff,"%*s %i", &min_gc);
if(strcmp(tag,"lowercase")==0) sscanf(buff,"%*s %i", &lowercase_allowed);
if(strcmp(tag,"threshold")==0) sscanf(buff,"%*s %lf",&threshold);
if(strcmp(tag,"samewindow")==0) sscanf(buff,"%*s %i", &SAMEWINDOW);
if(strcmp(tag,"limit")==0) sscanf(buff,"%*s %i", &length_limit);
if(strcmp(tag,"species")==0) {
file_name[n_species] = (char*)malloc(sizeof(char)*MAXBUFFLENGTH);
sscanf(buff,"%*s %s %lf", &file_name[n_species][0], &weight[n_species]);
tot_weight+=weight[n_species];
n_species++;
}
}
fclose(configfile);
}
if(strcmp(pc+1,"maf") == 0) sscanf(argv[++i],"%s",&maffilename[0]);
if(strcmp(pc+1,"r") == 0) restriction = new subset(argv[++i]);
if(strcmp(pc+1,"o") == 0) sscanf(argv[++i], "%s", &metacalcfilename[0]);
if(strcmp(pc+1,"verbose") == 0) verbose = 0;
if(strcmp(pc+1,"rc") == 0) reverse_complement = 1;
if(strcmp(pc+1,"log")==0) {
logfile = fopen(argv[++i], "w");
if(logfile==NULL) logfile = stderr;
}
}
}
if(halfsize<2 || gap>3) {
if(verbose) fprintf(logfile,"Word size or gap are incorrect, exiting\n");
exit(1);
}
metacalc = fopen(metacalcfilename,"wb");
if(metacalc==NULL) {
if(verbose) fprintf(logfile,"Output metacalc file cannot be opened, exiting\n");
exit(1);
}
/***************************************************************************************************************************************/
if(threshold==0) threshold = 0.5;
if(verbose) fprintf(logfile, "[Numeric parameters are: pattern=%i-%i-%i, minGC=%i, repeat=%i, threshold=%2.1lf%%]\n", halfsize, gap, halfsize, min_gc, repeat_length, threshold*100);
if(verbose) fprintf(logfile, "[Boolean parameters are: lowercase=%s, reverse_complement=%s]\n",yesno(lowercase_allowed), yesno(reverse_complement));
if(verbose) fprintf(logfile, "[Extra parameters are: SAMEWINDOW=%i, sequence length limit=%i]\n",SAMEWINDOW,length_limit);
wordexp(path, &exp_result, 0);
sprintf(&path[0],"%s",exp_result.we_wordv[0]);
/***************************************************************************************************************************************/
filter = new dictionary<ATOMIC>(halfsize,gap);
filter->mask_low_complexity(repeat_length);
if(min_gc>0) filter->mask_low_GCcontent(min_gc);
for(i=0;i<n_species;i++) {
dict[i] = new dictionary<ATOMIC>(halfsize,gap);
dict[i]->filter = filter;
}
if(maffilename[0]==0) {
for(i=0;i<n_species;i++) {
p_file_name = getfullname(path,file_name[i],suffix);
if(verbose) fprintf(logfile,"[Reading %s: ",p_file_name);
dict[i]->read_from_suf(p_file_name, restriction, reverse_complement,length_limit);
dict[i]->check();
cons[i] = new conservation_table(dict[i]->max_key);
cons[i]->before = dict[i]->fill_cons();
if(verbose) fprintf(logfile,", weight=%2.1lf]\n",weight[i]);
}
}
else {
if(verbose) fprintf(logfile,"[Reading %s: ", maffilename);
dictionary<ATOMIC>::read_from_muf(maffilename, dict, restriction, file_name, n_species, reverse_complement,length_limit);
if(verbose) fprintf(logfile,"]\n");
for(i=0;i<n_species;i++) {
if(verbose) fprintf(logfile,"[%s",file_name[i]);
dict[i]->info();
dict[i]->check();
cons[i] = new conservation_table(dict[i]->max_key);
cons[i]->before = dict[i]->fill_cons();
if(verbose) fprintf(logfile,", weight=%2.1lf]\n",weight[i]);
}
}
dictionary<ATOMIC>::intersect_many(dict, n_species, weight, threshold*tot_weight, (char*)"Intersect ");
if(verbose) fprintf(logfile,"[Compute conservation rates:");
for(i=0;i<n_species;i++) {
if(verbose) fprintf(logfile," %s",file_name[i]);
cons[i]->after = dict[i]->fill_cons();
}
if(verbose) fprintf(logfile,"]\n");
if(verbose) fprintf(logfile,"[Metacalc: saving data to %s]\n",metacalcfilename);
fprintf(metacalc,"%i %i %i %lf\n", halfsize, gap, n_species, threshold);
for(i=0;i<n_species;i++) {
if(verbose) fprintf(logfile,"[Saving %s",file_name[i]);
dict[i]->check();
dict[i]->info();
fprintf(metacalc,"%s %lf\n", file_name[i], weight[i]);
dict[i]->save(metacalc);
cons[i]->save(metacalc);
if(verbose) fprintf(logfile,"]\n");
}
fclose(metacalc);
timestamp_report();
return(0);
}
/*
* change the device name to a block device name
*/
char *
getfullblkname(char *cp)
{
struct stat64 buf;
char *dp;
char *new_path;
dev_t raw_dev;
if (cp == NULL)
return (strdup(""));
/*
* Create a fully qualified name.
*/
if ((cp = getfullname(cp)) == NULL)
return (NULL);
if (*cp == '\0')
return (cp);
if (stat64(cp, &buf) != 0) {
free(cp);
return (strdup(""));
}
if (S_ISBLK(buf.st_mode))
return (cp);
if (!S_ISCHR(buf.st_mode)) {
free(cp);
return (strdup(""));
}
if ((dp = getvfsspecial(cp, GET_BLK)) != NULL) {
free(cp);
return (strdup(dp));
}
raw_dev = buf.st_rdev;
/*
* We have a raw device name, go find the block name.
*/
if ((dp = strstr(cp, "/rdsk/")) == NULL &&
(dp = strstr(cp, "/" LOFI_CHAR_NAME "/")) == NULL &&
(dp = strstr(cp, "/" RD_CHAR_NAME "/")) == NULL &&
(dp = strstr(cp, "/" SNAP_CHAR_NAME "/")) == NULL &&
(dp = strrchr(cp, '/')) == NULL) {
/* this is not really possible */
free(cp);
return (strdup(""));
}
dp++;
if (*dp != 'r') {
dp = getblkcomplete(cp, &buf);
free(cp);
return (dp);
}
if ((new_path = malloc(strlen(cp))) == NULL) {
free(cp);
return (NULL);
}
(void) strncpy(new_path, cp, dp - cp);
/* fill in the rest of the unraw name */
(void) strcpy(new_path + (dp - cp), dp + 1);
if (test_if_blk(new_path, raw_dev)) {
free(cp);
/* block name was found, return it here */
return (new_path);
}
free(new_path);
dp = getblkcomplete(cp, &buf);
free(cp);
return (dp);
}