int main(int argc, char* argv[]) {
char out_file_name[MAXBUFFLENGTH]="";
char input_file_name[MAXBUFFLENGTH]="";
char idx_file_name[MAXBUFFLENGTH];
char dbx_file_name[MAXBUFFLENGTH];
long offset;
long seqlen;
long intronic_window = 150;
long exonic_window = 0;
char filename[MAXBUFFLENGTH];
char name[MAXBUFFLENGTH];
char chr_name[MAXBUFFLENGTH];
char buff[MAXBUFFLENGTH];
char longbuff[MAXLONGBUFFLENGTH];
char longbuffm[MAXLONGBUFFLENGTH];
FILE *idx_file;
FILE *dbx_file;
FILE *input_file;
FILE *outfile;
int b,i,j,q,k,n,a,m,s;
char c;
long position,y;
int strand;
long** pos;
int** str;
char** typ;
char*** ids;
long p,l;
int record_count[MAXCHR];
int record_idx[MAXCHR];
int cis = 0;
int coord = 0;
int all=0;
int warnings = 0;
char format[][64] = {"%*s %*i %*i %s %li %i %*s %s %c", "%s %li %i %*s %s %c"};
if(argc==1) {
fprintf(stderr,"This routine get sequence segments from a custom compressed FASTA repository (see transf)\n");
fprintf(stderr,"Last update by Dmitri Pervouchine ([email protected]) on Mar 22, 2013\n");
fprintf(stderr," -in <aln_file>\n -dbx <database_file>\n -idx <index_file>\n -out <output_file>\n");
fprintf(stderr," -we <exonic_window> [default=%i]\n -wi <intronic_window> [default=%i]\n -cis [use colunms 1-3] [default=%i]\n", exonic_window, intronic_window, cis);
fprintf(stderr," -quiet <suppress verbose output> [default=no]\n -all <include all sites>\n -coord <offset for 3'-sites> [default=%i]\n",coord);
exit(1);
}
timestamp_set();
for(i=1;i<argc;i++) {
if(strcmp(argv[i],"-in")==0) {
sscanf(argv[++i], "%s", &input_file_name[0]);
}
if(strcmp(argv[i],"-dbx")==0) {
sscanf(argv[++i], "%s", &dbx_file_name[0]);
}
if(strcmp(argv[i],"-idx")==0) {
sscanf(argv[++i], "%s", &idx_file_name[0]);
}
if(strcmp(argv[i],"-out")==0) {
sscanf(argv[++i], "%s", &out_file_name[0]);
}
if(strcmp(argv[i],"-we")==0) {
sscanf(argv[++i], "%li", &exonic_window);
}
if(strcmp(argv[i],"-wi")==0) {
sscanf(argv[++i], "%li", &intronic_window);
}
if(strcmp(argv[i],"-coord")==0) {
sscanf(argv[++i], "%i", &coord);
}
if(strcmp(argv[i],"-quiet")==0) {
verbose = 0;
}
if(strcmp(argv[i],"-cis")==0) {
cis = 1;
}
if(strcmp(argv[i],"-all")==0) {
all = 1;
}
}
if(out_file_name[0]==0) {
fprintf(stderr,"[WARNING: output file not specified, redirect to stdout]\n");
outfile = stdout;
}
else {
outfile = fopen(out_file_name,"w");
if(outfile == NULL) {
fprintf(stderr,"[ERROR: output file %s cannot be opened for writing, exiting]\n", out_file_name);
exit(1);
}
if(verbose) fprintf(stderr,"[>%s]\n",out_file_name);
}
input_file = fopen(input_file_name,"r");
if(input_file == NULL) {
fprintf(stderr,"[ERROR: cannot access %s, exiting]\n", input_file_name);
exit(1);
}
if(verbose) fprintf(stderr,"[<%s, pass 1",input_file_name);
while(fgets(buff,MAXBUFFLENGTH,input_file)) {
if(strlen(buff)<2) break;
sscanf(buff, format[cis], &chr_name[0], &position, &strand, &name[0], &c);
n = assign_code(chr_name);
record_count[n]++;
}
if(verbose) fprintf(stderr,"]\n");
pos = (long**) malloc(sizeof(long*)*(N_CHR_NAMES+1));
str = (int**) malloc(sizeof(int*)*(N_CHR_NAMES+1));
typ = (char**) malloc(sizeof(char*)*(N_CHR_NAMES+1));
ids = (char***)malloc(sizeof(char**)*(N_CHR_NAMES+1));
if(pos==NULL || str==NULL || typ==NULL || ids==NULL) {
fprintf(stderr,"[ERROR: failed to create index tables, exiting]\n");
exit(1);
}
for(i=0;i<N_CHR_NAMES;i++) {
if(record_count[i]>0) {
pos[i] = (long*) malloc(sizeof(long)*(record_count[i]+1));
str[i] = (int*) malloc(sizeof(int)*(record_count[i]+1));
typ[i] = (char*) malloc(sizeof(char)*(record_count[i]+1));
ids[i] = (char**) malloc(sizeof(char*)*(record_count[i]+1));
if(pos[i]==NULL || str[i]==NULL || typ[i]==NULL || ids[i]==NULL) {
fprintf(stderr,"[ERROR: failed to create index tables, exiting]\n");
exit(1);
}
record_idx[i]=0;
}
}
if(verbose) fprintf(stderr,"[<%s, pass 2",input_file_name);
fseek(input_file, 0, SEEK_SET);
while(fgets(buff,MAXBUFFLENGTH,input_file)) {
if(strlen(buff)<2) break;
sscanf(buff, format[cis], &chr_name[0], &position, &strand, &name[0], &c);
i = get_chr_code(chr_name);
j = record_idx[i];
pos[i][j] = position + (c=='D' ? coord*strand : 0);
str[i][j] = strand;
typ[i][j] = c;
ids[i][j] = (char*) malloc(sizeof(char)*(strlen(name)+1));
strcpy(ids[i][j],name);
record_idx[i]++;
}
if(verbose) fprintf(stderr,"]\n");
if(verbose) fprintf(stderr,"[<%s,%s",idx_file_name,dbx_file_name);
idx_file = fopen(idx_file_name,"r");
dbx_file = fopen(dbx_file_name,"r");
if(idx_file == NULL || dbx_file == NULL) {
fprintf(stderr,"[ERROR: cannot access %s or %s, exiting]\n", idx_file_name, dbx_file_name);
exit(1);
}
offset = 0;
while(fgets(buff,MAXBUFFLENGTH,idx_file)) {
if(strlen(buff)<2) break;
sscanf(buff,"%s" , &name[0]);
while(fgets(buff,MAXBUFFLENGTH,idx_file)) {
if(strlen(buff)<2) break;
sscanf(buff,"%s %li" , &chr_name[0], &seqlen);
i = get_chr_code(chr_name);
for(k=0;k<record_count[i];k++) {
if(pos[i][k]>seqlen) {
warnings++;
continue;
}
l = exonic_window + intronic_window;
if(typ[i][k]=='D' || typ[i][k]=='A' || all) {
if(str[i][k]>0) {
p = pos[i][k] - 1 - (typ[i][k]=='D' ? exonic_window : intronic_window);
}
else {
p = pos[i][k] - (typ[i][k]=='D' ? intronic_window : exonic_window);
}
fget_segment(longbuff, dbx_file, offset, p, l);
if(str[i][k]<0) {
rev1(longbuff);
}
if(is_all_n(longbuff)) continue;
fprintf(outfile,"%s\t%s\t%li\t%li\t%i\t%li\t%s\t%c\n",ids[i][k], chr_name, (str[i][k]>0 ? p + 1 : seqlen - (p + l)), l, str[i][k], seqlen, longbuff,typ[i][k]);
}
}
offset+= (seqlen % 8 == 0) ? seqlen/8 : (seqlen/8 + 1);
}
}
fclose(outfile);
fclose(idx_file);
fclose(dbx_file);
if(verbose) fprintf(stderr,"]\n");
if(verbose && warnings>0) fprintf(stderr,"[WARNING: %i windows were out of range, they were ignored]\n", warnings);
timestamp_report();
exit(0);
}
int main(int argc, char* argv[]) {
char cpsfilename[MAXBUFFLENGTH];
char chainfilename[MAXBUFFLENGTH];
char outfilename[MAXBUFFLENGTH]="";
int marginlength = 0;
int MAXREC;
char c;
char *pc;
int x;
char buff[MAXBUFFLENGTH+1];
char aux[MAXBUFFLENGTH+1];
long score;
int start1,end1,len1,start2,end2,len2;
char strand1, strand2, chr1[MAXBUFFLENGTH], chr2[MAXBUFFLENGTH];
int *size, *dq, *dt;
int a,b,k,i,j,s,m;
int *position;
char *strand;
int *ids;
int *idg;
char *type;
int chridx[MAXCHR+1];
int chroff[MAXCHR+1];
char resstr;
int rescrd;
if(argc==1) {
fprintf(stderr,"Finds matches of the given set of sites (CPS file) in the BLASTZ chain alignment (CHAIN file)\n");
fprintf(stderr,"Last update by (dp) on Sep 21, 2011\n");
fprintf(stderr,"Keys:\n -i CPS file (remember to sort by position in ascending order)\n -d CHAIN alignment file\n -o output file\n");
fprintf(stderr," -m margin length [0]\n -v suppress verbose output [NO]\n");
exit(1);
}
timestamp_set();
for(i=1;i<argc;i++) {
pc = argv[i];
if(*pc != '-') continue;
if(*(pc+1) == 'i') {
sscanf(argv[++i], "%s", &cpsfilename[0]);
}
if(*(pc+1) == 'd') {
sscanf(argv[++i], "%s", &chainfilename[0]);
}
if(*(pc+1) == 'o') {
sscanf(argv[++i], "%s", &outfilename[0]);
}
if(*(pc+1) == 'm') {
sscanf(argv[++i], "%i", &marginlength);
}
if(*(pc+1) == 'v') {
verbose=0;
}
}
if(outfilename[0]==0) {
fprintf(stderr,"No output file privided, exiting\n");
exit(1);
}
outfile = fopen(outfilename,"w");
if(outfile == NULL) {
fprintf(stderr,"Can't open output file, exiting\n");
exit(1);
}
for(i=0;i<MAXCHR;i++) {
chridx[i]=chroff[i]=0;
}
MAXREC = 0;
cpsfile= fopen(cpsfilename,"r");
if(cpsfile==NULL) {
fprintf(stderr,"Can't access CPS file. Exiting\n");
exit(1);
}
if(verbose) fprintf(stderr,"Reading CPS input pass 1");
while(!feof(cpsfile)) {
buff[0]=0;
fgets(buff,MAXBUFFLENGTH,cpsfile);
if(strlen(buff)<2) break;
sscanf(buff,"%s" , aux);
chridx[assign_code(aux)]++;
MAXREC++;
}
fclose(cpsfile);
for(s=i=0;i<MAXCHR;i++) {
x = chridx[i];
chridx[i] =s;
s+=x;
}
chridx[i] = s;
position = (int*) malloc(sizeof(int)*(s+4));
strand = (char*) malloc(sizeof(char)*(s+4));
type = (char*) malloc(sizeof(char)*(s+4));
ids = (int*) malloc(sizeof(int)*(s+4));
idg = (int*) malloc(sizeof(int)*(s+4));
if(position==NULL || strand==NULL || type==NULL || ids==NULL || idg==NULL) {
fprintf(stderr,"Not enough memory. Terminated\n");
exit(1);
}
cpsfile= fopen(cpsfilename,"r");
if(verbose) fprintf(stderr,", records = %i\nReading CPS input pass 2",MAXREC);
while(!feof(cpsfile)) {
buff[0]=0;
fgets(buff,MAXBUFFLENGTH,cpsfile);
if(strlen(buff)<2) break;
sscanf(buff,"%s" , aux);
i = assign_code(aux);
m = chridx[i]+chroff[i];
sscanf(buff,"%*s %i %c %i %i %c" , position+m, strand+m, idg+m, ids+m, type+m);
chroff[i]++;
}
fclose(cpsfile);
if(verbose) fprintf(stderr,"\nSorting segments");
/*
for(i=0;i<MAXCHR;i++) {
quickSort_ic(position,strand,chridx[i],chridx[i+1]-1);
}
*/
for(i=0;i<MAXCHR;i++) {
k=1;
while(k) {
k=0;
for(j=chridx[i];j<chridx[i+1]-1;j++) {
if(position[j]>position[j+1]) {
k=1;
swapi(position+j,position+j+1);
swapc(strand+j,strand+j+1);
swapc(type+j,type+j+1);
swapi(ids+j,ids+j+1);
swapi(idg+j,idg+j+1);
}
}
}
}
if(verbose) fprintf(stderr," done\nProcessing chains");
/**********************************************************************************************/
size = (int*) malloc(sizeof(int)*MAXALN);
dq = (int*) malloc(sizeof(int)*MAXALN);
dt = (int*) malloc(sizeof(int)*MAXALN);
if(size ==0 || dq ==0 || dt==0) {
fprintf(stderr,"Not enough memory for such long chains. Terminated\n");
exit(1);
}
/**********************************************************************************************/
chainfile = fopen(chainfilename,"r");
while(!feof(chainfile)) {
buff[0]=0;
fgets(buff,MAXBUFFLENGTH,chainfile);
if(strlen(buff)<2) break;
buff[5]=0;
if(strcmp(buff,"chain")==0) {
sscanf(buff+6,"%li %s %i %c %i %i %s %i %c %i %i",&score, &chr1[0], &len1, &strand1, &start1, &end1, &chr2[0], &len2, &strand2, &start2, &end2);
k=0;
while(!feof(chainfile)) {
buff[0]=0;
fgets(buff,MAXBUFFLENGTH,chainfile);
if(strlen(buff)<2) break;
sscanf(buff,"%i %i %i",&size[k],&dt[k],&dq[k]);
k++;
if(k>MAXALN) {
fprintf(stderr,"Chain length exceeded. Terminating");
exit(1);
}
}
x = get_chr_code(chr1);
if(x<0) continue;
a=start1;b=start2;
j=0;
for(i=chridx[x];i<chridx[x+1] && position[i]<start1;i++);
for(;i<chridx[x+1]&& position[i]<end1;i++) {
while(position[i]>a+size[j]+dt[j] && j<k){
a+=size[j]+dt[j];
b+=size[j]+dq[j];
j++;
}
if(j>=k) break;
if(position[i]-a > marginlength && a+size[j]-position[i] >= marginlength) {
if(strand1==strand2) {
resstr = strand[i];
rescrd = position[i] - a + b;
}
else {
resstr = (strand[i]=='+') ? '-' : '+';
rescrd = len2 - (position[i] - a + b - 1) ;
}
fprintf(outfile,"%s\t%i\t%c\t%s\t%i\t%c\t%i\t%i\t%c\t%li\n",chr1, position[i], strand[i],chr2,rescrd, resstr, idg[i], ids[i],type[i],score);
}
}
}
}
if(verbose) fprintf(stderr," done\n");
fclose(chainfile);
fclose(outfile);
timestamp_report();
exit(0);
}
int main(int argc, char* argv[]) {
char cps_file_name[MAXBUFFLENGTH];
char chain_file_name[MAXBUFFLENGTH];
char out_file_name[MAXBUFFLENGTH]="";
int marginlength = 0;
char buff[MAXBUFFLENGTH+1];
char aux[MAXBUFFLENGTH+1];
long score;
int start1,end1,len1,start2,end2,len2;
char strand1, strand2, chr1[MAXBUFFLENGTH], chr2[MAXBUFFLENGTH];
int *size, *dq, *dt;
int a,b,k,i,j,s,m,x;
int *position;
int *strand;
int *idg;
int *ids;
char *type;
char c;
int chridx[MAXCHR+1];
int chroff[MAXCHR+1];
char resstr;
int rescrd;
long chain_id;
if(argc==1) {
fprintf(stderr,"This utility does liftOver of coordinates (cps) by using chain alignment\n");
fprintf(stderr,"Gene information is included in the output\n");
fprintf(stderr,"Last update by Dmitri Pervouchine ([email protected]) on Mar 22, 2013\n");
fprintf(stderr,"Usage: %s -in <cps_file> -chain <chain_alignment_file> [-margin <length>] [-quiet]\n", argv[0]);
fprintf(stderr," -in cps6, i.e. chr1/position1/strand1/gene/site/type tab-delimited file, strand is +/-\n");
fprintf(stderr," -chain UCSC chain alignment file, species1=>2\n");
fprintf(stderr," -out <output_file> [default=stdout]\n");
fprintf(stderr," -margin margin length [default=0]\n -quiet suppress verbose output [default=NO]\n");
fprintf(stderr,"NOTE: Input has to be sorted by position!\n");
fprintf(stderr,"Output format cps3+cps6: chr1/position1/strand1/chr2/position2/strand2/gene/site/type/score\n");
exit(1);
}
timestamp_set();
for(i=1;i<argc;i++) {
if(strcmp(argv[i],"-in")==0) {
sscanf(argv[++i], "%s", &cps_file_name[0]);
}
if(strcmp(argv[i],"-chain")==0) {
sscanf(argv[++i], "%s", &chain_file_name[0]);
}
if(strcmp(argv[i],"-out")==0) {
sscanf(argv[++i], "%s", &out_file_name[0]);
}
if(strcmp(argv[i],"-margin")==0) {
sscanf(argv[++i], "%i", &marginlength);
}
if(strcmp(argv[i],"-quiet")==0) {
verbose=0;
}
}
if(out_file_name[0]==0) {
fprintf(stderr,"[WARNING: output file not specified, redirect to stdout]\n");
out_file = stdout;
}
else {
out_file = fopen(out_file_name,"w");
if(out_file == NULL) {
fprintf(stderr,"[ERROR: output file %s cannot be opened for writing, exiting]\n", out_file_name);
exit(1);
}
if(verbose) fprintf(stderr,"[>%s]\n",out_file_name);
}
cps_file= fopen(cps_file_name,"r");
if(cps_file==NULL) {
fprintf(stderr,"[ERROR: cannot access %s, exiting]\n", cps_file_name);
exit(1);
}
for(i=0;i<MAXCHR;i++) chridx[i] = chroff[i] = 0;
if(verbose) fprintf(stderr,"[<%s, pass 1",cps_file_name);
while(fgets(buff,MAXBUFFLENGTH,cps_file)) {
if(strlen(buff)<2) break;
sscanf(buff,"%s" , aux);
chridx[assign_code(aux)]++;
}
if(verbose) fprintf(stderr,"]\n");
for(s=i=0;i<MAXCHR;i++) {
x = chridx[i];
chridx[i] =s;
s+=x;
}
chridx[i] = s;
position = (int*) malloc(sizeof(int)*(s + ARRAY_MARGIN));
strand = (int*) malloc(sizeof(int)*(s + ARRAY_MARGIN));
ids = (int*) malloc(sizeof(int)*(s + ARRAY_MARGIN));
idg = (int*) malloc(sizeof(int)*(s + ARRAY_MARGIN));
type = (char*) malloc(sizeof(char)*(s + ARRAY_MARGIN));
if(position==NULL || strand==NULL || type==NULL || ids==NULL || idg==NULL) {
fprintf(stderr,"[ERROR: failed to create index tables, exiting]\n");
exit(1);
}
fseek (cps_file, 0, SEEK_SET);
if(verbose) fprintf(stderr,"[<%s, pass 2", cps_file_name);
while(fgets(buff,MAXBUFFLENGTH,cps_file)) {
if(strlen(buff)<2) break;
sscanf(buff,"%s" , aux);
i = assign_code(aux);
m = chridx[i]+chroff[i];
sscanf(buff,"%*s %i %c %i %i %c" , &position[m], &c,&idg[m],&ids[m],&type[m]);
strand[m] = strand_c2i(c);
chroff[i]++;
}
fclose(cps_file);
if(verbose) fprintf(stderr,"]\n");
if(verbose) fprintf(stderr,"[Sort by position (if not done before)");
for(i=0;i<MAXCHR;i++) {
k=1;
while(k) {
k=0;
for(j=chridx[i];j<chridx[i+1]-1;j++) {
if(position[j]>position[j+1]) {
k=1;
swapi(position+j,position+j+1);
swapi(strand+j,strand+j+1);
swapi(idg+j,idg+j+1);
swapi(ids+j,ids+j+1);
swapc(type+j,type+j+1);
}
}
}
}
if(verbose) fprintf(stderr,"]\n");
/**********************************************************************************************/
size = (int*) malloc(sizeof(int)*(MAXALN + ARRAY_MARGIN));
dq = (int*) malloc(sizeof(int)*(MAXALN + ARRAY_MARGIN));
dt = (int*) malloc(sizeof(int)*(MAXALN + ARRAY_MARGIN));
if(size ==0 || dq ==0 || dt==0) {
fprintf(stderr,"[ERROR: not enough memory for chains, exiting]\n");
exit(1);
}
/**********************************************************************************************/
chain_file = fopen(chain_file_name,"r");
if(chain_file==NULL) {
fprintf(stderr,"[ERROR: cannot access %s, exiting]\n", chain_file_name);
exit(1);
}
fseek(chain_file, 0, SEEK_END);
unsigned int last_pos = ftell(chain_file);
fseek(chain_file, 0, SEEK_SET);
while(fgets(buff,MAXBUFFLENGTH,chain_file)) {
if(strlen(buff)<2) break;
buff[5]=0;
if(strcmp(buff,"chain")==0) {
sscanf(buff+6,"%li %s %i %c %i %i %s %i %c %i %i %li",&score, &chr1[0], &len1, &strand1, &start1, &end1, &chr2[0], &len2, &strand2, &start2, &end2, &chain_id);
k=0;
while(fgets(buff,MAXBUFFLENGTH,chain_file)) {
if(strlen(buff)<2) break;
progressbar(ftell(chain_file), last_pos-1, (char*)"Processing ", verbose);
sscanf(buff,"%i %i %i",size + k, dt + k, dq + k);
k++;
if(k>=MAXALN) {
fprintf(stderr,"[ERROR: chain too long, exiting]\n");
exit(1);
}
}
x = get_chr_code(chr1);
if(x<0) continue;
a=start1;b=start2;
j=0;
for(i=chridx[x];i<chridx[x+1] && position[i]<start1;i++);
for(;i<chridx[x+1]&& position[i]<end1;i++) {
while(position[i]>a+size[j]+dt[j] && j<k){
a+=size[j]+dt[j];
b+=size[j]+dq[j];
j++;
}
if(j>=k) break;
if(position[i]-a > marginlength && a+size[j]-position[i] >= marginlength) {
if(strand1==strand2) {
resstr = strand[i];
rescrd = position[i] - a + b;
}
else {
resstr = -strand[i];
rescrd = len2 - (position[i] - a + b - 1) ;
}
fprintf(out_file,"%s\t%i\t%c\t%s\t%i\t%c\t%i\t%i\t%c\t%li\n",chr1, position[i], strand_i2c(strand[i]), chr2, rescrd, strand_i2c(resstr), idg[i], ids[i],type[i],score);
}
}
}
}
fclose(chain_file);
fclose(out_file);
timestamp_report();
free(size);
free(dq);
free(dt);
free(position);
free(strand);
exit(0);
}
